bluuebunny/crossref_metadata_2025 huggingface dataset:
Architectural complexity of a carbonate transgressive systems tract induced by basement physiography
Authors: MATEU‐VICENS GUILLEM , POMAR LUIS , TROPEANO MARCELLO
Published: June 2008

Three‐dimensional exposure of the Plio‐Pleistocene Calcarenite di Gravina Formation around Matera Horst, Italy, permits analysis of the architecture and internal complexities of carbonate sedimentary bodies around a palaeoisland. Spatial organization of the different lithosomes, along with their skeletal composition, sedimentary structures and bedding patterns, helps decipher the key factors that controlled platform architecture and distribution of heterogeneities: basement physiography, type and loci of carbonate production, bottom currents and changes in accommodation. Relative sea‐level changes resulted from high‐frequency glacioeustatic cycles that punctuated an overall tectonically induced transgression. Topographic relief, fragmentation of the limestone basement and wave energy controlled lithoclastic supply. Basement physiography and relative sea‐level changes determined the area available for carbonate‐producing biotas, and thus the amount and type of skeletal sediments. On the moderately dipping south‐western margin, waves and associated currents re‐distributed the lithoclasts derived from coastal abrasion. Bioclasts mostly derived from epiphytic seaweed production in the shoreface. Infralittoral prisms resulted from downdip transport (progradation) and longshore transport, which controlled along strike continuity of the prisms. Where basement continuity was interrupted at the margin of the palaeoisland, a lithoclastic fan was deposited from dumping sediments carried by shore‐parallel currents. Fan‐shaped skeletal bodies coalesced to form an apron on the steeper northern side of the palaeoisland, when a structural platform was flooded and epiphytic carbonates were shed. Red algae contribution depended on the available oligophotic area which, in turn, was controlled by high‐frequency sea‐level cycles, basement physiography and apron aggradation. The internal architecture of this apron resembles a low stand wedge but it accumulated during transgression. Deeper‐water, contour‐parallel currents formed a lithosome at the foot of the structural relief. Interpreted as drift deposits, it is composed of shallow‐water benthonic skeletal components, planktonic foraminifera and some limeclasts.
Improved long‐term graft function in pediatric transplant renal recipients with chronic allograft nephropathy
Authors: Kerecuk Larissa , Horsfield Catherine , Taylor Judy
Published: June 2008

Abstract:  CAN is the leading cause of graft loss in pediatric renal transplant recipients. A retrospective single centre analysis of pediatric transplant patients with CAN treated with MMF in conjunction with CNI minimisation/withdrawal is reported. 35 children were successfully started on MMF. The mean age at transplant was 7.9 ± 0.1 years. MMF was introduced 3.5 ± 0.1 years after transplantation and patients were followed up for a mean of 32.2 ± 0.5 months. CAN was confirmed on biopsy in 31 patients. CNI was stopped in 23 patients at a mean time of 16.5 ± 0.6 months after MMF introduction and minimised in the remaining patients. Prior to MMF introduction, GFR was deteriorating by 21.6 ± 0.07 ml/min/1.73 m2/yr. After MMF, there was an overall improvement in GFR of 4.0 ± 0.03 ml/min/1.73 m2/yr. This was most marked in the first six months when the GFR improved by 20.8 ± 0.06 ml/min/1.73 m2/day. Mean acute rejection episode rate prior to MMF was significantly reduced after MMF introduction. MMF was discontinued in a total of 4 patients due to adverse effects. CNI minimisation/withdrawal with MMF introduction is safe and leads to significant initial improvement with subsequent stabilisation of GFR and improved long term graft survival in pediatric renal transplant recipients with CAN.
Expression Patterns in Mouse Embryos of Neuroleukin/Glucose‐6‐Phosphate Isomerase and Autocrine Motility Factor Receptor
Authors: Repiso A. , Andrés R. , Climent F. , Ureña J. M.
Published: June 2008

The pattern of expression by using in situ hybridization in whole mouse embryos of the neuroleukin/glucose‐6‐phosphate isomerase (NK/GPI) gene and its receptor (AMF‐R) is reported. NK/GPI expression was first seen at embryonic day 9 whereas AMF‐R was detected at embryonic day 8; both were detected up to day 12 with NK/GPI showing peaking in the limbs around day 11. The main regions of expression are limb buds, spinal cord and brain. This work contributes to understanding how both proteins act in the development of somatosensory and motoric neural structures.
Representation of echo roughness and its relationship to amplitude‐modulation processing in the bat auditory midbrain
Authors: Borina Frank , Firzlaff Uwe , Schuller Gerd , Wiegrebe Lutz
Published: June 2008

Bats use natural landmarks such as trees for orientation. Echoes reflected by a tree are stochastic and complex. The degree of irregular loudness fluctuations of perceived echoes, i.e. the echo roughness, may be used to classify natural objects reliably. Bats are able to discriminate and classify echoes of different roughness. A neural correlate of the psychophysical roughness sensitivity has been described in the auditory cortex of the bat Phyllostomus discolor. Here, the role of the inferior colliculus of P.  discolor is explored in the neural representation of echo roughness. Using extracellular recording techniques, responses were obtained to simulated stochastic echoes of different roughness. The representation of these irregular loudness fluctuations in echoes is compared to the representation of periodic loudness fluctuations elicited by sinusoidal amplitude modulation (SAM) and to the shape of the peri‐stimulus time histogram in response to pure tones. About half the recorded units responded significantly differently to echoes with different roughness. Roughness sensitivity was related to the units’ sensitivity to the depth of an SAM: units that responded best to strong SAMs also responded best to echoes of high roughness. In response to pure tones, these units were typically characterized as Onset units. In contrast to the auditory cortex experiments, the responses of many units in the inferior colliculus decreased with increasing echo roughness. These units typically preferred weak SAMs and showed a sustained response to pure tones. The data show that auditory midbrain sensitivity to SAM is an important prerequisite for the neural representation of echo roughness as an ecologically important echo‐acoustic parameter.
Investigation of Adducin 2 (beta) DNA polymorphisms in genetic predisposition to diabetic nephropathy in Type 1 diabetes
Authors: Currie D. , Maxwell A. P. , Sadlier D. , McKnight A. J. ,   The Warren 3/UK GoKinD Study Group
Published: June 2008

Aims  Adducin 2 (beta) (ADD2) is a biological and positional candidate gene proposed to confer genetic risk for diabetic nephropathy. This study aimed to comprehensively investigate all common and putatively functional polymorphisms in the genomic region encompassing this gene.

Methods  Tag single nucleotide polymorphisms (n = 23) derived from phase II of the International HapMap Project and in silico functional variants (n = 2) were genotyped in 1467 White individuals from the British Isles (cases, n = 718; control subjects, n = 749) by a combination of Sequenom iPLEX and TaqMan technologies.

Results  χ2 analysis of genotype and allele frequencies in cases vs. control subjects revealed weak evidence for association of one variant at the 5% level of significance (rs10164951, P = 0.02). Adjusting for multiple testing in the present case–control collection negated this association.

Conclusions  We selected an appropriate subset of variants suitable for genetic investigations of the ADD2 gene and report the first investigation of polymorphisms in ADD2 with diabetic nephropathy. Our results suggest that common polymorphisms and putatively functional variants in the ADD2 gene do not strongly influence genetic susceptibility to diabetic nephropathy in this White population with Type 1 diabetes.
POSSIBLE GIRLS
Authors: SINHABABU NEIL
Published: June 2008

Abstract:  I argue that if David Lewis’ modal realism is true, modal realists from different possible worlds can fall in love with each other. I offer a method for uniquely picking out possible people who are in love with us and not with our counterparts. Impossible lovers and trans‐world love letters are considered. Anticipating objections, I argue that we can stand in the right kinds of relations to merely possible people to be in love with them and that ending a trans‐world relationship to start a relationship with an actual person isn't cruel to one's otherworldly lover.
DOING AND ALLOWING, THREATS AND SEQUENCES
Authors: WOOLLARD FIONA
Published: June 2008

Abstract:  The distinction between doing and allowing appears to have moral significance, but the very nature of the distinction is as yet unclear. Philippa Foot's ‘pre‐existing threats’ account of the doing/allowing distinction is highly influential. According to the best version of Foot's account an agent brings about an outcome if and only if his behaviour is part of the sequence leading to that outcome. When understood in this way, Foot's account escapes objections by Warren Quinn and Jonathan Bennett. However, more analysis is required to show what makes a relevant condition part of a sequence. Foot's account is promising, but incomplete.
On Gene Ranking Using Replicated Microarray Time Course Data
Authors: Chuan Tai Yu , Speed Terence P.
Published: June 2008

Summary Consider the ranking of genes using data from replicated microarray time course experiments, where there are multiple biological conditions, and the genes of interest are those whose temporal profiles differ across conditions. We derive a multisample multivariate empirical Bayes' statistic for ranking genes in the order of differential expression, from both longitudinal and cross‐sectional replicated developmental microarray time course data. Our longitudinal multisample model assumes that time course replicates are independent and identically distributed multivariate normal vectors. On the other hand, we construct a cross‐sectional model using a normal regression framework with any appropriate basis for the design matrices. In both cases, we use natural conjugate priors in our empirical Bayes' setting which guarantee closed form solutions for the posterior odds. The simulations and two case studies using published worm and mouse microarray time course datasets indicate that the proposed approaches perform satisfactorily.
A New Approach to Amino Acid Racemization in Enamel: Testing of a Less Destructive Sampling Methodology*
Authors: Griffin Rebecca C. , Moody Howard , Penkman Kirsty E.H. , Fagan Michael J. , Curtis Neil , Collins Matthew J.
Published: June 2008

Abstract:  Aspartic acid racemization has been found to be an accurate measure of age at death for recent forensic material. This paper examines the practicality of using acid etching of the tooth surface to extract amino acids from the enamel for racemization analysis. By serial etching of the tooth and contamination of the teeth with bovine serum albumin prior to etching, the ability of etching to remove contamination was assessed. The destructiveness of the method was visualized and quantified using micro‐computed tomography (micro‐CT). By bleaching the teeth and by deeper etching it was possible to obtain more consistent values. While etching had little effect on the enamel at the macroscale, it did have an impact at the microscale. The quantities of enamel removed varied depending upon the tooth morphology, but were not large. Acid etching of enamel thus appears to be a promising new method for extracting proteins for amino acid racemization age estimation noninvasively.
The effect of irritant dermatitis on cutaneous bioavailability of a metronidazole formulation, investigated by microdialysis and dermatopharmacokinetic method
Authors: García Ortiz Patricia , Hansen Steen Honoré , Shah Vinod P. , Menné Torkil , Benfeldt Eva
Published: June 2008

Background:  Determination of drug penetration in diseased skin represents a challenge.

Objective:  To compare dermal microdialysis and tape‐strip sampling of drug penetration in normal skin and skin with irritant dermatitis.

Methods:  The two methodologies were employed simultaneously in 16 healthy volunteers. Samples were collected in a study of the penetration of a metronidazole cream formulation (Flagyl® 1%) applied to forearm skin in both areas with irritant dermatitis and normal skin. Barrier perturbation and the depth of microdialysis probes were quantified by non‐invasive bioengineering methods.

Results:  Microdialysis showed a significant threefold increase in metronidazole penetration in skin with irritant dermatitis compared with unmodified skin. Conversely, the concentration of metronidazole in tape‐strip samples was significantly decreased in irritant dermatitis.

Conclusion:  The selection of sampling methodology should be based on the skin layer of interest as well as the integrity of the skin barrier. Whenever the dermal tissue is the target for topical treatment, microdialysis sampling should be the method of choice.
Involvement of the bulge region in primary scarring alopecia
Authors: Pozdnyakova Olga , Mahalingam Meera
Published: June 2008

While the pathogenesis of most scarring alopecias is poorly understood, one recent study indicates destruction of follicular stem cells as a possible mechanism in lichen planopilaris, the prototypic scarring alopecia. The aim of this cross‐sectional study was to ascertain the target of inflammation and to more precisely characterize the inflammatory infiltrate in various stages of primary scarring alopecias. Immunohistochemical studies were performed using a panel of antibodies that included anti‐cytokeratin 15, an antibody that specifically targets follicular bulge stem cells and CD4, CD8, CD1a and human leukocyte antigen‐DR to characterize the inflammatory infiltrate. Our data showing absence of follicular bulge stem cells in cases with moderate to heavy inflammation suggest involvement of the bulge region in ‘early’ active stages of primary scarring alopecia. The paucity of CD8+ T cells in the inflammatory infiltrate in the majority of these cases argues against a cell‐mediated cytotoxic destruction of follicular bulge stem cells. Preservation of CK15+ cells in ‘late’ fibrotic stages of primary scarring alopecia further supports this and implies that the irreversible loss of hair follicles, the sine qua non of primary scarring alopecia, is not necessarily a consequence of T cell‐mediated destruction of follicular bulge stem cells.
WHO Atlas on Global Resources for Persons with Intellectual Disabilities 2007: Key Findings Relevant for Low‐ and Middle‐Income Countries
Authors: Mercier Céline , Saxena Shekhar , Lecomte Jocelin , Cumbrera Marco Garrido , Harnois Gaston
Published: June 2008

Abstract  The World Health Organization (WHO) Atlas‐ID project was designed to collect, compile, and disseminate information on intellectual disabilities (ID) services and resources from across the world. This paper aims at selecting findings in the Atlas‐ID that can be used as a tool for advocacy, human rights awareness, development planning, and monitoring changes regarding resources for persons with intellectual disabilities and their families in countries with the lowest levels of income in the world. After consultation with experts in the field of ID, a questionnaire and its accompanying glossary were developed. This questionnaire was completed by national respondents from 147 countries, areas, and territories that are WHO members (response rate of 74.6% corresponding to 94.6% of the world population). Cross‐tabulations were calculated according to WHO region that the countries belong to as well as their levels of income. The data from the Atlas‐ID allowed for documenting similarities and differences among the poorest and the richest countries of the world in relation to ID. The most striking differences pertain to the areas of information, judicial protection, government benefits, financing, availability, and access to services. The Atlas‐ID allowed the identification of similarities and differences in resources and services between the four World Bank categories of countries income, and it demonstrated the extent of unmet needs in low‐income and low‐middle‐income countries, as well as some critical gaps between these countries and the high‐level income countries.
Growth of an NGO: The Indian Institute of Cerebral Palsy from 1974 to 2006
Authors: Sen Reena , Goldbart Juliet , Kaul Sudha
Published: June 2008

Abstract  The Indian Institute for Cerebral Palsy (IICP) has been providing education and other services in Kolkata, Eastern India, for children and young adults with cerebral palsy and related disabilities for over 30 years. IICP started by providing education for just two children, and was highly dependent on western expertise. Described is the history of the IICP and the strategy this organization used to develop itself into a primary service provider in Eastern India. Developments in recent years have demonstrated that IICP has moved from a small regional service, focusing on education of children with multiple disabilities to a large and complex organization. This has been possible because of the long‐standing commitment of its founding members, a close working relationship with partner organizations, mobilization of governmental support, and accessing financial aid from Indian and international donors. Throughout, the organization has set its own goals based on careful needs assessments and has used culturally appropriate methods in attaining them. It has established model projects and placed particular emphasis on education and provision, from parent education to degree level programs. It has fostered research and international dissemination, been in the forefront in informing and influencing government policy, and has supported self‐advocacy for people with disabilities to represent themselves. This case study approach is reflective of the manner that nongovernmental organizations—with local or regional responsibility to develop model services—can organize services and provides a “lesson's learned” model for organizations to undertake similar development.
Downregulation of protease‐activated receptor‐1 in human lung fibroblasts is specifically mediated by the prostaglandin E2 receptor EP2 through cAMP elevation and protein kinase A
Authors: Sokolova Elena , Hartig Roland , Reiser Georg
Published: June 2008

Many cellular functions of lung fibroblasts are controlled by protease‐activated receptors (PARs). In fibrotic diseases, PAR‐1 plays a major role in controlling fibroproliferative and inflammatory responses. Therefore, in these diseases, regulation of PAR‐1 expression plays an important role. Using the selective prostaglandin EP2 receptor agonist butaprost and cAMP‐elevating agents, we show here that prostaglandin (PG)E2, via the prostanoid receptor EP2 and subsequent cAMP elevation, downregulates mRNA and protein levels of PAR‐1 in human lung fibroblasts. Under these conditions, the functional response of PAR‐1 in fibroblasts is reduced. These effects are specific for PGE2. Activation of other receptors coupled to cAMP elevation, such as β‐adrenergic and adenosine receptors, does not reproduce the effects of PGE2. PGE2‐mediated downregulation of PAR‐1 depends mainly on protein kinase A activity, but does not depend on another cAMP effector, the exchange protein activated by cAMP. PGE2‐induced reduction of PAR‐1 level is not due to a decrease of PAR‐1 mRNA stability, but rather to transcriptional regulation. The present results provide further insights into the therapeutic potential of PGE2 to specifically control fibroblast function in fibrotic diseases.
Is computer‐assisted audiometry as reliable as manual audiometry in an NHS setting?
Authors: Ho T.P. , Hildreth T. , Lindsey L
Published: June 2008

Objectives.  The Otogram™ is a computer‐assisted audiometer.1 It assesses air conduction and bone conduction thresholds and administers masking when appropriate1. There has been no published research in a peer‐reviewed journal, validating it's use in a British population.2 We propose to investigate the reliability of the Otogram™ in an NHS setting.

Method.  This is a prospective non‐randomised study of 48 patients referred to an NHS Otology clinic. Each patient had two pure tone audiograms (PTAs). The first 16 patients had two manual PTAs performed by audiologists. Hearing thresholds were ascertained by audiologists and by the Otogram™ for the second group of 16 patients. The third group of 16 patients had two PTAs, each performed by the Otogram.

Results.  Ninety‐four percent of air conduction thresholds and 91% of bone conduction thresholds measured by the Otogram™ fell within 10 dB of thresholds measured by an audiologist. There was a high level of agreement in air conduction thresholds (κ = 0.96, 95%CI 0.95–0.97) and bone conduction thresholds (κ = 0.92, 95%CI 0.90–0.95) between audiologist and Otogram™. This compares favourably with the inter‐rater agreement between our audiologists for air conduction (κ = 0.94, 95%CI 0.92–0.95) and bone conduction (κ = 0.86, 95%CI 0.81–0.91).

Conclusions.  There is evidence that the Otogram™ is a reliable automated audiometer in the clinical setting. The Otogram™ has the potential to reduce NHS patient waiting times and to help audiology departments to reach their 18‐week Department of Health target.

References.  1 http://www.tympany.net

2 D’Agostino M.A. & Lee J. (2004) Manual audiometry vs. Self‐Automated Otogram : a comparison of testing outcomes. Otolaryngol.Head Neck Surg. 131, 81–82
Mulberry Anthocyanin Extracts Inhibit LDL Oxidation and Macrophage‐Derived Foam Cell Formation Induced by Oxidative LDL
Authors: Liu L.‐K. , Lee H.‐J. , Shih Y.‐W. , Chyau C.‐C. , Wang C.‐J.
Published: June 2008

ABSTRACT:  Low‐density lipoprotein (LDL) oxidation plays a role in atherosclerosis; therefore the lower the formation of oxidative LDL (oxLDL), the lower the occurrence of coronary heart diseases (CHD). Mulberry, the fruit of Morus alba L., is used effectively in Chinese medicines for prevention of CHD. However, the mechanism of this action is unclear. Two extracts, MWEs (mulberry water extracts) and MACs (mulberry anthocyanin‐rich extracts), which exhibit antioxidative and anti‐atherosclerogensis abilities in vitro. Data showed that MWEs and MACs were able to inhibit (P < 0.05) the relative electrophoretic mobility (REM), ApoB fragmentation, and thiobarbituric acid reaction substances (TBARS) formation in Cu2+‐mediated oxidation LDL. MWEs and MACs also had the ability of 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) radical scavenging for reducing the formation of free radicals mediated by copper ions. Furthermore, we observed that MWEs and MACs could decrease (P < 0.05) macrophage death induced by oxLDL. In addition, the MWEs and MACs also could inhibit (P < 0.05) the formation of foam cells. Both MWEs and MACs showed a great ability of scavenging radicals, inhibition of LDL oxidation, and decrease in atherogenic stimuli in macrophages, while the efficacy of MACs is 10‐fold greater than that of MWEs. It also demonstrated that anthocyanin components in mulberry extracts were regarded as the prevention of atherosclerosis.
Prevalence of optic disc drusen in an adult Chinese population: the Beijing Eye Study
Authors: You Qi Sheng , Xu Liang , Wang Ya Xing , Jonas Jost B.
Published: June 2008

Purpose:  This study aimed to determine the prevalence of optic disc drusen and their associations with ocular and general parameters.

Methods:  The Beijing Eye Study included 4439 of 5324 subjects invited to participate (response rate 83.4%). All subjects were aged ≥ 40 years. The present investigation involved 8594 (96.8%) eyes of 4324 (97.4%) subjects from whom readable fundus photographs of at least one eye were available. The main outcome parameter was the presence of optic disc drusen defined as round, whitish bodies.

Results:  Optic disc drusen were detected in nine (0.1 ± 0.05%) eyes of eight subjects (five women). The prevalence rate was 0.2 ± 0.07% (95% confidence interval 0.07−0.33%) per subject. Optic disc drusen were significantly associated with small optic discs (p < 0.001). They were not statistically associated with age (p = 0.90), gender (p = 0.73), intraocular pressure (p = 0.97), refractive error (p = 0.71), visual field defects (p = 0.47) or corrected visual acuity (p = 0.84).

Conclusions:  Optic disc drusen are present in about two in 1000 adult Chinese people in Northern China. The main associated factor is a small optic disc.
A Velocity Approach to Elasto-Plastic and Elasto-Viscoplastic Calculation by the Finite Element Method
Authors: Chenot J. L. , Bellet M.
Published: June 2008

A second order scheme for the time discretization of the elasto-plastic or elasto-viscoplastic behavior is proposed, based on a velocity approach. The complete set of equations is given for the evolution problem in the case of small rotations approximation. The method is quite general and may be applied to a large class of constitutive equations. The finite element discretization is briefly outlined and it is shown that the procedure is quite similar to that of previous displacement formulations. A numerical example concerning the sheet metal forming process, with an elasto-viscoplastic behavior and a membrane approximation, is presented. The numerical tests show a considerable improvement in accuracy for a given increment of time.
A Transient Electromagnetic Flowmeter and Calibration Facility
Authors: Lefebvre P. J. , Durgin W. W.
Published: June 2008

An electromagnetic flowmeter was developed to measure transient flows at a data rate of 60 Hz. The approach taken was to develop suitable electronics to replace the electronics of a commercially available electromagnetic flowmeter normally used for steady-state operation. Use of the commercially available flowmeter body, which includes the magnetic coils, core, and signal electrodes, provided a relatively economical means of fabricating the transient flowmeter. A transient flow calibration facility consisting of a free-falling water column was also designed and built. Results of the calibrations are presented and show that the flowmeter can accurately measure transient flows up to the maximum observed acceleration of approximately 1 g.
Impaired Naive and Memory B-Cell Responsiveness to TLR9 Stimulation in Human Immunodeficiency Virus Infection
Authors: Jiang Wei , Lederman Michael M. , Mohner Richard J. , Rodriguez Benigno , Nedrich Todd M. , Harding Clifford V. , Sieg Scott F.
Published: June 2008

Toll-like receptor 9 (TLR9) agonists such as unmethylated bacterial CpG DNAs activate B lymphocytes directly, potentially influencing their function and homeostasis. To assess B-cell responsiveness to TLR9 agonists in human immunodeficiency virus (HIV) disease, we examined the ability of naive and memory B cells to proliferation and to increase surface expression of CD80 in response to CpG oligonucleotides (ODN). CpG ODN induced expression of CD80 similarly in B cells from HIV-infected persons and from healthy controls. In contrast, proliferation responses to CpG ODN were markedly impaired in both naive and memory B-cell subsets from HIV-infected persons. Naive B-cell proliferation defects were related to plasma HIV RNA and, among memory B cells, to the frequencies of CD21-negative cells. Importantly, TLR9 mRNA levels were significantly diminished in freshly prepared naive B cells and especially so in memory B cells from HIV-positive viremic donors, suggesting a possible underlying mechanism for the observed functional impairments. Dose-response studies indicated that optimal induction of CD80 expression was achieved with much lower concentrations of CpG ODN than optimal induction of proliferation. We propose that the relatively low threshold of activation that is required for CD80 induction by CpG ODN might explain the preservation of this response in B cells from HIV-infected persons despite diminished TLR9 expression. Impaired responsiveness to TLR9 agonists may contribute to defects in humoral immunity in HIV infection.
Regulation of Cytokine Production by Virus-Specific CD8 T Cells in the Lungs
Authors: Fulton Ross B. , Olson Matthew R. , Varga Steven M.
Published: June 2008

Inflammation and the elimination of infected host cells during an immune response often cause local tissue injury and immunopathology, which can disrupt the normal functions of tissues such as the lung. Here, we show that both virus-induced inflammation and the host tissue environment combine to influence the capacity of virus-specific CD4 and CD8 T cells to produce cytokines in various tissues. Decreased production of cytokines, such as IFN-γ and TNF-α, by antigen-specific T cells is more pronounced in peripheral tissues, such as the lung and kidney, than in secondary lymphoid organs, such as the spleen or lymph nodes. We also demonstrate that tissues regulate cytokine production by memory T cells independently of virus infection, as memory T cells that traffic into the lungs of naïve animals exhibit a reduced ability to produce cytokines following direct ex vivo peptide stimulation. Furthermore, we show that cytokine production by antigen-specific memory CD4 and CD8 T cells isolated from the lung parenchyma can be rescued by stimulation with exogenous peptide-pulsed antigen-presenting cells. Our results suggest that the regulation of T-cell cytokine production by peripheral tissues may serve as an important mechanism to prevent immunopathology and preserve normal tissue function.
EcoR124I: from Plasmid-Encoded Restriction-Modification System to Nanodevice
Authors: Youell James , Firman Keith
Published: June 2008

Plasmid R124 was first described in 1972 as being a new member of incompatibility group IncFIV, yet early physical investigations of plasmid DNA showed that this type of classification was more complex than first imagined. Throughout the history of the study of this plasmid, there have been many unexpected observations. Therefore, in this review, we describe the history of our understanding of this plasmid and the type I restriction-modification (R-M) system that it encodes, which will allow an opportunity to correct errors, or misunderstandings, that have arisen in the literature. We also describe the characterization of the R-M enzyme EcoR124I and describe the unusual properties of both type I R-M enzymes and EcoR124I in particular. As we approached the 21st century, we began to see the potential of the EcoR124I R-M enzyme as a useful molecular motor, and this leads to a description of recent work that has shown that the R-M enzyme can be used as a nanoactuator. Therefore, this is a history that takes us from a plasmid isolated from (presumably) an infected source to the potential use of the plasmid-encoded R-M enzyme in bionanotechnology.
Balance between Phytoplankton Production and Plankton Respiration in Lakes
Authors: Giorgio Paul A. del , Peters Robert H.
Published: June 2008

We analyzed published rates of algal photosynthesis and plankton community respiration to test the hypothesis that the ratio of planktonic primary production to community (P/R) varies systematically with lake trophy. Regression analyses show that algal production and plankton respiration are closely related to chlorophyll concentrations for lakes spanning a wide trophic range. More surprisingly, plankton respiration exceeds algal photosynthesis in oligotrophic lakes, and P/R rises above unity only when chlorophyll concentrations are above 17 mg∙m−3. A simple allometric model based on the predicted biomasses of the different planktonic component yield rates of community respiration that are in good agreement with measured values. Moreover, the model suggest that in oligotrophic lakes, microbial respiration may greatly exceed the current estimates based on bacterial production data and that heterotrophs contribute proportionately more to total plankton metabolism than they do in eutrophic lakes. Because such high respiration rates require external energy subsidies, these results; challenge the view that pelagial communities of most lakes are even approximately self-supporting.
Seasonal Changes of Dissolved Oxygen and Plant Nutrients in Seawater near Salmonid Net Pens in the Macrotidal Bay of Fundy
Authors: Wildish D. J. , Keizer P. D. , Wilson A. J. , Martin J. L.
Published: June 2008

Seasonal observations for tidal periods of 12 or 24 h in, or near, Bay of Fundy salmonid mariculture sites were made. Variables measured included dissolved oxygen, salinity, temperature, chlorophyll a, current velocity, dissolved inorganic nitrogen, phosphate, and silicate. Circumstantial evidence suggests that the following processes were most important in controlling levels of dissolved oxygen: advection which supplies oxygen-saturated water and removes dissolved oxygen deficits; photosynthetic oxygen production which supersaturates seawater with dissolved oxygen during the spring and summer; and chemical and biological oxidation processes which could be dominant in removing dissolved oxygen during the night and in the late summer/fall when temperatures remain high but photosynthetic activity is low. Levels of nitrate, phosphate, and silicate were not increased by the salmonid mariculture industry above those typical of the oligotrophic Bay of Fundy, although ammonia levels were higher near the salmon net pens. During the summer, levels of silicate and dissolved inorganic nitrogen were diminished coincident with uptake by the microalgal bloom.
Instruments for Measuring Subice Algal Profiles and Productivity in situ
Authors: Herman A. W. , Knox D. F. , Conrad J. , Mitchell M. R.
Published: June 2008

Instruments have been developed for the in situ measurement of concentration and productivity of bottom ice algal layers in Resolute Passage, eastern Canadian Arctic. Measurements are accomplished by deploying an instrument on an arm articulated remotely through a hole in the ice, sampling the subice surface, and finally recovering the instrument and sample. The first instrument is an incubation system that is used to measure in situ productivity of a subice core. Results show the extent and range of productivity in bottom ice, with low and high biomass at the commencement of the algal bloom and near the end of the bloom period, respectively. The second instrument is a reflectance meter that can be used to measure chlorophyll profiles at the subice surface. The meter was calibrated against measured chlorophyll concentrations of extracted cores. After calibration the instrument can be used to measure integrated chlorophyll (milligrams per square metre) and profiles (milligrams per cubic metre) rapidly and synoptically. Deployment of the arm coupled with a plankton pump sampler is also briefly described.
Genetic, Environmental, and Interaction Effects on Growth and Stress Response of Chinook Salmon (Oncorhynchus tshawytscha) Fry
Authors: Heath Daniel D. , Bernier Nicholas J. , Heath John W. , Iwama George K.
Published: June 2008

Eight full- and half-sib families of chinook salmon (Oncorhynchus tshawytscha) were held during egg development at two temperatures (8.0 and 10.2 °C). As fry, these families were measured for relative growth rate, initial and final wet weight, hematocrit values before and 2 h after a 30-s handling stress, and plasma cortisol and glucose concentrations before and after stress. Significant sire effects were found for all measured traits, and significant dam effects were found for all traits except for the poststress increases in cortisol concentrations. There were significant genotype-by-environment interactions for all traits except unstressed (control) plasma glucose concentrations. Incubation temperature had a significant effect on relative growth rate and final wet weight only. We found a significant correlation between poststress plasma glucose concentration and relative growth rate for all fish, independent of family, while resting plasma cortisol concentration and poststress hematocrit correlated with wet weight only when analyzed within the eight individual families. Genetic contributions to stress-related parameters and genotype-by-environment interactions should be considered as a factor in stress-related research with fish.
Comparison of trichloroacetic acid with other protein-precipitating agents in enriching abnormal prion protein for Western blot analysis
Authors: LeBrun Matthew , Huang Hongsheng , He Runtao , Booth Stephanie , Balachandran Aru , Li Xuguang
Published: June 2008

Detection of the abnormal or the pathogenic form of prion protein (PrPSc) by Western blot (WB) is challenging, especially, for samples derived from cell cultures that contain low levels of PrPSc. A variety of PrPSc concentration methods have been reported with various PrPSc recovery efficiencies. Ultracentrifugation is one of the methods used frequently to enrich the pathogenic form of PrPSc prior to WB analyses. The resulting PrPSc pellet is extremely insoluble and often requires sonication to be dissolved, potentially generating aerosols. We modified the common protein-precipitating protocol using trichloroacetic acid to concentrate PrPSc by slow-speed centrifugation, followed by solubilization of the pellets with 6 mol/L urea prior to sodium dodecyl sulphate – polyacrylamide gel electrophoresis and WB analyses. Comparative studies suggest this simple trichloroacetic acid protocol was more effective in enriching PrPSc presented in cell cultures and brain homogenates than other reported protein-precipitating methods. Furthermore, incorporation of the urea treatment step to dissolve the precipitated PrPSc pellets helped to reduce the infectivity of PrPSc.
Quantitatively evaluating mistaken clone assignments by RFLP analysis of 16S rRNA genes: a case study
Authors: Zhang Han-Bo , Xu Chan-Wen , Wang Miao-Miao , Li Tao , Zhao Zhi-Wei
Published: June 2008

We quantitatively evaluated the errors of clone assignment based on the restriction fragment length polymorphism (RFLP) pattern of 16S rRNA genes. Eighty clones were randomly selected from a 16S rRNA gene library and were categorized into 35 operational taxonomic units (OTU) based on their indistinguishable enzyme restriction patterns of 3 tetrameric restriction enzymes RsaI, BsuRI, and HinfI. All of these clones were then sequenced and were reassigned into 36–53 OTUs using the DOTUR program when sequence similarities of 95%–100% were used. The number of the identically assigned clones ranged from 53 to 61 and the percentage varied from 66.3% to 76.3%. The Shannon–Weaver index for the bacterial community observed by RFLP analysis was 2.75, equal to that estimated by DOTUR at a 97% sequence similarity. Compared with clones assigned with the DOTUR program at a 97% sequence similarity, only 61 clones (76.3%) were correctly assigned by RFLP analysis. Six clones (7.5%) were assigned mistakenly at the phylum level, and the positions of 13 clones (16.2%) were phylogenetically different at a lower taxonomic rank.
Characterization of the promoter activity of a poxvirus conserved element
Authors: Eaton Heather E. , Metcalf Julie , Brunetti Craig R.
Published: June 2008

The conserved sequence element (CSE) is a highly conserved 42-bp poxvirus sequence that can function as a poxvirus promoter element. The CSE is composed of 2 repeats, each containing the highly conserved late poxvirus promoter sequence TAAAT. To define the location of the nucleotides critical for promoter function, polymerase chain reaction was carried out using primers that inserted modified versions of the CSE upstream of the green fluorescent protein (GFP), and the constructs were transiently transfected into cells by using GFP levels as a measure of promoter function. The results of this analysis revealed that the second TAAAT sequence, but not the first TAAAT sequence, is critical for promoter function of the CSE. Furthermore, deletion of half of the intervening sequence, i.e., from 10 to 5 nt, increases the promoter strength of the CSE as compared with the wild-type CSE. These results indicate the potential of this novel poxvirus promoter for driving high levels of gene expression.
A NEW IRREGULARITY CRITERION FOR DISCRIMINATION OF STOCHASTIC AND DETERMINISTIC TIME SERIES
Authors: OMIDVARNIA AMIR H. , NASRABADI ALI M.
Published: June 2008

In this paper, a new irregularity criterion based on fractal dimensions is introduced. In fact, this criterion (which is called ONH criterion) is the state space version of Higuchi fractal dimension, which can discriminate stochastic and deterministic time series from each other. To compute this criterion, we have exploited "the amount of state vectors fluctuations" in embedding space. By varying the reconstruction delay in embedding space, one can obtain a logarithmic diagram of overall changes corresponding to reconstructed state space versus delays. The slope of the linear region of this diagram could be considered as a new irregularity criterion. To discriminate random and deterministic time series, this criterion is adopted as a new statistic for hypothesis testing. Probability density function of this statistic under H0hypothesis is constructed and regarding to a certain confidence level, one can determine whether randomness is accepted or rejected.
THE MULTIFRACTAL DIMENSION FUNCTIONS OF HOMOGENEOUS MORAN MEASURE
Authors: XIAO JIAQING , WU MIN
Published: June 2008

In this paper we attain the multifractal dimension functions of Moran measure associated with homogeneous Moran fractals and give a sufficient condition which ensures the multifractal spectrum of Moran measure is equal to the Legendre transform of the multifractal dimension functions. As an application of this method, we give an example and a counterexample about the validity of the multifractal formalism of Moran measure.
Sampling of cardiovascular data; how often and how much?
Authors: Guild Sarah-Jane , Barrett Carolyn J. , McBryde Fiona D. , Van Vliet Bruce N. , Malpas Simon C.
Published: June 2008

Long-term measurement of cardiovascular variables by telemetry in laboratory animals has become indispensable in recent years. However, limited battery life and management of large volumes of recorded data are major drawbacks. These limitations can often be overcome by intermittent sampling of data. The question is, how much data does one need to collect to accurately reflect the underlying average value? To investigate this, 24-h continuous recordings of rabbit heart rate, arterial pressure, and integrated renal sympathetic nerve activity (RSNA) were resampled using a variety of protocols that differed with respect to the number of individual sampling periods used and the total amount of time that was sampled. The absolute percentage errors of estimates of the daily mean, standard deviation, and interquartile range were calculated for each sampling protocol. A similar analysis was repeated using arterial pressure data from rats. The results show that the number of sampling periods spread throughout the day had more effect than the total amount of data recorded. For example, just 2 h of total sampling time spread over 12 evenly spaced 10-min periods gave estimates of the daily mean of blood pressure and heart rate with < 1% error and RSNA with < 3% error. We show that accurate estimates of the daily mean of arterial pressure, heart rate, and RSNA can all be made using scheduled recording, and we recommend recording a minimum of 2 h/day spread over a number of periods throughout the day.
α-Adducin mutations increase Na/K pump activity in renal cells by affecting constitutive endocytosis: implications for tubular Na reabsorption
Authors: Torielli Lucia , Tivodar Simona , Montella Rosa Chiara , Iacone Roberto , Padoani Gloria , Tarsini Paolo , Russo Ornella , Sarnataro Daniela , Strazzullo Pasquale , Ferrari Patrizia , Bianchi Giuseppe , Zurzolo Chiara
Published: June 2008

Genetic variation in α-adducin cytoskeletal protein is implicated in the polymerization and bundling of actin and alteration of the Na/K pump, resulting in abnormal renal sodium transport and hypertension in Milan hypertensive rats and humans. To investigate the molecular involvement of α-adducin in controlling Na/K pump activity, wild-type or mutated rat and human α-adducin forms were, respectively, transfected into several renal cell lines. Through multiple experimental approaches (microscopy, enzymatic assays, coimmunoprecipitation), we showed that rat and human mutated forms increased Na/K pump activity and the number of pump units; moreover, both variants coimmunoprecipitate with Na/K pump. The increased Na/K pump activity was not due to changes in its basolateral localization, but to an alteration of Na/K pump residential time on the plasma membrane. Indeed, both rat and human mutated variants reduced constitutive Na/K pump endocytosis and similarly affected transferrin receptor trafficking and fluid-phase endocytosis. In fact, α-adducin was detected in clathrin-coated vesicles and coimmunoprecipitated with clathrin. These results indicate that adducin, besides its modulatory effects on actin cytoskeleton dynamics, might play a direct role in clathrin-dependent endocytosis. The constitutive reduction of the Na/K pump endocytic rate induced by mutated adducin variants may be relevant in Na-dependent hypertension.
Mechanical Behaviour and Microstructure of Aluminum-Steel Sheets Joined by FSSW
Authors: Bozzi S. , Etter A. L. , Baudin T. , Robineau A. , Goussain J. C.
Published: June 2008

At the prospect of a lightening of the automobile
structures, welded spots have been realized on a stacking of
two sheets (a 6008 aluminum alloy on steel) Friction Stir
Spot welding (FSSW). Different process parameters have been
tested, but only the influence of the dwell time will be
described in the present paper. The dwell time corresponds to
the time during which the probe stays in rotation at its
bottom location before extracting. A study of the
microstructures and textures associated to mechanical tests
(tensile shear tests) allowed determining the best set of
welding parameters. The recrystallized area around the welding
spot has been characterized by electron back-scattered
diffraction (EBSD). A mechanism of continuous dynamic
recrystallization has been identified since the misorientation
of subboundaries increases close to the weld, and this is for all
the dwell times tested. Elsewhere, the increase of the dwell
time induced a larger recrystallized zone. It has also been
found that a long dwell time induced a larger welded area but
also a higher quantity of intermetallic compounds (especially
FeAl, Fe2Al7, and FeAl2) with high-microhardness values (up to 800 Hv). Thus, the dwell time must not exceed a certain value, otherwise it can weaken the weld.