bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oscillatory Neural Networks
Authors: Ermentrout G Bard 
Published: January 2011

Abstract

Oscillatory neural networks are found throughout the nervous system. They are responsible for many repetitive motor activities and have recently been shown to play a role in cognition. In spite of the many different mechanisms that underlie neural oscillations, they can be understood using a common mathematical framework. Most neural oscillators arise from slow or delayed negative feedback. The timing of groups of oscillators depends both on the arrangement of their connections and their intrinsic properties and, in particular, on their phase resetting curve. Linear chains of oscillators can produce travelling waves, and these waves control undulatory movement in many animals. There are many mechanisms for generating waves in a chain including asymmetry in coupling, heterogeneities and pacemakers.

Key Concepts:

The mechanisms for the creation of neural oscillators generally involve delayed negative feedback.

Coordination of neural oscillations occurs through coupling that can take many forms including direct electrical coupling and chemical synaptic transmission.

The phase‐response curve of an oscillator shows how perturbations shift to timing and how the oscillator responds to stimuli.

The timing patterns produced by networks of oscillators depend on the nature of the coupling, the internal dynamics of the oscillator and the connectivity pattern.

Metachronal waves, for example, found in the swimming of the lamprey or the leech can be viewed as a chain of coupled neural oscillators item. Cortical oscillations may play a role in attention and enhancement of sensory coding. However, unlike the simple CPGs described in most of this article, the role of rhythms in higher brain regions remains controversial and is not yet settled.
Regeneration of the Vertebrate Tail
Authors: Ferretti Patrizia 
Published: January 2011

AbstractSome vertebrates can regenerate their tail, a complex process which involves recruitment and proliferation of progenitor cells from the stump and their subsequent differentiation into the various tissues of the tail. Regeneration is observed only in tails that contain the spinal cord and their ability to regenerate varies among species and with age. Adult tailed amphibians (urodeles) have the most striking regenerative capability and frogs (anurans) can regenerate at larval stages. The spinal cord provides neural progenitor cells from which a new spinal cord will form and in urodeles has a key role in differentiation and morphogenesis of other tail tissues. In anuran tadpoles tail regeneration requires also the presence of the notochord to proceed. Tail regeneration occurs also in lizards, though less faithfully than in urodeles. Recent establishment of effective tracking techniques in amphibians and cloning of their genome is starting to fill the gap in our knowledge of the mechanistic control of tail regeneration.Key Concepts:The presence of the nervous system is crucial to tail regeneration.Caudal autotomy is associated with regenerative ability in lizards but not in urodeles.Paedomorphosis does not appear to be causally associated with regenerative ability, but continuous growth throughout adulthood correlates with high regenerative capability of all tissue tails including the spinal cord.Neural progenitor cells for regeneration in amphibians maintain an intermediate phenotype between radial glia and ependyma and are likely to be multipotent.Cells in regenerating tails largely maintain their identity and position of origin.Redeployment of certain developmental mechanisms underlies patterning in the regenerating tail.
Regeneration of Mammalian Skin
Authors: Metcalfe Anthony D , Ferguson Mark WJ 
Published: January 2011

Abstract

Regeneration and repair of tissue injury in mammalian skin is an intricate process in which cellular, biochemical and molecular interactions occur. These interactions are the foundations of new therapeutics and approaches designed to facilitate tissue repair. The ultimate goal is to regenerate skin such that the complete structural and functional properties of the wounded area are restored to the levels before injury without a scar. Novel pharmaceutical approaches to scar reduction are under development, with the furthest progressed being avotermin (Juvista; transforming growth factor beta 3 (TGFβ3)). In addition, new synthetic biomaterials are constantly being developed that may in future enable some control over the capacity for tissues to regenerate by manipulating stem cells, cell adhesion, growth and differentiation for optimal tissue development. The success of these new approaches to skin regeneration is likely to be underpinned by the manipulation of the mechanisms responsible for wound repair and regeneration.

Key Concepts:

Like other animals such as newts and salamanders, mammals have the ability to regenerate tissues.

Many wound signals probably control more than one cell activity, and regeneration probably constitutes an orchestrated response to a mixture of such signals.

The processes involved during wound healing can trigger an embryonic state in the skin which makes it receptive to regenerative cues and signals.

New approaches to skin regeneration are likely to be underpinned by our understanding of the mechanisms responsible for wound repair.

Skin wounds on early mammalian embryos heal perfectly with no scars, whereas wounds to adult mammals scar.

The growth factor profile in a healing embryonic wound is very different from that in an adult wound.

TGF‐β3 has the ability to elicit a scar‐reducing effect and thus a regenerative healing response in mammalian skin.

Scars can have a significant psychological impact on patients, irrespective of whether or not they are hidden by clothing.

Scarring may no longer be an inevitable consequence of modern injury or surgery; a pharmaceutical approach to the prevention of human scarring is now possible.
Immune System: Evolutionary Pressure of Infectious Agents
Authors: Kasahara Masanori 
Published: January 2011

AbstractLike all other biologic systems, the immune system emerged as a consequence of evolution. A major force that has driven the evolution of the immune system and shaped its current organisation was the needs to fight pathogens. Key elements of adaptive immunity, such as antigen receptors and major histocompatibility complex molecules, show evidence of selective pressures exerted by pathogens. Conversely, immune responses mounted by the host have also imposed strong selective pressures on pathogens. To escape immune attack from the host, pathogens have developed immune evasion tactics such as antigenic variation (as typically seen in influenza viruses) and the production of immune evasion proteins (as typically seen in herpesviruses). Mutation is the key genetic mechanism underlying the co‐evolution of the immune system and pathogens.Key Concepts:The immune system of vertebrates has evolved to fight pathogens.Pathogens have exerted intense selective pressures on the evolution of the immune system.Key elements of the adaptive immune system, such as antigen receptors and major histocompatibility complex molecules, show evidence of such selective pressures.Immune responses by the host exert strong selective pressures on pathogens.To escape immune attack, pathogens change their antigenicity or produce immune evasion proteins.Mutation is the key genetic mechanism underlying the co‐evolution of the immune system and pathogens.
Cytochrome P450 (

CYP

) Gene Superfamily
Authors: Nelson David R , Nebert Daniel W 
Published: January 2011

Abstract

Cytochrome P450
, which was first named a ‘pigment in the cell’ having an absorption maximum of 450 nm when reduced and bound to carbon monoxide, was thought to be a single enzyme in the early 1960s. P450 was correlated with drug and steroid metabolism by the late 1960s and recognised eventually to comprise an ancient gene superfamily encoding numerous ubiquitous enzymes that participate in countless essential life processes. More than 12 000 P450 genes are named across all kingdoms of life. Nearly all eukaryotes require sterols in their membranes for essential fluidity and lipid‐packing characteristics.
CYP51
is the sterol
14α‐demethylase
that makes these sterols; thus, it is fundamental to eukaryotic life. Cytochromes P450 evolved novel functions in chordates leading to the origin of steroid hormones. In conjunction with steroid hormone receptors, these novel regulatory pathways distinguish chordates from other animals. Defects in many of the 57 human functional

CYP

genes are involved in some inborn errors of metabolism and other clinical diseases.

Key Concepts:

Cytochromes P450 (CYPs) are haeme‐containing membrane proteins in the endoplasmic reticulum (ER) or mitochondrial inner membrane.

Most CYPs require a source of electrons from an electron transfer chain to function: NADPH‐cytochrome P450 oxidoreductase (POR) in the ER and ferredoxin (FDX) plus ferredoxin reductase (FDXR) in mitochondria.

CYP functions can be divided into oxidation/reduction of endogenous or exogenous compounds (e.g. drugs, chemicals, pollutants, etc.).

Endogenous P450 substrates are mainly lipids including steroids, lanosterol, bile acids, vitamin D, retinoic acid, eicosanoids, fatty acids and some haeme breakdown products.

In 2010, 13 of 57 human P450s remain as orphans without known substrates.

Cytochromes P450 in humans (and most vertebrates) are divided into 18 CYP gene families based on sequence similarity.

Polymorphism in CYP genes can alter a person's ability to metabolise drugs (poor, intermediate, efficient or ultra‐rapid metaboliser).

CYP2D6 and CYP3A4 are the major drug‐metabolising enzymes in humans. CYP2D6 appears to be the most polymorphic.

Alterations in CYP drug metabolism are often responsible for adverse drug reactions – especially when multiple drugs are taken.

The triazole antifungal drugs ketoconazole, fluconazole and itraconazole target the fungal CYP51 required for fungal sterol biosynthesis. Drug resistance may occur by mutations in this gene.
Meganucleases and Their Biomedical Applications
Authors: Molina Rafael , Montoya Guillermo , Prieto Jesús 
Published: January 2011

Abstract

Homing endonucleases and zinc‐finger nucleases are double‐stranded meganucleases that target large
deoxyribonucleic acid
(DNA) recognition sites, a feature that means only a few such sites are likely to be present in a mammalian‐sized genome. Several homing endonucleases have been used as templates to engineer tools that cleave DNA sequences other than their original wild‐type targets. Indeed, zinc‐finger nucleases have been designed to recognise specific genes. These custom meganucleases can be used to stimulate double‐strand break homologous recombination in cells, thereby inducing the repair of defective genes with very low toxicity levels. The use of tailored meganucleases opens up new possibilities for gene therapy in patients with monogenic diseases that can be treated

ex vivo

. This review provides an overview of recent advances in this field.

Key Concepts:

Meganucleases are double‐stranded DNAses that target large recognition sites.

Meganucleases promote efficient gene targeting through double‐strand‐break‐induced homologous recombination.

Homologous recombination and nonhomologous end joining are the two pathways that can be used to repair DNA double‐strand breaks.

Meganucleases encompass homing endonucleases and zinc‐finger nucleases.

Meganucleases are ideal scaffolds to engineer enzymes that accurately cleave DNA and induce recombination.

Meganucleases can recognise unique sites of cleavage within a genome, permitting their use for therapeutic purposes in human diseases.

X‐ray diffraction of crystallised proteins allows us to understand the relationship between the structure and function of biomolecules.
Copper‐Mediated and Copper‐Catalyzed Addition and Substitution Reactions of Extended Multiple Bond Systems
Authors: Krause Norbert , Aksin‐Artok Özge 
Published: January 2011

AbstractIntroductionCopper‐Mediated and Copper‐Catalyzed Addition Reactions to Extended Michael AcceptorsCopper‐Mediated and Copper‐Catalyzed Substitution Reactions of Extended SubstratesConclusion
Increases in global tropospheric ozone following an El Niño event: examining stratospheric ozone variability as a potential driver
Authors: Voulgarakis A. , Hadjinicolaou P. , Pyle J. A. 
Published: January 2011

AbstractThe stratosphere can strongly influence the interannual variability of tropospheric ozone. It has been discussed previously that tropospheric ozone can increase following an El Niño event, due to enhanced stratosphere/troposphere exchange (STE) of ozone. Here, we run a chemical‐transport model for 5 years, covering a period including a strong El Niño event (1997–1998), and find that variability of ozone in the stratosphere is an almost negligible driver of modelled post‐El Niño increases of ozone STE and tropospheric ozone abundances. Changes in the dynamics, affecting the cross‐tropopause air‐mass flux, may be far more important in driving these anomalies. Copyright © 2011 Royal Meteorological Society
Stereoselective Single (Copper) or Double (Platinum) Boronation of Alkynes Catalyzed by Magnesia‐Supported Copper Oxide or Platinum Nanoparticles
Authors: Grirrane Abdessamad , Corma Avelino , Garcia Hermenegildo 
Published: January 2011

AbstractCopper(II) oxide nanoparticles supported on magnesia have been prepared from CuII supported on magnesia by hydrogen reduction at 400 °C followed by storage under ambient conditions. X‐ray photoelectron spectroscopy of the material clearly shows that immediately after the reduction copper(0)–metal nanoparticles are present on the magnesia support, but they undergo fast oxidation to copper oxide upon contact with the ambient for a short time. TEM images show that the catalytically active CuO/MgO material is formed of well‐dispersed copper oxide nanoparticles supported on fibrous MgO. CuO/MgO exhibits a remarkable catalytic activity for the monoborylation of aromatic, aliphatic, terminal, and internal alkynes, the products being formed with high regio‐ (borylation at the less substituted carbon) and stereoselectivity (trans‐configured). CuO/MgO exhibits complete chemoselectivity towards the monoborylation of alkynes in the presence of alkenes. Other metal nanoparticles such as gold or palladium are inactive towards borylation, but undergo undesirable oligomerization or partial hydrogenation of the CC triple bond. In contrast, platinum, either supported on magnesia or on nanoparticulate ceria, efficiently promotes the stereoselective diborylation of alkynes to yield a cis‐configured diboronate alkene. By using platinum as the catalyst we have developed a tandem diborylation/hydrogenation reaction that gives vic‐diboronated alkanes from alkynes in one pot.
How does macroinvertebrate taxonomic resolution influence ecohydrological relationships in riverine ecosystems
Authors: Monk Wendy A. , Wood Paul J. , Hannah David M. , Extence Chris A. , Chadd Richard P. , Dunbar Michael J. 
Published: January 2011

AbstractThe taxonomic resolution of macroinvertebrate community data needs careful consideration, to ensure that research objectives in pure and applied freshwater scientific research are met. The level of taxonomy used may be driven by time and financial restrictions associated with the increasing resources and effort needed to identify organisms to a lower taxonomic resolution. This paper aims to assess the influence of taxonomic resolution on the understanding of long‐term (1985–2006) benthic macroinvertebrate community response to changes in the hydrological regime. There were marked differences in the number of taxa included in the analysis when comparing ‘species’‐ and ‘family’‐level data used to derive lotic‐invertebrate index for flow evaluation (LIFE) scores, particularly among species rich orders, such as Ephemeroptera, Plecoptera, Trichoptera and Coleoptera. The performance of the partial least squares (PLS) regression models of hydrological variables and the LIFE scores derived for different taxonomic levels were compared. Coefficients of determination were higher for species‐level LIFE data than for the same data resolved to family level. Results demonstrate that the species‐level LIFE data produced significant model components while those derived from family‐level data were not; although both models indicated the dominance of hydrological indices quantifying the duration and magnitude of the hydrological events. We conclude that there is a growing need to resolve faunal data to species level to adequately fulfil operational and legislative obligations for river management and conservation purposes. Copyright © 2011 John Wiley & Sons, Ltd.
Design of neo‐glycoconjugates that target the mannose receptor and enhance TLR‐independent cross‐presentation and Th1 polarization
Authors: Singh Satwinder Kaur , Streng‐Ouwehand Ingeborg , Litjens Manja , Kalay Hakan , Burgdorf Sven , Saeland Eirikur , Kurts Christian , Unger Wendy W. , van Kooyk Yvette 
Published: January 2011

AbstractCross‐presentation is an important mechanism by which DCs present exogenous antigens on MHC‐I molecules, and activate CD8+ T cells, cells that are crucial for the elimination of tumors. We investigated the feasibility of exploiting the capacity of the mannose receptor (MR) to improve both cross‐presentation of tumor antigens and Th polarization, processes that are pivotal for the anti‐tumor potency of cytotoxic T cells. To this end, we selected two glycan ligands of the MR, 3‐sulfo‐LewisA and tri‐GlcNAc (N‐acetylglucosamine), to conjugate to the model antigen OVA and assessed in vitro the effect on antigen presentation and Th differentiation. Our results demonstrate that conjugation of either 3‐sulfo‐LewisA or tri‐GlcNAc specifically directs antigen to the MR. Both neo‐glycoconjugates showed, even at low doses, improved uptake as compared with native OVA, resulting in enhanced cross‐presentation. Using MR−/− and MyD88‐TRIFF−/− bone marrow‐derived DCs (BMDCs), we show that the cross‐presentation of the neo‐glycoconjugates is dependent on MR and independent of TLR‐mediated signaling. Whereas proliferation of antigen‐specific CD4+ T cells was unchanged, stimulation with neo‐glycoconjugate‐loaded DCs enhanced the generation of IFN‐γ‐producing T cells. We conclude that modification of antigen with either 3‐sulfo‐LewisA or tri‐GlcNAc enhances cross‐presentation and permits Th1 skewing, through specific targeting of the MR, which may be beneficial for DC‐based vaccination strategies to treat cancer.
IL‐22 is produced by γC‐independent CD25+ CCR6+ innate murine spleen cells upon inflammatory stimuli and contributes to LPS‐induced lethality
Authors: Dumoutier Laure , de Heusch Magali , Orabona Ciriana , Satoh‐Takayama Naoko , Eberl Gerard , Sirard Jean‐Claude , Di Santo James P. , Renauld Jean‐Christophe 
Published: January 2011

AbstractIL‐22 is a Th17 cytokine that plays a key role in immune responses against extracellular bacteria. In mucosal lymphoid tissues, IL‐22 production is mainly due to an IL‐23‐responsive NK‐like cell subset that shares some markers with lymphoid tissue inducer (LTi) cells. Here, we identified a new spleen cell population responsible for IL‐22 production upon either in vitro stimulation by anti‐CD3 antibodies or in vivo stimulation by lipopolysaccharide (LPS) via IL‐2‐ and an IL‐23‐dependent mechanisms, respectively. These cells represent 1% of spleen cells from recombination activating gene (Rag2)‐deficient mice, and correspond to a discrete innate lymphoid cell population expressing CD25, CCR6 and IL‐7R. This population comprises 60–70% CD4+ cells, which produce IL‐22, and are still present in common γ chain‐deficient mice; the CD4− subset coexpresses IL‐22 and IL‐17, and is common γ chain‐dependent. The importance of IL‐22 production for the LPS‐triggered response is highlighted by the fact that IL‐22‐deficient mice are more resistant to LPS‐induced mortality.
The high‐frequency limit of usable response spectral ordinates from filtered analogue and digital strong‐motion accelerograms
Authors: Akkar Sinan , Kale Özkan , Yenier Emrah , Bommer Julian J. 
Published: January 2011

AbstractThe range of response frequencies for which spectral ordinates obtained from accelerograms may be considered reliable is limited by several factors, primary among them being the effects of filters that are routinely applied to remove noise from the records. Considerable attention has been focused on the low‐frequency limit of the usable spectral ordinates because of various engineering applications requiring long‐period spectral accelerations or displacements but only recently have rational approaches to selecting the high‐frequency limit been proposed. Since there are applications for which the high‐frequency spectral ordinates are important, the approaches to this issue presented in the recent studies are reviewed and their application to the ground‐motion database from Europe and the Middle East is explored. On the basis of the results of these analyses, it is concluded that a large proportion of this dataset can be used to provide reliable estimates of response spectral ordinates at much shorter periods than may have previously been considered feasible. Copyright © 2011 John Wiley & Sons, Ltd.
Seismic reliability of traditional and innovative concentrically braced frames
Authors: Giugliano Maria Teresa , Longo Alessandra , Montuori Rosario , Piluso Vincenzo 
Published: January 2011

AbstractStructural engineering problems are always affected by many sources of uncertainty, such as aleatory of material properties, applied loads and earthquake intensity, therefore, seismic assessment of structures should be based on probabilistic methods. Since PBSD (Performance‐based Seismic Design) philosophy was formulated, many researches have been conducted in this field in order to develop simple and accurate procedures for evaluating structural reliability. An important contribution has been provided by Jalayer and Cornell, who have developed a closed‐form expression to evaluate the mean annual frequency of exceeding a defined limit state. In this paper, by assuming the record‐to‐record variability as the only source of uncertainty, the seismic reliability of concentrically braced frames designed according to traditional and innovative methodologies is investigated, and a comparison between their performances is presented. In particular, two design methodologies have been applied: Eurocode 8 provisions and a new design methodology based on a rigorous application of ‘capacity design’ criteria. The innovative reduced section solution strategy, based on the reduction of cross sections at bracing member ends, has also been analysed. Copyright © 2011 John Wiley & Sons, Ltd.
Control of Noise in Chemical and Biochemical Information Processing
Authors: Privman Vladimir 
Published: January 2011

AbstractWe review models and approaches for error control in order to prevent the buildup of noise when gates for digital chemical and biomolecular computing based on (bio)chemical reaction processes are utilized to realize stable, scalable networks for information processing. Solvable rate equation models illustrate several recently developed methodologies for gate‐function optimization. We also survey future challenges and possible new research avenues.