Local and semilocal density functional computations for crystals of 1-alkyl-3-methyl-imidazolium salts

The accuracy and reliability of popular density functional approximations for the compounds giving origin to room temperature ionic liquids have been assessed by computing the T=0 K crystal structure of several 1-alkyl-3-methyl-imidazolium salts. Two prototypical exchange-correlation approximations have been considered, i.e., the local density approximation (LDA) and one gradient corrected scheme [PBE-GGA, Phys. Rev. Lett. 77, 3865 (1996)]. Comparison with low-temperature x-ray diffraction data shows that the equilibrium volume predicted by either approximations is affected by large errors, nearly equal in magnitude (~10%), and of opposite sign. In both cases the error can be traced to a poor description of the intermolecular interactions, while the intramolecular structure is fairly well reproduced by LDA and PBE-GGA. The PBE-GGA optimization of atomic positions within the experimental unit cell provides results in good agreement with the x-ray structure. The correct system volume can also be restored by supplementing PBE-GGA with empirical dispersion terms reproducing the r-6 attractive tail of the van der Waals interactions.

BACE1 Polymorphisms Do Not Influence Platelet Membrane β-secretase Activity or Genetic Susceptibility for Alzheimer’s Disease in the Northern Irish Population

ß-Site amyloid precursor protein (APP)-cleaving enzyme 1 (BACE1) is a biological and positional candidate gene for Alzheimer’s disease (AD). BACE1 is a protease that catalyses APP cleavage at the ß-secretase site. We evaluated all common and putatively functional polymorphisms in the genomic region encompassing BACE1 for an association with AD, and for functional effects on platelet ß-secretase activity. Tag SNPs (n = 10) derived from phase II of the International HapMap Project, and a nonsynonymous variant, were successfully genotyped in 901 Caucasian individuals from Northern Ireland using Sequenom iPLEX and TaqMan technologies. APOE genotyping was performed by PCR-RFLP. Platelet membrane ß-secretase activity was assayed in a subset of individuals (n = 311). Hardy–Weinberg equilibrium was observed for all variants. Evidence for an association with AD was observed with multi-marker haplotype analyses (P = 0.01), and with rs676134 when stratified for APOE genotype (P = 0.02), however adjusting for multiple testing negated the evidence for association of this variant with AD. ?2 analysis of genotype and allele frequencies in cases versus controls for individual SNPs revealed no evidence for association (5% level). No genetic factors were observed that significantly influenced platelet membrane ß-secretase activity. We have selected an appropriate subset of variants suitable for comprehensive genetic investigation of the BACE1 gene. Our results suggest that common BACE1 polymorphisms and putatively functional variants have no significant influence on genetic susceptibility to AD, or platelet ß-secretase activity, in this Caucasian Northern Irish population.

Spontaneous spin polarization and electron localization in constrained geometries: The Wigner transition in nanowires

The Wigner transition in a jellium model of cylindrical nanowires has been investigated by density-functional computations using the local spin-density approximation. A wide range of background densities rho(b) has been explored from the nearly ideal metallic regime (r(s)=[3/4 pi rho(b)](1/3)=1) to the high correlation limit (r(s)=100). Computations have been performed using an unconstrained plane wave expansion for the Kohn-Sham orbitals and a large simulation cell with up to 480 electrons. The electron and spin distributions retain the cylindrical symmetry of the Hamiltonian at high density, while electron localization and spin polarization arise nearly simultaneously in low-density wires (r(s)similar to 30). At sufficiently low density (r(s)>= 40), the ground-state electron distribution is the superposition of well defined and nearly disjoint droplets, whose charge and spin densities integrate almost exactly to one electron and 1/2 mu(B), respectively. Droplets are arranged on radial shells and define a distorted lattice whose structure is intermediate between bcc and fcc. Dislocations and grain boundaries are apparent in the droplets' configuration found by our simulations. Our computations aim at modeling the behavior of experimental low-carried density systems made of lightly doped semiconductor nanostructures or conducting polymers.

General trends in the barriers of catalytic reactions on transition metal surfaces

A catalyst preparation by design is one of the ultimate goals in chemistry. The first step towards this goal is to understand the origin of reaction barriers. In this study, we have investigated several catalytic reactions on some transition metal surfaces, using density functional theory. All the reaction barriers have been determined. By detailed analyses we obtain some insight into the reaction barrier. Each barrier is related to (i) the potential energy surface of reactants on the surface, (ii) the total chemisorption energy of reactants, and (iii) the metal d orbital occupancy and the reactant valency. (C) 2001 American Institute of Physics.

The consequences of resistance training for movement control in older adults

Older adults who undertake resistance training are typically seeking to maintain or increase their muscular strength with the goal of preserving or improving their functional capabilities. The extent to which resistance training adaptations lead to improved performance on tasks of everyday living is not particularly well understood. Indeed, studies examining changes in functional task performance experienced by older adults following periods of resistance training have produced equivocal findings. A clear understanding of the principles governing the transfer of resistance training adaptations is therefore critical in seeking to optimize the prescription of training regimes that have as their aim the maintenance and improvement of functional movement capacities in older adults. The degenerative processes that occur in the aging motor system are likely to influence heavily any adaptations to resistance training and the subsequent transfer to functional task performance. The resulting characteristics of motor behavior, such as the substantial decline in the rate of force development and the decreased steadiness of force production, may entail that specialized resistance training strategies are necessary to maximize the benefits for older adults. In this review, we summarize the alterations in the neuromuscular system that are responsible for the declines in strength, power, and force control, and the subsequent deterioration in the everyday movement capabilities of older adults. We examine the literature concerning the neural adaptations that older adults experience in response to resistance training, and consider the readiness with which these adaptations will improve the functional movement capabilities of older adults.

Resistance training enhances the stability of sensorimotor coordination

Strategics for the control of human movement are constrained by the neuroanatomical characteristics of the motor system. In particular, there is evidence that the capacity of muscles for producing force has a strong influence on the stability of coordination in certain movement tasks. In the present experiment, our aim was to determine whether physiological adaptations that cause relatively long-lasting changes in the ability of muscles to produce force can influence the stability of coordination in a systematic manner. We assessed the effects of resistance training on the performance of a difficult coordination task that required participants to synchronize or syncopate movements of their index finger with an auditory metronome. Our results revealed that training that increased isometric finger strength also enhanced the stability of movement coordination. These changes were accompanied by alterations in muscle recruitment patterns. In Particular, the trained muscles were recruited in a more consistent fashion following the programme of resistance training. These results indicate that resistance training produces functional adaptations of the neuroanatomical constraints that underlie the control of voluntary movement.

Abnormal Functional Connectivity of Hippocampus During Episodic Memory Retrieval Processing Network in Amnestic Mild Cognitive Impairment.

BACKGROUND: Functional connectivity magnetic resonance imaging technique has revealed the importance of distributed network structures in higher cognitive processes in the human brain. The hippocampus has a key role in a distributed network supporting memory encoding and retrieval. Hippocampal dysfunction is a recurrent finding in memory disorders of aging such as amnestic mild cognitive impairment (aMCI) in which learning- and memory-related cognitive abilities are the predominant impairment. The functional connectivity method provides a novel approach in our attempts to better understand the changes occurring in this structure in aMCI patients. METHODS: Functional connectivity analysis was used to examine episodic memory retrieval networks in vivo in twenty 28 aMCI patients and 23 well-matched control subjects, specifically between the hippocampal structures and other brain regions. RESULTS: Compared with control subjects, aMCI patients showed significantly lower hippocampus functional connectivity in a network involving prefrontal lobe, temporal lobe, parietal lobe, and cerebellum, and higher functional connectivity to more diffuse areas of the brain than normal aging control subjects. In addition, those regions associated with increased functional connectivity with the hippocampus demonstrated a significantly negative correlation to episodic memory performance. CONCLUSIONS: aMCI patients displayed altered patterns of functional connectivity during memory retrieval. The degree of this disturbance appears to be related to level of impairment of processes involved in memory function. Because aMCI is a putative prodromal syndrome to Alzheimer's disease (AD), these early changes in functional connectivity involving the hippocampus may yield important new data to predict whether a patient will eventually develop AD.

Regulatory Planning for Economic Development in the Countryside

This article examines the interaction between development control and economic development in the countryside within the context of contemporary debates on shifts in the agricultural sector from productivism to multi-functionality. Using planning application decisions from the case of Northern Ireland for the period 1994–95 to 2005–06, together with insights from high-level key informants with planning, economic development and environmental management expertise, the article critiques a perception that regulatory planning is in line with rural development ambitions to foster a multi-functional countryside. While the quantitative data indicate a high approval rate for economic development projects, the qualitative evidence points to limitations within the policy content and operational practices of the planning system. The article argues that regulatory planning must engage more deeply with rural development objectives.

The role of PET/CT scanning in radiotherapy planning

The introduction of functional data into the radiotherapy treatment planning process is currently the focus of significant commercial, technical, scientific and clinical development. The potential of such data from positron emission tomography (PET) was recognized at an early stage and was integrated into the radiotherapy treatment planning process through the use of image fusion software. The combination of PET and CT in a single system (PET/CT) to form an inherently fused anatomical and functional dataset has provided an imaging modality which could be used as the prime tool in the delineation of tumour volumes and the preparation of patient treatment plans, especially when integrated with virtual simulation. PET imaging typically using F-Fluorodeoxyglucose (F-FDG) can provide data on metabolically active tumour volumes. These functional data have the potential to modify treatment volumes and to guide treatment delivery to cells with particular metabolic characteristics. This paper reviews the current status of the integration of PET and PET/CT data into the radiotherapy treatment process. Consideration is given to the requirements of PET/CT data acquisition with reference to patient positioning aids and the limitations imposed by the PET/CT system. It also reviews the approaches being taken to the definition of functional/ tumour volumes and the mechanisms available to measure and include physiological motion into the imaging process. The use of PET data must be based upon a clear understanding of the interpretation and limitations of the functional signal. Protocols for the implementation of this development remain to be defined, and outcomes data based upon clinical trials are still awaited. © 2006 The British Institute of Radiology.

The response of small mammals to natural and human-altered edges associated with Afromontane forests of South Africa

An increase in edge area reduces the effective size of habitat fragments and thus the area available for habitat-interior specialists. However, it is unclear how edge effects compare at different ecotones in the same system. We investigated the response of a small mammal community associated with Afromontane forests to edge effects at three different habitat transitions: natural forest to grassland (natural edge, structurally different vegetation types), natural forest to mature plantation (human-altered edge, structurally similar vegetation types) and natural forest to harvested plantation (human-altered edge, structurally different vegetation types). We predicted that edge effects should be less severe at natural ecotones and at similarly structured contiguous vegetation types than human-altered ecotones and differently structured contiguous vegetation types, respectively. We found that forest species seemed to avoid all habitat edges in our study area. Surprisingly, natural edges supported a less diverse small mammal community than human-altered forest edges. However, edge effects were observed deeper into native forests surrounded by mature alien plantations (and more so at harvested plantations) than into native forests surrounded by native grasslands. The net effect of mature plantations was therefore to reduce the functional size of the natural forest by creating a larger edge. We suggest that when plantations are established a buffer zone of natural vegetation be left between natural forests and newly established plantations to mitigate the negative effects of plantation forestry.

The Colorectal cancer disease-specific transcriptome may facilitate the discovery of more biologically and clinically relevant information

BACKGROUND: To date, there are no clinically reliable predictive markers of response to the current treatment regimens for advanced colorectal cancer. The aim of the current study was to compare and assess the power of transcriptional profiling using a generic microarray and a disease-specific transcriptome-based microarray. We also examined the biological and clinical relevance of the disease-specific transcriptome.

METHODS: DNA microarray profiling was carried out on isogenic sensitive and 5-FU-resistant HCT116 colorectal cancer cell lines using the Affymetrix HG-U133 Plus2.0 array and the Almac Diagnostics Colorectal cancer disease specific Research tool. In addition, DNA microarray profiling was also carried out on pre-treatment metastatic colorectal cancer biopsies using the colorectal cancer disease specific Research tool. The two microarray platforms were compared based on detection of probesets and biological information.

RESULTS: The results demonstrated that the disease-specific transcriptome-based microarray was able to out-perform the generic genomic-based microarray on a number of levels including detection of transcripts and pathway analysis. In addition, the disease-specific microarray contains a high percentage of antisense transcripts and further analysis demonstrated that a number of these exist in sense:antisense pairs. Comparison between cell line models and metastatic CRC patient biopsies further demonstrated that a number of the identified sense:antisense pairs were also detected in CRC patient biopsies, suggesting potential clinical relevance.

CONCLUSIONS: Analysis from our in vitro and clinical experiments has demonstrated that many transcripts exist in sense:antisense pairs including IGF2BP2, which may have a direct regulatory function in the context of colorectal cancer. While the functional relevance of the antisense transcripts has been established by many studies, their functional role is currently unclear; however, the numbers that have been detected by the disease-specific microarray would suggest that they may be important regulatory transcripts. This study has demonstrated the power of a disease-specific transcriptome-based approach and highlighted the potential novel biologically and clinically relevant information that is gained when using such a methodology.

BRCA1 transcriptionally regulates genes associated with the basal-like phenotype in breast cancer

Expression profiling of BRCA1-deficient tumours has identified a pattern of gene expression similar to basal-like breast tumours. In this study, we examine whether a BRCA1-dependent transcriptional mechanism may underpin the link between BRCA1 and basal-like phenotype. In methods section, the mRNA and protein were harvested from a number of BRCA1 mutant and wild-type breast cancer cell lines and from matched isogenic controls. Microarray-based expression profiling was used to identify potential BRCA1-regulated transcripts. These gene targets were then validated (by in silico analysis of tumour samples) by real-time PCR and Western blot analysis. Chromatin immunoprecipitation (ChIP) assays were used to confirm recruitment of BRCA1 to specific promoters. In results, we demonstrate that functional BRCA1 represses the expression of cytokeratins 5(KRT5) and 17(KRT17) and p-Cadherin (CDH3) in HCC1937 and T47D breast cancer cell lines at both mRNA and protein level. ChIP assays demonstrate that BRCA1 is recruited to the promoters of KRT5, KRT17 and CDH3, and re-ChIP assays confirm that BRCA1 is recruited independently to form c-Myc and Sp1 complexes on the CDH3 promoter. We show that siRNA-mediated inhibition of endogenous c-Myc (and not Sp1) results in a marked increase in CDH3 expression analogous to that observed following the inhibition of endogenous BRCA1. The data provided suggest a model whereby BRCA1 and c-Myc form a repressor complex on the promoters of specific basal genes and represent a potential mechanism to explain the observed overexpression of key basal markers in BRCA1-deficient tumours.

The potential of electron beam radiation for simultaneous surface modification and bioresorption control of PLLA

Bioresorbable polymers have been widely investigated as materials exhibiting significant potential for successful application in the fields of tissue engineering and drug delivery. Further to the ability to control degradation, surface engineering of polymers has been highlighted as a key method central to their development. Previous work has demonstrated the ability of electron beam (e-beam) technology to control the degradation profiles and bioresorption of a number of commercially relevant bioresorbable polymers (poly-l-lactic acid (PLLA), Llactide/DL-lactide co-polymer (PLDL) and poly(lactic-co-glycolic acid (PLGA)). This work investigates the further potential of ebeam technology to impart added biofunctionality through the manipulation of polymer (PLLA) surface properties. PLLA samples were subjected to e-beam treatments in air, with varying beam energies and doses. Surface characterization was then performed using contact angle analysis, X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and atomic force microscopy. Results demonstrated a significant increase in surface wettability post e-beam treatment. In correlation with this, XPS data showed the introduction of oxygen-containing functional groups to the surface of PLLA. Raman spectroscopy indicated chain scission in the near surface region of PLLA (as predicted). However, e-beam effects on surface properties were not shown to be dependent on beam energy or dose. E-beam irradiation did not seem to affect the surface roughness of PLLA as a direct consequence of the treatment.

A novel dual-fluorescence strategy for functionally validating microRNA targets in 3-prime untranslated regions: regulation of the inward rectifier potassium channel Kir2.1 by miR-212.

Gene targeting by microRNAs is important in health and disease. We developed a functional assay for identifying microRNA targets and applied it to the K+ channel Kir2.1 (KCNJ2) which is dysregulated in cardiac and vascular disorders. The 3'UTR was inserted downstream of the mCherry red fluorescent protein coding sequence in a mammalian expression plasmid. MicroRNA sequences were inserted into the pSM30 expression vector which provides enhanced green fluorescent protein as an indicator of microRNA expression. HEK293 cells were co-transfected with the mCherry-3'UTR plasmid and a pSM30-based plasmid with a microRNA insert. The principle of the assay is that functional targeting of the 3'UTR by the microRNA results in a decrease in the red/green fluorescence intensity ratio as determined by automated image analysis. The method was validated with miR-1, a known downregulator of Kir2.1 expression, and was used to investigate targeting of the Kir2.1 3'UTR by miR-212. Red/green ratio was lower in miR-212-expressing cells compared to non-targeting controls, an effect that was attenuated by mutating the predicted target site. MiR-212 also reduced inward rectifier current and Kir2.1 protein in HeLa cells. This novel assay has several advantages over traditional luciferase-based assays including larger sample size, amenability to time course studies and adaptability to high-throughput screening.

Ecological impacts of an invasive predator explained and predicted by comparative functional responses

Forecasting the ecological impacts of invasive species is a major challenge that has seen little progress, yet the development of robust predictive approaches is essential as new invasion threats continue to emerge. A common feature of ecologically damaging invaders is their ability to rapidly exploit and deplete resources. We thus hypothesized that the 'functional response' (the relationship between resource density and consumption rate) of such invasive species might be of consistently greater magnitude than those of taxonomically and/or trophically similar native species. Here, we derived functional responses of the predatory Ponto-Caspian freshwater 'bloody red' shrimp, Hemimysis anomala, a recent and ecologically damaging invader in Europe and N. America, in comparison to the local native analogues Mysis salemaai and Mysis diluviana in Ireland and Canada, respectively. This was conducted in a novel set of experiments involving multiple prey species in each geographic location and a prey species that occurs in both regions. The predatory functional responses of the invader were generally higher than those of the comparator native species and this difference was consistent across invaded regions. Moreover, those prey species characterized by the strongest and potentially de-stabilizing Type II functional responses in our laboratory experiments were the same prey species found to be most impacted by H. anomala in the field. The impact potential of H. anomala was further indicated when it exhibited similar or higher attack rates, consistently lower prey handling times and higher maximum feeding rates compared to those of the two Mysis species, formerly known as 'Mysis relicta', which itself has an extensive history of foodweb disruption in lakes to which it has been introduced. Comparative functional responses thus merit further exploration as a methodology for predicting severe community-level impacts of current and future invasive species and could be entered into risk assessment protocols.