bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological Data Centres
Authors: Stafford Phillip , Lee HoJoon
Published: January 2010

The age of genomics has pushed the cost of sequencing much lower than typical cost/ technology curves would predict. Sanger sequencing, next‐gen sequencing (ABI SOLiD sequencing, Illumina GA, Roche 454) and even whole‐chromosome imaging are providing sequence data faster than most laboratories can analyse or store. The biological data infrastructure that was established in the early 1990s is still in place, mostly because it was very well planned in terms of future needs. The three main biological data centres are NCBI (
http://www.ncbi.nlm.nih.gov/
), DDJB (
http://www.ddbj.nig.ac.jp/
) and EBI/EMBL (
http://www.ebi.ac.uk/embl/
). These centres will be discussed in the context of new types of high‐density biological data, such as microarrays of various sorts. This article will discuss history, the tools that are provided to the public, other biological databases that support and integrate with sequencing databases and a projection of biology in the future.

Key concepts:

Biological data is much denser today than it was even 10 years ago.

Sequencing DNA is faster, cheaper and more accurate today than it was 6 months ago, and far faster than it was 10 years ago. Data repositories have struggled to keep up.

Three main DNA sequence repositories exist: USA, Europe and Japan. These are mirrors of each other, but are also distinct.

Web‐based sequence analysis tools are presented.

Other high‐density databases are listed including GEO, BIND, pdb, HapMap, KEGG and GO.
Neutron Diffraction
Authors: Bradshaw Jeremy P
Published: January 2010

Neutron diffraction, a technique analogous to X‐ray diffraction, is well‐suited to the study of biological materials. By differentiating between hydrogen and its heavier isotope, deuterium, neutron diffraction is able to provide detailed information about the hydrogen atoms within biological macromolecules. It allows biologists to study solvation effects, protonation–deprotonation equilibria and hydrogen bonding, all of which are invisible to X‐ray techniques. Recent years have seen the construction of new neutron research facilities, notably the Spallation Neutron Source in the USA, the World's brightest neutron source. Even with such high‐flux sources, the intensity of neutrons hitting the sample is several orders of magnitude lower than a typical X‐ray experiment. However, the nonionizing nature of neutrons means that beam damage to the specimen is low, even over extended exposure times.

Key Concepts:

Neutron diffraction is closely related to the complementary technique of X‐ray crystallography, a method that led to a revolution in biological sciences.

Hydrogen plays a central role in many biological processes, but is invisible to X‐rays.

Neutrons are able to distinguish between hydrogen and deuterium, so selective deuteration of a single molecule or group can be used to locate it within a complex macromolecular assembly.

The neutron‐scattering contrast of samples can be controlled by changing the deuterium content of the solvent (water‐heavy water exchange).

Neutrons have the ability to discriminate between nitrogen, carbon and oxygen, which can be difficult with X‐rays.

Neutron experiments are carried out at large scale, national or international neutron research centres, because production of the neutrons requires a nuclear reactor or a spallation source.
Informed Consent and Multiplex Genetic Screening
Authors: Avard Denise , Harmsen Eef
Published: January 2010

Recent advances in genome‐wide genotyping together with new technologies provide unprecedented opportunities for multiplex screening. These advances provide insight into diseases, hold promises to improve clinical practices to address lifestyle changes, inform reproductive decisions, identify newborns at risk as well as possibly move genetic screening out of the realm of the clinics into direct‐to‐consumer market forces. Advances in multiplex genetic screening raise ethical issues with regard to consent. Some of the concerns that may arise include how to: manage the incidental and excess information; integrate information about susceptibility testing into the clinic, given the complexity of the information; address the psychosocial impact and educate health professionals about the meaning of the results. If multiplex screening is used in genomic research and made available in the clinic, each ethical issue deserves consideration in the consent process and should be discussed.

Key concepts:

Become aware of new technologies that are being used to expand screening.

Understand the distinction between testing and screening.

Describe a spectrum of social, ethical issues that are involved in multiplex testing and screening.

Know why multiplex screening/testing requires informed consent.

Familiarize the reader with the concept of broad consent.

Identify the emerging issues relevant to multiplex screening/testing.

Consider whether multiplex screening/testing will shift the clinical approach towards a ‘direct‐to‐consumer’ model.
Using Evolutionary Biology in the Medical Sciences
Authors: Antolin Michael F
Published: January 2010

Applying evolutionary thinking to medical practice can lead to unraveling ultimate causes of disease and in improving diagnostics and therapies. Genetic variation is central: adaptations evolve by natural selection of inherited differences linked to survival and reproduction. Thus we may ask why diseases persist. Genetic diseases recur because long‐term population size and histories of selection influence the number of disease‐causing mutations patients carry. Individuals present different symptoms because mutations interact with environmental and genetic backgrounds. Some diseases like diabetes and hypertension persist because of mismatches between previous adaptation and modern environments. For infectious diseases, rapid evolution in microbes underlies the drug resistance blocking improvement of public health and prevents design of vaccines with long‐lasting protection against human‐adapted pathogens like influenza and malaria. A key is that diseases represent convergence of several evolutionary histories: the patient's legacy of inherited mutations and adaptations, and the microbes' history of infection, pathogenicity and transmission.

Key Concepts

Evolutionary thinking in medicine distinguishes between proximate and ultimate evolutionary causes of disease.

Mutations that cause disease in modern times may have been adaptive in the past, and thus produce traits that are maladaptive (mismatched) in modern environments.

Early developmental problems may lead to disease in adults because of trade‐offs in early versus late life history traits.

Weak selection on diseases related to ageing explains their persistence in modern times especially as post‐reproductive longevity increases.

The evolutionary potential of microbes ensures that infectious diseases will evade therapies and vaccines in the future.

Disease symptoms may represent adaptations to slow pathogen reproduction, so treating symptoms may prolong the course of infections and opportunities for pathogen transmission.

The evolutionary potential of microbes makes it likely that new diseases will continue to emerge from reservoirs in wild animal populations.

Medical research on therapies and diagnostics depends on testing animals most closely related and thus most similar to humans.

Individual patients’ presentation of disease will depend on complex interactions at the convergence of patients’ genetic legacies, the evolutionary history of pathogens to which they are exposed, and the environmental context where the patients and pathogens meet.
Bioethics in Asia: in Transition
Authors: Bhardwaj Minakshi
Published: January 2010

Bioethics in Asia is in transformation. In parallel with technological innovations in medicine and other fields the importance of bioethics is gradually recognized. Asia is a vast continent with huge diversity of religious, social, cultural and political values. Asian perspectives are equally diverse in moral reasoning and ethical decision‐making. Research developments in biomedicine and technological advancements in genomics have brought new dimensions to debates on informed consent, privacy for example, and new concepts are developed as an attempt to integrate local values in global issues. Bioethics in Asia is explored both from country perspectives and conceptualized from religious and philosophical views. As much as Buddhist and Confucian views have dominated Bioethics debates in Asia, gradually Islamic, Hindu and Jain perspectives are beginning to surface. This article attempts to provide an overview of contemporary bioethical debates in Asia, and how such debates within the region are also influencing global debates.

Key Concepts

Asian perspectives are diverse in moral reasoning and ethical decision‐making.

Islamic, Hindu and Sikh perspectives are beginning to surface in bioethics debates in Asia where Buddhist and Confucian perspectives traditionally dominated in academic debates.

Integration of local cultural values is encouraged in global issues, such as informed consent.

Family and community values dominate decision‐making.

There is a huge gap between biomedical research and clinical applications.

Genetics is increasingly becoming understood in the public domain.

There is a growing momentum to compete with the west in medical research.

Questions are raised if there is ‘one’ Asian Bioethics, given the multicultural societies within Asia.
Stable Isotope Ecology
Authors: Newton Jason
Published: January 2010

Stable isotope geochemistry has proved to be an extremely useful tool in elucidating many ecological problems, with stable isotope ecology comprising the theme of a series of international conferences (
http://www.isoecol.org
). Stable isotopes can be used as biological tracers in the following ways: (i) to identify sources, for instance in determining the identity of basal carbon in a food web; (ii) to distinguish sources, for example to determine whether a breeding animal is using local resources or its own reserves; (iii) to quantify relative inputs in a system, for example determining the proportions of different prey items to a consumer's diet. When utilized carefully, stable isotope geochemistry provides some advantages over conventional methods, and provides an additional device for the ecologist. The following article provides a short reference for ecologists considering the inclusion of stable isotope analysis as part of their methodology.

Key concepts:

Stable isotopes are useful tracers of ecological processes.

Carbon stable isotopes are useful for tracing carbon sources and plant physiology.

Nitrogen stable isotope ratios in animal tissues are useful indicators of trophic level.

Combined carbon and nitrogen isotope ratios in animal tissues elucidate food webs and trophic niche.

Hydrogen and oxygen isotope ratios in animals reflect those of local precipitation.
Electron Tomography
Authors: He Wanzhong , Fernández José‐Jesús
Published: January 2010

Electron tomography (ET) is an emerging electron microscopy (EM) technique for the three‐dimensional (3D) visualization of the cellular architecture and molecular organization in native cells at nanometer scale. ET thus bridges the gap between the low‐resolution imaging techniques and the high‐resolution structural techniques. In ET a series of images is taken from a single specimen at different projecting orientations. The 3D map computed from these images is subsequently subjected to visualization and interpretation. Thanks to several recent innovations in EM, including improved specimen preparation techniques, novel EM hardware and software, reliable genetic and molecular labelling approaches, ET is rapidly becoming a powerful bioimaging tool for precisely dissecting the macromolecular organizations and cellular events captured from living cells in health and disease. Thus many previously unanswered molecular mechanisms responsible for the specific cellular functions could be clearly elucidated by the ET technology.

Key concepts:

Electron tomography allows visualization of cellular architecture and molecular organization in native cells at nanometer scale in 3D.

Electron tomography bridges the resolution gap between the low resolution imaging techniques and the high‐resolution structural techniques.

The biological specimen has to be specially prepared before it is imaged in the electron microscope.

Data acquisition strategies have to be used to obtain reasonable image contrast and reduce the electron‐dose damage.

The 3D map is calculated from a series of 2D EM projection images recorded from the specimen at different projecting orientations.

Several post‐processing stages are intended to facilitate the interpretation of the complex 3D maps.
Scale‐dependence in Ecological Systems
Authors: Hewitt Judi E , Thrush Simon F , Lundquist Carolyn
Published: January 2010

Scale has a profound influence on how we conduct ecological studies, interpret results and understand the links between processes operating at different rates. All of these factors profoundly influence our ability to predict responses to change. The ecological patterns and variability we observe range from millimetres to across ocean basins and from seconds to the expanse of evolutionary history. Patterns apparent at one scale can collapse to noise when viewed from other scales, indicating that perceptions of the importance of different processes vary in a scale‐dependent manner. Moreover, rather than the environment simply providing an arena within which organisms are born grow and die, many organisms interact with the environment, altering it for both for themselves and for other species. Because of these factors, studying ecological systems is far from simple and scale needs to be considered in study design and analysis.

Key concepts:

The pattern you see depends on the scale at which you study it.

Threats from human activities occur at varying scales, from small point sources to large diffuse threats and changes in disturbance regimes across landscapes.

How organisms interact with the environment depends on how they perceive it and how patchy it is.

How an organism moves and how far it can move is crucial to how an organism perceives and responds to their environment.

Many organisms can alter their environment, both for themselves and for other species.

Because most processes are scale‐dependent, studies must explicitly consider scale in their design.

Understanding both the scale of threats and the scale over which species live are essential for successful management and conservation.
Biobanking: Social, Political and Ethical Aspects
Authors: Tutton Richard
Published: January 2010

Prospective, population‐based biobanks designed for research into genetic, environmental and lifestyle factors associated with common, complex diseases or the genetic basis of drug response have garnered significant interest over the past 10 years from bioethicists, social scientists, lawyers and other commentators. There are a series of interrelated but distinct social, political and ethical issues raised by biobanking: the challenges of creating governance structures that win public confidence in these novel and uncertain scientific initiatives; the establishment of appropriate systems of consent; determining the rights of ownership, commercial exploitation and benefit‐sharing among different stakeholders and the ways biobanks invoke ideas about human population differences and might serve to help address the health needs of minority groups in society.

Key concepts:

Biobanking is an activity that spans research and clinical contexts and is undertaken by public sector agencies, charities and commercial actors.

Biobanks should be understood as ‘sociotechnical’ enterprises that need to bring about novel arrangements for governance, gain the support of funders and the public, as well to develop scientific and technical procedures and infrastructures.

Biobanks are situated on the blurred lines of ‘public’ and ‘private’ and raise significant, controversial issues about the role of commercial interests in biomedical research and the distribution of benefits from the use of human tissue and information on individuals.

With the prospect of international networking of biobanks, questions of data sharing, consent, privacy and governance will remain significant and still need to be further debated and resolved.
The Development of Fluorescence Microscopy
Authors: Masters Barry R
Published: January 2010

The fluorescence microscope (wide‐field, scanning, confocal, one‐photon excitation, multiphoton excitation) is an extremely useful and ubiquitous instrument in biological and medical laboratories. The fluorescence microscope provides enhanced contrast, single protein specificity and single molecule sensitivity. Progress in the technical development over more than 100 years of instrument design and fluorescent probe synthesis has contributed to the continuing widespread utility of the fluorescence microscope. Modern advances in instrumentation include the use of continuous wave and pulsed laser light sources, dichroic filters, photomultipliers, avalanche photodetectors and charge‐coupled device detectors. The invention of the two‐photon excitation microscope provides for microscopic imaging of live cells and whole organisms. The development of specific dyes, physiological probes and molecular probes (intrinsic and extrinsic) stimulated the widespread use of fluorescence microscopy in the life sciences. Recently, genetically expressed fluorescent proteins and quantum dots provide new research capabilities for the intravital fluorescence microscope.

Key concepts:

The reader will gain an understanding of the development of both the fluorescence microscope instrumentation and the field of fluorescent probe synthesis, development, limitations and applications to the life sciences.

The fluorescence microscope can provide single molecule detection sensitivity.

The fluorescence microscope can provide single protein selectivity.

A major advance in fluorescence microscope is the development of multiphoton excitation microscopy.

Recent instrument advances include the following: laser light sources, dichroic mirror filters, different types of photodetectors and imaging cameras.

Recent advances in fluorescent probe development include the following: genetically expressed fluorescent proteins and quantum dots.

The limitations of the fluorescence microscope include the following: optical resolution, noise and aberrations; photon‐induced cell and tissue damage; the bleaching of fluorescent probes.

There are microscopic techniques that do not depend on fluorescent probes, but have alternative contrast mechanisms, that is, coherent anti‐Stokes Raman microscopy and second‐harmonic generation microscopy.
Light Microscopy Imaging Facilities
Authors: Sanderson Jeremy
Published: January 2010

Historically core imaging facilities have been associated with electron microscopes. With the very widespread use of fluorescent markers for both fixed and living cells and tissues the light microscope facility has emerged in its own right. Well‐run core light microscope imaging facilities are focal points within research institutions. Researchers want to do science, acquire images and manipulate data for publication; for them, the microscope and the computing infrastructure within the imaging facility are merely tools. Staff provide organization, continuity, tuition and knowledge and maintenance of equipment, which encompass the needs of both novice and advanced users. Increasingly, imaging facilities are considered from the outset as a component in the design of a new research building, and must recover the costs of operation. This article discusses the need for optical sectioning, the role of the light microscopy facility and points to consider in its design.

Key Concepts:

Fluorescent labelling is widely used in life science to study organelles, structures and proteins of interest within cells and tissues.

Fluorescent cells and tissues are self‐luminous and light up throughout their thickness. This is often greater than the depth of field (thickness of the in‐focus object plane) of the microscope objective, thus most of the image is composed of scattered light and out‐of‐focus blur which obscures the in‐focus detail and drastically reduces the signal‐to‐noise ratio (SNR).

Optical sectioning microscopy ‘cleans up’ the image at each point of focus, so allowing a sharply defined 3D Z‐stack to be constructed and analysed.

The light microscopes required to acquire multidimensional images over time, and the software packages needed to analyse the data, are both expensive and complex. Core image facilities provide the instrumentation and specialist staff to assist in this process.

The design and operation of a core light microscopy imaging facility which is capable of effectively supporting a research institution requires some forethought.
Brain
Authors: Oscar‐Berman Marlene , Mosher Susan M.
Published: January 2010

The human brain is a complex aggregate of billions of cells working together to process stimuli, to monitor needs, and to direct behavior. Developmentally, the brain begins at the most rostral extension of the neural tube; it bends over and convolutes as it expands within the confines of the skull (cranium). The brain's expansion is disproportionate relative to the growth of the spinal cord, the most caudal extension of the central nervous system. Figure 1 illustrates the development of the human brain, showing its major subdivisions.
C
hina, Psychology in
Authors: Yang Yufang
Published: January 2010

Modern Chinese psychology was founded in the early years of the twentieth century. The Chinese reformer and educator Yuanpei Cai studied in Wilhelm Wundt's Leipzig laboratory between the years 1908 and 1911, returned to China, and became President of Peking University in 1917. In the same year, Daqi Chen, with Cai's support, established the first psychological laboratory in China. This marked the beginning of modern Chinese psychology. In the ensuing years many departments of psychology were established in various universities in China. The Chinese Psychological Society was founded in 1921, and in 1922 the first journal,
Psychology
, was published. The Institute of Psychology under Academia Sinica was established in 1929. The outbreak of the Sino‐Japanese war in 1937 caused a major setback to progress of psychology until the end of World War II.
Cognitive Therapy
Authors: Beck Judith S.
Published: January 2010

Cognitive therapy (CT), a system of psychotherapy with an operationalized treatment, is based on an elaborated theory of psychopathology and personality. The theory has been empirically validated in hundreds of cognitive science studies, and the therapy itself has been demonstrated to be effective in hundreds of randomized controlled trials for a wide variety of psychiatric disorders, psychological problems, and medical conditions with psychological components (Beck, 2005). Research has shown that CT is highly effective in helping patients not only overcome their disorders but also in preventing relapse (Hollon et al., 2005).
Drug Addiction
Authors: Koob George F.
Published: January 2010

Substance dependence can be defined as a chronically relapsing disorder characterized by (1) compulsion to seek and take the drug, (2) loss of control in limiting intake, and (3) emergence of a negative emotional state (e.g., dysphoria, anxiety, irritability) when access to the drug is prevented (defined here as withdrawal). Addiction and substance dependence, as currently defined by the
Diagnostic and Statistical Manual of Mental Disorders
(DSM‐IV‐TR; American Psychiatric Association, 2000), are used interchangeably in this article to refer to a final stage of a usage process that moves from drug use to abuse to addiction. The term
dependence
has two meanings: (1) an acute withdrawal syndrome (defined here as dependence with a little “d”), and (2) a syndrome in which a subject meets the criteria for substance dependence. In addiction, drug‐taking behavior progresses from impulsivity to compulsivity in a three‐stage cycle consisting of binge/intoxication, withdrawal/negative affect, and preoccupation/anticipation.
Evidence‐Based Practice
Authors: Spring Bonnie , Hitchcock Kristin
Published: January 2010

Evidence‐based practice (EBP) describes a process of decision making for high‐quality client care. The idea of basing practice on evidence was introduced in medicine as a way to promote clinical decision making that followed a rational process rather than intuition (Evidence‐Based Medicine Working Group, 1992). EBP was defined as “the conscientious, explicit, judicious use of current best evidence in making decisions about the care of individual patients” (Sackett, Rosenberg, Gray, Haynes, & Richardson, 1996). From the outset, EBP was seen as based on more than research alone. Research was depicted as one of three overlapping circles or data streams to be considered in clinical decision making. Sackett and colleagues (1996) defined EBP as “the integration of best research evidence with clinical expertise and patient values.”
Black and gold howler monkeys (Alouatta caraya) as sentinels of ecosystem health: patterns of zoonotic protozoa infection relative to degree of human–primate contact
Authors: Kowalewski Martin M. , Salzer Johanna S. , Deutsch Joseph C. , Raño Mariana , Kuhlenschmidt Mark S. , Gillespie Thomas R.
Published: January 2010

Exponential expansion of human populations and human activities within primate habitats has resulted in high potential for pathogen exchange creating challenges for biodiversity conservation and global health. Under such conditions, resilient habitat generalists such as black and gold howler monkeys (Alouatta caraya) may act as effective sentinels to overall ecosystem health and alert us to impending epidemics in the human population. To better understand this potential, we examined noninvasively collected fecal samples from black and gold howler monkeys from remote, rural, and village populations in Northern Argentina. We examined all samples (n=90) for the zoonotic protozoaCryptosporidiumsp. andGiardiasp. via immunofluorescent antibody (IFA) detection. All samples were negative forCryptosporidiumsp. The prevalence ofGiardiasp. was significantly higher at the rural site (67%) compared with the remote forest (57%) and village (40%) sites. A lack ofCryptosporidiumsp. in all samples examined suggests that this pathogen is not a natural component of the howler parasite communities at these sites and that current land‐use patterns and livestock contact are not exposing Argentine howler monkeys to this pathogen. High prevalence ofGiardiasp. at all sites suggests that howler monkeys may serve as a viable reservoir forGiardia.Significantly higher prevalence ofGiardiasp. at the rural site, where primate–livestock contact is highest, suggests the presence of multipleGiardiaclades or increased exposure toGiardiathrough repeated zoonotic transmission among nonhuman primates, livestock, and/or people. These results highlight the need for future research into the epidemiology, cross‐species transmission ecology, and clinical consequences ofGiardiaand other infectious agents not only in humans and livestock, but also in the wild animals that share their environments. Am. J. Primatol. 73:75–83, 2011. © 2010 Wiley‐Liss, Inc.
Observations by a university anatomy teacher and a suggestion for curricular change: Integrative anatomy for undergraduates
Authors: Darda David M.
Published: January 2010

The observation that anatomical course offerings have decreased in undergraduate biology curricula is supported by a survey of undergraduate institutions in the state of Washington. This reduction, due partially to increased emphasis in other areas of the biology curriculum, along with the lack of anatomy prerequisites for admission to most medical and dental schools, has resulted in many biology majors who have little or no exposure to the anatomical sciences. This is a disservice to our students who need to understand organismal form and function to better connect our rapidly expanding knowledge of life at the cell and molecular level to our understanding of the role of organisms in ecosystems and as the primary target of natural selection in evolutionary change. Undergraduate anatomical courses can also serve as an extension of the anatomy curriculum in professional healthcare programs, where anatomical sciences are also experiencing a reduced allocation of instructional time. Given the importance of anatomical knowledge along with the many demands and constraints on biology curricula, what can we do? One suggestion, a course in integrative anatomy for undergraduates, is proposed and discussed. Anat Sci Educ 3:73–76, 2010. © 2010 American Association of Anatomists.
Advanced biofuel production in microbes
Authors: Peralta‐Yahya Pamela P. , Keasling Jay D.
Published: January 2010

The cost‐effective production of biofuels from renewable materials will begin to address energy security and climate change concerns. Ethanol, naturally produced by microorganisms, is currently the major biofuel in the transportation sector. However, its low energy content and incompatibility with existing fuel distribution and storage infrastructure limits its economic use in the future. Advanced biofuels, such as long chain alcohols and isoprenoid‐ and fatty acid‐based biofuels, have physical properties that more closely resemble petroleum‐derived fuels, and as such are an attractive alternative for the future supplementation or replacement of petroleum‐derived fuels. Here, we review recent developments in the engineering of metabolic pathways for the production of known and potential advanced biofuels by microorganisms. We concentrate on the metabolic engineering of genetically tractable organisms such as Escherichia coli and Saccharomyces cerevisiae for the production of these advanced biofuels.
A weak degeneracy revealing decomposition for the CANDECOMP/PARAFAC model
Authors: Rocci Roberto , Giordani Paolo
Published: January 2010

The CANDECOMP/PARAFAC (CP) model is a well known and frequently used tool for extracting substantial information from a three‐way data array. It has several useful characteristics and usually gives meaningful insights about the underlying structure of the data. However, in some cases it has a ‘strange’ behaviour suffering from the so‐called ‘degenerate solutions’, i.e. solutions where the components show a diverging pattern and are meaningless. Several authors have investigated the causes of degeneracy concluding that the phenomenon is due to a lack of minimum of the loss function. In this paper, we study the degeneracy of CP limiting our attention to the two‐component case. The study is done by introducing a canonical form, called 2DR, which is ‘weakly degeneracy revealing’. On the ground of this framework, degeneracy is studied along with some of the remedies proposed in the literature by using a Tucker3 model having a core in the 2DR form. The analysis gives new insights about the behaviour of the CP model and suggests new ideas on how to deal with degeneracy. Copyright © 2010 John Wiley & Sons, Ltd.
Local chemometrics for samples and variables: optimizing calibration and standardization processes
Authors: Igne Benoit , Hurburgh Charles R.
Published: January 2010

The ability of five sample selection methods for local chemometrics and three variable selection algorithms were compared for the development and the transfer of whole soybeans protein and oil near infrared prediction models. Two new methods based on a similarity index considering Euclidian distance among Fourier coefficients were introduced and tested against more common approaches (locally weighted regression, LOCAL). Genetic algorithms were also challenged with the development of models based on particle swarm optimization (PSO). A modification to the original PSO model was introduced. Sample and variable selection methods, as well as their combinations, were tested in the transfer of models in intra‐ and inter‐brand situations using two Foss Infratecs and two Bruins OmegAnalyzerGs. For each brand, a master was designated and its models transferred onto the second unit of its network and the two units of the second brand. Calibration models were proven transferable from brand to brand with similar or better precisions than when all instruments were calibrated on their own calibration sets (relative predictive determinant (RPD) improving from 10.42 to 12.76 and 12.39 in intra‐brand standardization for Infratec network with local and variable selection methods respectively). These methods provided contrasted results depending on the instrument, the parameter, and the variability of interest. Copyright © 2010 John Wiley & Sons, Ltd.
Multivariate calibration leverages and spectralF‐ratios via the filter factor representation
Authors: Andries Erik , Kalivas John H.
Published: January 2010

Diagnostics are fundamental to multivariate calibration (MC). Two common diagnostics are leverages and spectralF‐ratios and these have been formulated for many MC methods such as partial least square (PLS), principal component regression (PCR) and classical least squares (CLS). While these are some of the most common methods of calibration in analytical chemistry, ridge regression is also common place and yet spectralF‐ratios have not been developed for it. Noting that ridge regression is a form of Tikhonov regularization (TR) and using the unifying filter factor representation for MC, this paper develops the filter factor form of leverages and spectralF‐ratios. The approach is applied to a spectral data set to demonstrate computational speed‐up advantages and ease of implementation for the filter factor representation. Copyright © 2010 John Wiley & Sons, Ltd.
Construction and Photophysical Properties of Organic–Inorganic Nanonetworks Based on Oligo(phenylenevinylene) and Functionalized Gold Nanoparticles
Authors: Yang Jien , Liu Xiaofeng , Huang Changshui , Zhou Chunjie , Li Yuliang , Zhu Daoben
Published: January 2010

Novel organic–inorganic nanonetworks of oligo(phenylenevinylene) (OPV) and gold nanoparticles (GNPs) have been synthesized by the amine‐based epoxide ring‐opening reaction. The resulting OPV–GNPs nanocomposites exhibit homogeneous and well‐defined interfaces between the organic ligands and the inorganic nanoparticles, thereby promoting efficient electronic interfacial interaction between the two constituents. The functionalized gold nanoparticles serve as chemical reagents for the construction of nanohybrids, while the epoxide‐terminated OPV acts as linkage between gold nanoparticles. The new architecture provides a facile methodology for fabrication of novel organic–inorganic nanohybrids under relatively mild conditions, which facilitates further applications of hybrid materials.
Characterization of gel grown iron‐manganese‐cobalt ternary levo‐tartrate crystals
Authors: Joshi S. J. , Tank K. P. , Parekh B. B. , Joshi M. J.
Published: January 2010

In the present investigation, iron–manganese–cobalt ternary levo‐tartrate crystals of different compositions have been grown by single‐diffusion gel growth technique in silica hydrogel medium. The metallic composition in the crystals was estimated by EDAX. The coloration of the crystals changed with composition of metallic content. The powder XRD study suggested the crystalline nature and indicated the presence of some extra phases. The grown crystals were characterized by FT‐IR spectroscopy, TGA, dielectric and Vibrating Sample Magnetometer (VSM) studies. The FT‐IR study suggested the presence of O‐H, C=O, C‐O and metal‐oxygen bonds. The effect of composition of metallic content was observed in certain absorption regions in FT‐IR spectra. The thermal stability of the crystals was studied by thermogravimetry and the kinetic and thermodynamic parameters of dehydration were calculated. The effect of composition of ternary levo‐tartrate was observed in dielectric study. The dielectric study was carried out in the frequency range of applied field from 500 Hz to 1 MHz. The variations in dielectric constant, dielectric loss, a.c. resistivity and a.c. conductivity with frequency of applied field were studied. VSM study suggested that all crystals were of paramagnetic nature. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical properties of 2‐aminopyridinium nitrato silver
Authors: Bhuvana K. P. , Robinson Jebas S. , Balasubramanian T.
Published: January 2010

Crystals of 2‐aminopyridinium nitrato silver have been synthesized by slow evaporation method. Grown crystals have been subjected to FTIR, Single crystal X‐Ray diffraction and UV‐Visible studies in order to investigate the structural and optical properties of the crystal. The FTIR spectrum reveals the presence of the functional group that corresponds to both 2‐aminopyridine and silver nitrate, suggesting the formation of the compound, 2‐aminopyridinium nitrato silver. From XRD it is observed that the crystal crystallizes in the structure of monoclinic with the space group of P21/c. The optical transmittance spectrum shows the maximum transparency of about 95% in the visible region is in consistent with the wide band gap, estimated as 4.738 eV. The optical constants n and k has also been determined from the transmittance data. The static dielectric constant is found to be 0.851. The wide band gap and the less dielectric constant suggest the suitability of this compound material for photoconductive applications. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of isothermal annealing on degree of crystallinity and mechanical properties of poly(l‐lactide‐co‐glycolide)
Authors: Zhao Na , Wang Liansong , Huang Dongling , Zhang Tianyao , Zhang Lifang , Xiong Chengdong
Published: January 2010

We investigated the effect of isothermal annealing on the degree of crystallinity and mechanical properties of a random copolymer‐poly(l‐lactide‐co ‐glycolide) (PLLGA)‐with monomer molar ratios of 85/15 (PLLGA85/15) by performing polarizing optical microscopy, differential scanning calorimetry, and X‐ray diffraction, and studying the tensile properties. Isothermal annealing of PLLGA at 130 °C was conducted to improve the degree of crystallinity of the copolymer; the maximum degree of crystallinity (44.5%) was achieved after 60 min of annealing. The crystal size/perfection was observed to increase with annealing time. The highest tensile strength of 65.8 MPa was achieved after 80 min of annealing. However, the degree of crystallinity and tensile strength can only reach to certain extent. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of a static magnetic field on silicon transport in liquid phase diffusion growth of SiGe
Authors: Armour N. , Dost S.
Published: January 2010

Liquid phase diffusion experiments have been performed without and with the application of a 0.4 T static magnetic field using a three‐zone DC furnace system. SiGe crystals were grown from the germanium side for a period of 72 h. Experiments have led to the growth of single crystal sections varying from 0 to 10 mm thicknesses. Examination of the processed samples (single and polycrystalline sections) has shown that the effect of the applied static magnetic field is significant. It alters the temperature distribution in the system, reduces mass transport in the melt, and leads to a much lower growth rate. The initial curved growth interface was slightly flattened under the effect of magnetic field. There were no growth striations in the single crystal sections of the samples. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Heterogeneous versus bulk nucleation of lysozyme crystals
Authors: Hodzhaoglu F. V. , Nanev C. N.
Published: January 2010

Heterogeneous (on‐glass) protein crystal nucleation was separated from the bulk one in systems of thin protein solution layers, confined between two glass plates of custom made quasi two‐dimensional all‐glass cells, as well as by applying forced protein solution flow. Two commercial samples of hen‐egg‐white lysozyme, Seikagaku and Sigma were used as model proteins. Applying the classical technique of separation in time of nucleation and growth stages with protein solution layers of thickness 0.05 cm we found that the on‐glass crystal nucleation prevailed highly with Seikagaku HEWL, while on the opposite, bulk nucleated crystals represented the main crystal fraction in Sigma solution. Also using 0.05 cm solution layers nucleation rates were measured separately for the on‐glass and bulk protein crystals. The process was investigated by varying solution layer thicknesses as well, from 0.05 down to 0.01, 0.0065 and 0.002 cm. Studying the influence of the forced protein solution flow on HEWL crystal nucleation the classical double‐pulse technique was modified by separating the nucleation and growth stages not only in time, but simultaneously also in place. In this case we found that the ratio of on‐glass formed crystal nuclei to bulk nuclei depended on the flow velocity, but in different manner with Seikagaku HEWL and Sigma HEWL. A plausible explanation of our experimental results is that the bulk crystal nucleation occurs on foreign surfaces as well, e.g. on rests of source biomaterial, which are always present in the protein solutions. Moreover, biomaterial seems to be more active nucleant than glass. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Kinetic study of ultrasonic antisolvent crystallization of sirolimus
Authors: Gandhi P. J. , Murthy Z. V. P.
Published: January 2010

Sirolimus, generally used in organ transplantation, is derived from bacterium Streptomyces hygroscopicus. Mass transfer controlled ultrasonic antisolvent method was used for determining the precipitation kinetics of sirolimus. The effect of temperature was determined on the particles size, percentage recovery, critical radius of nucleus, mass transfer coefficient, etc. for sirolimus dissolved in methanol and antisolvent water using ultrasonic treatment. The study was done using classical nucleation theory, which can also be applied to precipitation processes. Experiments were carried out at various temperatures; viz: 45, 50, 60 and 70 °C and the percentage recoveries of sirolimus were found to be 90.74, 91.5, 92.64 and 93.61%, respectively, for initial amount of 8 mg dissolved in 1 mL of solvent and further introduced into 12 mL of HPLC water. The final average diameters of crystals observed for the temperatures were 1371, 1287, 1063 and 863 nm, respectively. The systems were found to be mass transfer controlling and that the mass diffusivities were found to be about 3.97×10–9, 4.00×10–9, 3.01×10‐9 and 1.92×10–9 m2/s, respectively. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Efficient memory architecture for image processing
Authors: Perri Stefania , Corsonello Pasquale
Published: January 2010

This Letter presents a novel purpose‐designed architecture to realize efficient dual‐port memory structures for image processing applications. The main innovation proposed here is the exploitation of single‐port (SP) sub‐banks to achieve the same data bandwidth offered by a true dual‐port (TDP) memory, but significantly reducing the access time and resources requirement.

When compared with a conventional TDP memory bank, the proposed strategy requires up to 25% less silicon area and consumes up to 9% lower power. It also exhibits an access time up to 15% lower.

When used within an Actel FPGA RTAX device to realize an image compressor based on the 2D DWT and the SPIHT algorithm, the memory structure proposed here allows reaching an 11 Mpixels/s frame‐rate, which is 77% higher than that achieved by simply instantiating the SP memory banks available on chip. Copyright © 2010 John Wiley & Sons, Ltd.
Modeling of switching frequency instabilities in buck‐based DC–AC H‐bridge inverters
Authors: El Aroudi Abdelali , Rodriguez Enric , Orabi Mohamed , Alarcón Eduard
Published: January 2010

In this paper, the dynamical behavior of a full bridge DC–AC buck inverter controlled by fixed frequency and PWM is studied. After showing that the system can undergo both period‐doubling and Neimark–Sacker bifurcation at the fast scale (switching period) by using the exact switching model, an exact solution discrete‐time model able to predict both instability phenomena is derived. The model is obtained without making the quasi‐static approximation and it can be used to obtain the useful operation region in the multi‐dimensional design parameter space from time domain simulations in a very fast and accurate manner. Based on the study of the system, some design guidelines are provided. Copyright © 2010 John Wiley & Sons, Ltd.
A battery charger with maximum power point tracking function for low‐power photovoltaic system applications
Authors: Chiu Huang‐Jen , Lo Yu‐Kang , Lee Ting‐Peng , Chen Qing Su , Yu Wen Long , Lee Jian‐Xing , Shih Frank , Mou Shann‐Chyi
Published: January 2010

A battery charger with MPPT function for low‐power PV system applications is presented in this study. For effective miniaturization, the battery charger is designed with high‐frequency operation. Some current‐sensing techniques are studied, and their MPPT implementation is compared. A battery charging method is also designed to prolong battery lifetime without the use of battery current sensors. The operation principles and design considerations of the proposed PV charger are analyzed and discussed in detail. A laboratory prototype is implemented and tested to verify the feasibility of the proposed scheme. Experimental results show that high MPPT accuracy and conversion efficiency can be simultaneously achieved under high‐frequency operation. Copyright © 2010 John Wiley & Sons, Ltd.
Pyrosequencing‐based strategy for a successful SNP detection in two hypervariable regions: HV‐I/HV‐II of the human mitochondrial displacement loop
Authors: Anjum Ghulam Murtza , Du Weidong , Klein Rachel , Amara Umme , Huber‐Lang Markus , Schneider E. Marion , Wiegand Peter
Published: January 2010

Forensic analysis of mitochondrial displacement loop (D‐loop) sequences using Sanger sequencing or SNP detection by minisequencing is well established. Pyrosequencing has become an important alternative because it enables high‐throughput analysis and the quantification of individual mitochondrial DNAs (mtDNAs) in samples originating from more than one individual. DNA typing of the mitochondrial D‐loop region is usually the method of choice if STR analysis fails because of trace amounts of DNA and/or extensive degradation. The main aim of the present work was to optimize the efficiency of pyrosequencing. To do this, 31 SNPs within the hypervariable regions I and II of the D‐loop of human mtDNA were simultaneously analyzed. As a novel approach, we applied two sets of amplification primers for the multiplexing assay. These went in combination with four sequencing primers for pyrosequencing. This method was compared with conventional sequencing of mtDNA from blood and biological trace materials.
A new evaluation technique for the detection of impurities in purified proteins via CE with native UV‐LIF
Authors: Rodat Audrey , Couderc Bettina , Feurer Bernard , Couderc François
Published: January 2010

An analytical methodology for quality control analyses of IgG and their impurities is presented using a new UV‐LIF (266 nm) detector inside the cassette of a CE instrument and its performance was evaluated. The observed sensitivity was very close to that obtained by silver staining of slab gels (LOD of 25 ng/mL), while the sensitivity of the analysis is 80 times better than with CE/UV absorption (214 nm). Examples of the analysis of pharmaceutical and other commercial IgGs are provided and the kinetics of the reduction of IgG by β‐mercaptoethanol is reported, demonstrating the ease of performing the analysis.