bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction of CheY2 and CheY2‐P with the cognate CheA kinase in the chemosensory‐signalling chain of Sinorhizobium meliloti
Authors: Riepl Hubert , Maurer Till , Kalbitzer Hans Robert , Meier Veronika M. , Haslbeck Martin , Schmitt Rüdiger , Scharf Birgit
Published: June 2008

An unusual regulatory mechanism involving two response regulators, CheY1 and CheY2, but no CheZ phosphatase, operates in the chemotactic signalling chain of Sinorhizobium meliloti. Active CheY2‐P, phosphorylated by the cognate histidine kinase, CheA, is responsible for flagellar motor control. In the absence of any CheZ phosphatase activity, the level of CheY2‐P is quickly reset by a phospho‐transfer from CheY2‐P first back to CheA, and then to CheY1, which acts as a phosphate sink. In studying the mechanism of this phosphate shuttle, we have used GFP fusions to show that CheY2, but not CheY1, associates with CheA at a cell pole. Cross‐linking experiments with the purified proteins revealed that both CheY2 and CheY2‐P bind to an isolated P2 ligand‐binding domain of CheA, but CheY1 does not. The dissociation constants of CheA–CheY2 and CheA–CheY2‐P indicated that both ligands bind with similar affinity to CheA. Based on the NMR structures of CheY2 and CheY2‐P, their interactions with the purified P2 domain were analysed. The interacting surface of CheY2 comprises its C‐terminal β4‐α4‐β5‐α5 structural elements, whereas the interacting surface of CheY2‐P is shifted towards the loop connecting β5 and α5. We propose that the distinct CheY2 and CheY2‐P surfaces interact with two overlapping sites in the P2 domain that selectively bind either CheY2 or CheY2‐P, depending on whether CheA is active or inactive.
Cysteine proteases XCP1 and XCP2 aid micro‐autolysis within the intact central vacuole during xylogenesis in Arabidopsis roots
Authors: Avci Utku , Earl Petzold H. , Ismail Ihab O. , Beers Eric P. , Haigler Candace H.
Published: June 2008

Establishing the mechanisms regulating the autolysis of xylem tracheary elements (TEs) is important for understanding this programmed cell death process. These data demonstrate that two paralogous Arabidopsis thaliana proteases, XYLEM CYSTEINE PROTEASE1 (XCP1) and XCP2, participated in micro‐autolysis within the intact central vacuole before mega‐autolysis was initiated by tonoplast implosion. The data acquisition was aided by the predictable pattern of seedling root xylogenesis, the availability of single and double total knock‐out T‐DNA lines, anti‐sera that recognized XCP1 and XCP2, and the microwave‐assisted processing of whole seedlings prior to immunolabeling and observation in the transmission electron microscope. During secondary wall thickening, XCP1 and XCP2 (in wild type), XCP1 (in xcp2 seedlings) or XCP2 (in xcp1 seedlings) were imported into the TE central vacuole. Both XCP1 and XCP2 heavily labeled dense aggregates of material within the vacuole. However, because of XCP1 deficiency in xcp1 and xcp1 xcp2 TEs, non‐degraded cellular remnants first accumulated in the vacuole and then persisted in the TE lumen (longer than in the wild type) after the final mega‐autolysis was otherwise complete. This delayed TE clearing phenotype in xcp1 was rescued by complementation with wild‐type XCP1. Although TEs in the xcp2 single knock‐out cleared comparably with wild type, the non‐degraded remnants in xcp1 xcp2 TEs were more densely packed than in xcp1 TEs. Therefore, XCP2 has a minor but distinct role in micro‐autolysis. After tonoplast implosion, XCP1 and XCP2 remained associated with disintegrating cellular material as mega‐autolysis, aided by additional lytic enzymes, destroyed the bulk of the cellular contents.
Profile of vitiligo in the south of Tunisia
Authors: Akrem Jalel , Baroudi Aicha , Aichi Taher , Houch Fethi , Hamdaoui Mohamed Hédi
Published: June 2008

Background  Vitiligo is a depigmentation disorder characterized by the loss of melanocytes from cutaneous cells. Its pathogenesis has not yet been clarified.

Objective  To study the epidemiologic profile of vitiligo in Tunisia and analyze its characteristics.

Methods  The clinical presentation of vitiligo was examined in 60 patients [27 males (45%) and 33 females (55%)] attending the Médenine Hospital Center, a large hospital in the south of Tunisia.

Results  The lower limbs were the initial site of onset of vitiligo in the majority of patients (29.8%), followed by the upper limbs, head and neck, trunk, and mucosae. The most common clinical pattern observed was vitiligo vulgaris, followed by focal, acrofacial, mucosal, segmental, and universal types. Leukotrichia was observed in 23%, koebnerization in 18.5%, and a positive family history in 18%.

Conclusion  This study indicates that vitiligo vulgaris is the most common clinical type observed in the south of Tunisia. There were associated endocrine disorders in some patients, including diabetes, hypothyroidism, and alopecia.
Kindler syndrome: a study of five Egyptian cases with evaluation of severity
Authors: Nofal Eman , Assaf Magda , Elmosalamy Khaled
Published: June 2008

Background  Kindler syndrome (KS) is a rare genodermatosis characterized by four major features (acral blisters, photosensitivity, poikiloderma, and cutaneous atrophy) and many associated findings. The diagnosis of KS includes clinical features, ultrastructural findings, and, recently, immunostaining and genetic studies. Varying degrees of severity of the syndrome have been described.

Methods  Five patients with clinical features consistent with KS were included in this study. All patients were subjected to histopathologic and ultrastructural studies.

Results  Cases 1 and 2 presented with severe major features, severe mucosal involvement, and many other associated findings. Case 3 presented with severe major features, but mild and limited mucosal involvement and other associated findings. Cases 4 and 5 showed mild major features and few other findings. Histopathology revealed nonspecific poikiloderma. Marked thickening of the lamina densa and splitting of the lamina lucida were the main ultrastructural findings.

Conclusion  KS may be classified into mild, moderate, and severe according to the severity of the major features and mucosal involvement. Because histopathologic and ultrastructural findings are not pathognomonic, clinical features remain the mainstay for the diagnosis of KS, and the need for immunostaining with kindlin antibody and genetic studies may be restricted to early cases with incomplete features.
Diacylglycerol pyrophosphate inhibits the α‐amylase secretion stimulated by gibberellic acid in barley aleurone
Authors: Racagni Graciela , Villasuso Ana L. , Pasquaré Susana J. , Giusto Norma M. , Machado Estela
Published: June 2008

ABA plays an important regulatory role in seed germination because it inhibits the response to GA in aleurone, a secretory tissue surrounding the endosperm. Phosphatidic acid (PA) is a well‐known intermediary in ABA signaling, but the role of diacylglycerol pyrophosphate (DGPP) in germination processes is not clearly established. In this study, we show that PA produced by phospholipase D (E.C. 3.1.4.4) during the antagonist effect of ABA in GA signaling is rapidly phosphorylated by phosphatidate kinase (PAK) to DGPP. This is a crucial fact for aleurone function because exogenously added dioleoyl‐DGPP inhibits secretion of α‐amylase (E.C. 3.2.1.1). Aleurone treatment with ABA and 1‐butanol results in normal secretory activity, and this effect is reversed by addition of dioleoyl‐DGPP. We also found that ABA decreased the activity of an Mg2+‐independent, N‐ethylmaleimide‐insensitive form of phosphatidate phosphohydrolase (PAP2) (E.C. 3.1.3.4), leading to reduction of PA dephosphorylation and increased PAK activity. Sequence analysis usingArabidopsis thalianalipid phosphate phosphatase (LPP) sequences as queries identified two putative molecular homologues, termedHvLPP1andHvLPP2, encoding putative Lpps with the presence of well‐conserved structural Lpp domains. Our results are consistent with a role of DGPP as a regulator of ABA antagonist effect in GA signaling and provide evidence about regulation of PA level by a PAP2 during ABA response in aleurone.
Clinical reasoning in neurology: Use of the repertory grid technique to investigate the reasoning of an experienced occupational therapist
Authors: Kuipers Kathy , Grice James W.
Published: June 2008

Background/aim:  The aim of this paper is to describe the use of a structured interview methodology, the repertory grid technique, for investigating the clinical reasoning of an experienced occupational therapist in the domain of upper limb hypertonia as a result of brain injury.

Method:  Repertory grid interviews were completed before and after exposure to a protocol designed to guide clinical reasoning and decision‐making in relation to upper limb neurological rehabilitation. Data were subjected to both qualitative and quantitative analyses.

Results:  Qualitative analysis focussed on clinical reasoning content. Common themes across the pre‐ and post‐exposure interviews were the use of theoretical frameworks and practice models, the significance of clinical expertise, and discrimination of ‘broad’ and ‘specific’ aspects, as well as differentiation between ‘therapist and client‐related’ aspects of the clinical situation. Quantitative analysis indicated that for both pre‐ and post‐exposure repertory grids, clinical reasoning was structured in terms of two main concepts. In the pre‐exposure grid, these were related to the therapist's role, and to the ‘scope’ of practice tasks (either broad or specific). In the post‐exposure grid the two main concepts were upper limb performance, and client‐centred aspects of the therapy process.

Conclusions:  The repertory grid technique is proposed as an effective tool for exploring occupational therapy clinical reasoning, based on its capacity for accessing personal frames of reference, and elucidating both the meaning and the structure supporting clinical reasoning.
Systematic review of quality of life following laparoscopic and open colorectal surgery
Authors: Dowson H. M. , Cowie A. S. , Ballard K. , Gage H. , Rockall T. A.
Published: June 2008

Objective  To compare the health‐related quality of life (HRQoL) of patients following laparoscopic and open colorectal surgery.

Method  A systematic review was performed according to Quorum guidelines. Prospective studies comparing the HRQoL of patients after laparoscopic and open colorectal surgery were identified. The primary outcome measure was postoperative quality of life; performance status and cosmesis were secondary outcome measures.

Results  Twenty‐three studies were identified that satisfied the inclusion criteria; 18 assessed HRQoL, four performance status, and three cosmesis. It was not possible to perform a meta‐analysis due to study heterogeneity. The studies reported outcomes for 2946 patients. The most frequent HRQoL instruments employed were Short Form 36, European Organization for Research and Treatment of Cancer, and gastrointestinal quality of life index. Six studies, using a total of 12 separate measures, evaluated QoL during the first three postoperative months: 10 of these measures showed no significant difference, and two showed an improved HRQoL with laparoscopy. Twelve further studies evaluated HRQoL up to 5 years postoperatively: nine showed no difference between the two groups, and three demonstrated a benefit for laparoscopy. Three of four studies assessing performance status on discharge, and all three studies assessing cosmesis, reported benefits with the laparoscopic approach.

Conclusions  The current evidence suggests there is no significant difference in HRQoL following laparoscopic and open colorectal surgery, although there is a lack of good quality data. There is a trend towards improved quality of life outcomes and performance status with laparoscopy in the early postoperative period. There is a need for further research, particularly assessing quality of life in the early postoperative period.
PLACE‐MAKING AND ‘GREEN’ REUSES OF BROWNFIELDS IN THE RUHR
Authors: FRANZ MARTIN , GÜLES ORHAN , PREY GISELA
Published: June 2008

Depending on location, size and former use, brownfields in the Ruhr have different potentials. Besides brownfields where viable regeneration projects are possible there are many sites that are not attractive to the market. One type of use for this category is post‐industrial nature (e.g. industrial forests). Following the overall concept of sustainable development, these sites offer potentials for creative ‘place‐making’ by local residents. The approach of ‘place‐making’ is embedded in the discussion of establishing local governance in urban districts of the Ruhr. Introducing one best‐practice‐case (the Rheinelbe industrial forest in Gelsenkirchen), the paper focuses on the discussion of ‘place‐making’ as a strategy for innovative brownfield development and local governance using the example of the former Lohberg colliery in Dinslaken.
Metastatic Crohn's disease: a review
Authors: Palamaras I , El‐Jabbour J , Pietropaolo N , Thomson P , Mann S , Robles W , Stevens HP
Published: June 2008

Metastatic Crohn's disease (MCD) indicates the presence of non‐caseating granuloma of the skin at sites separated from the gastrointestinal tract by normal tissue and is the least common dermatologic manifestation of CD. In adults, MCD usually appears after the initial diagnosis of CD in 70% of cases, whereas in children, it appears at the same time as CD in almost half of the cases. The most frequent skin lesions in adults are nodules, plaques with or without ulceration on the extremities and ulcers on the genitals. In children, genital swelling with or without erythema is the most frequent presentation of MCD. Simultaneous presence of perianal CD affects more females (60%) and particularly children. Associated gastrointestinal symptoms are present in one third of the cases in adults and in half of the cases in children. Treatment is often unsatisfactory. Randomised controlled trials are lacking. Various chemotherapeutic agents have been used such as oral metronidazole, topical and/or oral steroids, azathioprine, cyclosporine, sulfasalazine, tetracyclines, topical or systemic tacrolimus, infliximab alone or with methotrexate, and surgical treatment with oral zinc sulphate. MCD represents another ‘great imitator’. This reviews the most relevant characteristics of this disease, in order to increase awareness and to avoid delay in diagnosis and improve management of the whole CD complex.
A Bayesian Spatial Multimarker Genetic Random‐Effect Model for Fine‐Scale Mapping
Authors: Tsai M.‐Y. , Hsiao C. K. , Wen S.‐H.
Published: June 2008

Multiple markers in linkage disequilibrium (LD) are usually used to localize the disease gene location. These markers may contribute to the disease etiology simultaneously. In contrast to the single‐locus tests, we propose a genetic random effects model that accounts for the dependence between loci via their spatial structures. In this model, the locus‐specific random effects measure not only the genetic disease risk, but also the correlations between markers. In other words, the model incorporates this relation in both mean and covariance structures, and the variance components play important roles. We consider two different settings for the spatial relations. The first is our proposal, relative distance function (RDF), which is intuitive in the sense that markers nearby are likely to correlate with each other. The second setting is a common exponential decay function (EDF). Under each setting, the inference of the genetic parameters is fully Bayesian with Markov chain Monte Carlo (MCMC) sampling. We demonstrate the validity and the utility of the proposed approach with two real datasets and simulation studies. The analyses show that the proposed model with either one of two spatial correlations performs better as compared with the single locus analysis. In addition, under the RDF model, a more precise estimate for the disease locus can be obtained even when the candidate markers are fairly dense. In all simulations, the inference under the true model provides unbiased estimates of the genetic parameters, and the model with the spatial correlation structure does lead to greater confidence interval coverage probabilities.
Three‐Dimensional Culture Environments Enhance Osteoblast Differentiation
Authors: Boehrs Jessica , Zaharias Rebecca S. , Laffoon John , Ko Y. Joon , Schneider Galen B.
Published: June 2008

Purpose: In previous work from our laboratory, we demonstrated that the three‐dimensional (3D) cell cultures developed in simulated microgravity environments enhanced osseous‐like aggregate formation and accelerated preosteoblast cell differentiation. Thus, as described here, we hypothesize that aggregate formation and mineralization would occur with fewer than 10 × 106 cells as previously described.

Materials and Methods: Human preosteoblastic cells were cultured at different concentrations in a rotary wall vessel to simulate microgravity for 7 days. Aggregate size was assessed, and mineralization and collagen expression detected using Von Kossa and Masson Trichrome staining. Scanning electron microscopy was used for structural and elemental analysis. Immunohistochemistry was used to detect expression of the osteogenic markers BSPII and osteopontin (OP).

Results: Size and calcium expression were dependent upon cultured cell number (p < 0.01). Calcium and collagen expression were detected throughout the aggregate, but organization was independent of cell number. Aggregates had similar microscopic structural patterns demonstrating organized development. Presence of BSPII and OP showed that the aggregates share common differentiation proteins with in vivo bone formation.

Conclusions: These results may lead to novel bone engineering techniques associated with dental treatment.
PerioGlas® Regulates Osteoblast RNA Interfering
Authors: Palmieri Annalisa , Pezzetti Furio , Spinelli Giuseppe , Arlotti Marzia , Avantaggiato Anna , Scarano Antonio , Scapoli Luca , Zollino Ilaria , Carinci Francesco
Published: June 2008

Purpose: PerioGlas® (PG) is an alloplastic material that has been used for grafting periodontal osseous defects since the 1990s. In animal models, it has been proven that PG achieves histologically good repairs of surgically created defects. In clinical trials, PG is effective as an adjunct to conventional surgery in the treatment of intrabony defects; however, how PG alters osteoblast activity to promote bone formation is poorly understood. We therefore attempted to address this question by using microRNA (miRNA) microarray techniques to investigate the translation process in osteoblasts exposed to PG.

Materials and Methods: By using miRNA microarrays containing 329 probes designed from human miRNA sequences, we identified several miRNA whose expression was significantly modified in osteoblast‐like cell lines (MG‐63) cultured with PG.

Results: There were ten up‐regulated miRNA (mir‐337, mir‐377, mir‐9, mir‐516, mir‐515‐3p, mir‐496, mir‐200b, mir‐489, mir‐25, mir‐423) and two down‐regulated miRNA (mir‐26a, mir‐30d).

Conclusion: PG acts on miRNAs, which in turn regulate several messengers. Among them there are mRNAs related to bone formation and skeletal and cartilage development. The vast majority of detected genes are down‐regulated, and some are homeobox genes like NOG, EN1, and CHRD. Other down‐regulated genes are receptors (like GHRHR) and extracellular matrix proteins (like COMP). Although the exact mechanism of PG action on osteoblasts is still incompletely understood, these data demonstrate that PG has not only an osteoconductive effect, but also regulates bone formation.
Dual Path: A Concept to Improve the Esthetic Replacement of Missing Anterior Teeth with a Removable Partial Denture
Authors: Carreiro Adriana da Fonte Porto , Machado Ana Lucia , Giampaolo Eunice Teresinha , Santana Ivone Lima , Vergani Carlos Eduardo
Published: June 2008

The dual path of insertion concept for removable partial denture (RPD) design may be used in esthetically demanding situations. When compared to conventional RPDs, the main advantage of this design is the minimal use of clasps. This clinical report describes the treatment of a patient with an anterior maxillary edentulous area using a dual path RPD. The diagnostic cast was surveyed to ensure the adequacy of the undercuts on the mesial surfaces of the anterior abutments, where rigid minor connectors were placed. Inverted V‐shaped canine cingulum rest seats were prepared to provide resistance to tooth movement during function. The dual path RPD concept allows excellent esthetic results, minimizes tooth preparation, and reduces the tendency toward plaque accumulation in a Kennedy class IV partially edentulous arch.
Imaging the Brain's Highways—Diffusion Tensor Imaging in Epilepsy
Authors: Duncan John S.
Published: June 2008

Diffusion tensor imaging evaluates the motion of water at the voxel level and can provide data on the structural integrity of brain tissue, with quantitative measures of diffusion and fractional anisotropy. Imaging of the orientation of preferential diffusion of water in the brain can visualize major white matter pathways and infer the structural basis of cerebral networks. Thus, how these pathways and networks may be altered in specific epilepsy syndromes and in consequence to therapies can be assessed with the aid of these images.
The Masquerades of Temporal Lobe Epilepsy in Childhood
Authors: Blume Warren T.
Published: June 2008

Age-Dependent Seizure Semiology in Temporal Lobe Epilepsy. Fogarasi A, Tuxhorn I, Janszky J, Janszky I, Rásonyi G, Kelemen A, Halász P. Epilepsia 2007;48(9):1697–1702. Epub 2007 May 23. OBJECTIVE: To examine the effects of age on different aspects of temporal lobe seizure semiology. METHODS: We performed a video analysis of 605 archived seizures from 155 consecutive patients (age 10 months to 49 years) selected by seizure freedom after temporal lobectomy. Eighty patients had hippocampal sclerosis (HS). Beside semiological seizure classification, we assessed age dependency of several axes of seizure semiology: ( 1 ) aura, ( 2 ) number of different lateralizing signs, occurrence of ictal ( 3 ) emotional signs, ( 4 ) autonomic symptoms, ( 5 ) automatisms, and ( 6 ) secondary generalization as well as ( 7 ) the ratio of motor seizure components. RESULTS: From the 155 patients, 117 reported aura, 39 had ictal emotional signs, 51 had autonomic symptoms, 130 presented automatisms, while 18 patients showed secondary generalization at least once during their seizures. Altogether 369 (median: 2/patient) different lateralizing signs were recorded. Frequency of HS (p < 0.001), ictal automatisms (p < 0.001), secondary generalization (p = 0.014), number of different lateralizing signs (p < 0.001) increased while the ratio of motor seizure component (p = 0.007) decreased by age. Auras, emotional symptoms, and autonomic signs occurred independently of patients’ ages. Hippocampal sclerosis adjusted linear models revealed that the frequency of automatisms and secondarily generalized seizures as well as the number of different lateralizing signs are HS-independent significant variables. CONCLUSION: Our findings support that brain maturation significantly influences the evolution of some important aspects (motor seizures, lateralizing signs) of temporal lobe seizure semiology. Conversely, other aspects (aura, emotional, and autonomic signs) are independent of the maturation process. This is the first report investigating age dependency of epileptic seizure semiology comparing all age groups.
Dual effects of melatonin on oxidative stress after surgical brain injury in rats
Authors: Lee Steve , Jadhav Vikram , Ayer Robert E. , Rojas Hugo , Hyong Amy , Lekic Tim , Tang Jiping , Zhang John H.
Published: June 2008

Abstract:  The purpose of this study was to evaluate the effect of melatonin on oxidative stress occurring in the brain after routine lobectomy neurosurgery procedures. Different concentrations of melatonin (5, 15 and 150 mg/kg) were administered 1 hr before lobectomy in a rodent surgical brain injury (SBI) model. Neurological outcomes were assessed 24 hr before the killing of the rodents, for evaluation of brain water content (brain edema) and lipid peroxidation (oxidative stress). The results showed that lower doses (5 and 15 mg/kg) failed to reduce brain edema, but the 15 mg/kg dose did lower oxidative stress and improved several neurological parameters. High concentration of melatonin (150 mg/kg) significantly increased brain edema and elevated oxidative stress when compared with the vehicle‐treated group. Furthermore, high‐dose melatonin also worsened neurological outcomes compared with other groups. The study suggests that melatonin has dual effects: low‐dose melatonin may provide neuroprotective effects against SBI but a high dose may aggravate some parameters after SBI.
Ubiquitylation is Required for Degradation of Transmembrane Surface Proteins in Trypanosomes
Authors: Chung Wei‐Lian , Leung Ka Fai , Carrington Mark , Field Mark C.
Published: June 2008

The surface of Trypanosoma brucei is dominated by glycosyl‐phosphatidylinositol (GPI)‐anchored proteins, and endocytosis is clathrin dependent. The vast majority of internalized GPI‐anchored protein is efficiently recycled, while the processes by which transmembrane domain (TMD) proteins are internalized and sorted are unknown. We demonstrate that internalization of invariant surface glycoprotein (ISG)65, a trypanosome TMD protein, involves ubiquitylation and also requires clathrin. We find a hierarchical requirement for cytoplasmic lysine residues in internalization and turnover, and a single position‐specific lysine is sufficient for degradation, surface removal and attachment of oligoubiquitin chains. Ubiquitylation is context dependent as provision of additional lysine residues by C‐terminal fusion of neuronal precursor cell‐expressed developmentally downregulated protein (NEDD)8 fails to support ubiquitylation. Attachment of NEDD8 leads to degradation by a second ubiquitin‐independent pathway. Moreover, degradation of ubiquitylated or NEDDylated substrate takes place in an acidic compartment and is proteosome independent. Significantly, in non‐opisthokont lineages, Rsp5p or c‐Cbl, the E3 ubiquitin ligases acting on endocytic cargo, are absent but Uba1 class genes are present and are required for cell viability and ISG65 ubiquitylation. Hence, ubiquitylation is an evolutionarily conserved mechanism for internalization of surface proteins, but aspects of the machinery differ substantially between the major eukaryotic lineages.
Isolation and characterization of eight polymorphic microsatellite loci in the endangered Hawaiian tree snail, Achatinella sowerbyana
Authors: ERICKSON P. B. , HADFIELD M. G.
Published: June 2008

Achatinella is a genus of highly endangered native Hawaiian tree snails. Eight polymorphic microsatellite markers were isolated for one species, Achatinella sowerbyana, to be used in assessing remaining genetic diversity and gene flow in the often small and isolated populations. All loci amplified consistently in every individual tested. The number of alleles per locus in a sample of 40 individuals varied from three to 13, and the observed heterozygosity ranged from 0.308 to 0.846. These markers will be used to assist in the development of conservation and management plans.
Development and characterization of 11 microsatellite loci for the Mona Island iguana (Cyclura cornuta stejnegeri)
Authors: ROSAS K. G. , PÉREZ‐BUITRAGO N. , ACEVEDO J. P. , MARTÍNEZ N. , FUNK S. M. , MCMILLAN W. O.
Published: June 2008

We isolated and characterized 11 microsatellite loci in the Mona Island iguana (Cyclura cornuta stejnegeri). Eleven loci exhibit moderate to high allelic diversity (two to 12 alleles, mean = 4.5) and polymorphism (mean observed heterozygosity, 0.56; range, 0.26 to 0.78) in 41 adults. This marker set has low probability of identity and high parentage exclusion power and will be suitable for studies of paternity, social organization and relatedness in this species.
Eleven novel microsatellite markers for the Asian oyster Crassostrea ariakensis
Authors: XIAO JIE , CORDES JAN F. , JONES KENNETH C. , REECE KIMBERLY S.
Published: June 2008

Clones from four partial genomic libraries of the Asian oyster Crassostrea ariakensis were screened to reveal 64 microsatellite‐containing sequences. Polymerase chain reaction primers were designed for 34 of these loci. Reactions were optimized for 11 primer pairs and markers were evaluated in eight family crosses and one wild population from northern China. Zero to three null alleles per locus were identified in family crosses, and two of the 11 loci showed allele frequency deviations from Hardy–Weinberg equilibrium in the wild population. These markers have proven useful for genetic studies of C. ariakensis.
Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach
Authors: TAYLOR D. LEE , BOOTH MICHAEL G. , MCFARLAND JACK W. , HERRIOTT IAN C. , LENNON NIALL J. , NUSBAUM CHAD , MARR THOMAS G.
Published: June 2008

High throughput sequencing methods are widely used in analyses of microbial diversity, but are generally applied to small numbers of samples, which precludes characterization of patterns of microbial diversity across space and time. We have designed a primer‐tagging approach that allows pooling and subsequent sorting of numerous samples, which is directed to amplification of a region spanning the nuclear ribosomal internal transcribed spacers and partial large subunit from fungi in environmental samples. To test the method for phylogenetic biases, we constructed a controlled mixture of four taxa representing the Chytridiomycota, Zygomycota, Ascomycota and Basidiomycota. Following cloning and colony restriction fragment length polymorphism analysis, we found no significant difference in representation in 19 of the 23 tested primers. We also generated a clone library from two soil DNA extracts using two primers for each extract and compared 456 clone sequences. Community diversity statistics and contingency table tests applied to counts of operational taxonomic units revealed that the two DNA extracts differed significantly, while the pairs of tagged primers from each extract were indistinguishable. Similar results were obtained using UniFrac phylogenetic comparisons. Together, these results suggest that the pig‐tagged primers can be used to increase ecological inference in high throughput sequencing projects on fungi.
Non‐invasive prospective targeting of arterial P in subjects at rest
Authors: Ito Shoji , Mardimae Alexandra , Han Jay , Duffin James , Wells Greg , Fedorko Ludwik , Minkovich Leonid , Katznelson Rita , Meineri Massimiliano , Arenovich Tamara , Kessler Cathie , Fisher Joseph A.
Published: June 2008

Accurate measurements of arterial P (P) currently require blood sampling because the end‐tidal P (P) of the expired gas often does not accurately reflect the mean alveolar P and P. Differences between P and P result from regional inhomogeneities in perfusion and gas exchange. We hypothesized that breathing via a sequential gas delivery circuit would reduce these inhomogeneities sufficiently to allow accurate prediction of P from P. We tested this hypothesis in five healthy middle‐aged men by comparing their P values with P values at various combinations of P (between 35 and 50 mmHg), P (between 70 and 300 mmHg), and breathing frequencies (f; between 6 and 24 breaths min−1). Once each individual was in a steady state, P was collected in duplicate by consecutive blood samples to assess its repeatability. The difference between P and average P was 0.5 ± 1.7 mmHg (P= 0.53; 95% CI −2.8, 3.8 mmHg) whereas the mean difference between the two measurements of P was −0.1 ± 1.6 mmHg (95% CI −3.7, 2.6 mmHg). Repeated measures ANOVAs revealed no significant differences between P and P over the ranges of P, f and target P. We conclude that when breathing via a sequential gas delivery circuit, P provides as accurate a measurement of P as the actual analysis of arterial blood.
The presence of pacemaker HCN channels identifies theta rhythmic GABAergic neurons in the medial septum
Authors: Varga Viktor , Hangya Balázs , Kránitz Kinga , Ludányi Anikó , Zemankovics Rita , Katona István , Shigemoto Ryuichi , Freund Tamás F. , Borhegyi Zsolt
Published: June 2008

The medial septum (MS) is an indispensable component of the subcortical network which synchronizes the hippocampus at theta frequency during specific stages of information processing. GABAergic neurons exhibiting highly regular firing coupled to the hippocampal theta rhythm are thought to form the core of the MS rhythm‐generating network. In recent studies the hyperpolarization‐activated, cyclic nucleotide‐gated non‐selective cation (HCN) channel was shown to participate in theta synchronization of the medial septum. Here, we tested the hypothesis that HCN channel expression correlates with theta modulated firing behaviour of MS neurons by a combined anatomical and electrophysiological approach. HCN‐expressing neurons represented a subpopulation of GABAergic cells in the MS partly overlapping with parvalbumin (PV)‐containing neurons. Rhythmic firing in the theta frequency range was characteristic of all HCN‐expressing neurons. In contrast, only a minority of HCN‐negative cells displayed theta related activity. All HCN cells had tight phase coupling to hippocampal theta waves. As a group, PV‐expressing HCN neurons had a marked bimodal phase distribution, whereas PV‐immunonegative HCN neurons did not show group‐level phase preference despite significant individual phase coupling. Microiontophoretic blockade of HCN channels resulted in the reduction of discharge frequency, but theta rhythmic firing was perturbed only in a few cases. Our data imply that HCN‐expressing GABAergic neurons provide rhythmic drive in all phases of the hippocampal theta activity. In most MS theta cells rhythm genesis is apparently determined by interactions at the level of the network rather than by the pacemaking property of HCN channels alone.
Tonic activation of GLUK5 kainate receptors decreases neuroblast migration in whole‐mounts of the subventricular zone
Authors: Platel Jean‐Claude , Heintz Tristan , Young Stephanie , Gordon Valerie , Bordey Angélique
Published: June 2008

In the postnatal subventricular zone (SVZ), neuroblasts migrate in chains along the lateral ventricle towards the olfactory bulb. AMPA/kainate receptors as well as metabotropic glutamate receptors subtype 5 (mGluR5) are expressed in SVZ cells. However, the cells expressing these receptors and the function of these receptors remain unexplored. We thus examined whether SVZ neuroblasts express mGluR5 and Ca2+‐permeable kainate receptors in mouse slices. Doublecortin (DCX)‐immunopositive cells (i.e. neuroblasts) immunostained positive for mGluR5 and GLUK5‐7‐containing kainate receptors. RT‐PCR from ∼10 GFP‐fluorescent cell aspirates obtained in acute slices from transgenic mice expressing green fluorescent protein (GFP) under the DCX promoter showed mGluR5 and GLUK5 receptor mRNA in SVZ neuroblasts. Patch‐clamp data suggest that ∼60% of neuroblasts express functional GLUK5‐containing receptors. Activation of mGluR5 and GLUK5‐containing receptors induced Ca2+ increases in 50% and 60% of SVZ neuroblasts, respectively, while most neuroblasts displayed GABAA‐mediated Ca2+ responses. To examine the effects of these receptors on the speed of neuroblast migration, we developed a whole‐mount preparation of the entire lateral ventricle from postnatal day (P) 20–25 DCX‐GFP mice. The GABAA receptor (GABAAR) antagonist bicuculline increased the speed of neuroblast migration by 27%, as previously reported in acute slices. While the mGluR5 antagonist MPEP did not affect the speed of neuroblast migration, the homomeric and heteromeric GLUK5 receptor antagonists, NS3763 and UB302, respectively, increased the migration speed by 38%. These data show that although both GLUK5 receptor and mGluR5 activations increase Ca2+ in neuroblasts, only GLUK5 receptors tonically reduce the speed of neuroblast migration along the lateral ventricle.
Study of Conceptual Design of the Extension Method for Mechanical Products
Authors: Zhao Yanwei , Zhang Guoxian
Published: June 2008

On the foundation summing up existing intelligent conceptual design method, this paper puts forward the research content, characters, path, and method of the conceptual design of extension for mechanical products. This paper rounds the core technology of intelligent conceptual design to research the modeling method of extension design in function-principle-layout-configuration. It includes the function expression, function decomposition and synthesis, function illation and decision. The computers are utilized to simulate the human dialectic thought when resolve problems in this method. The given example shows that the extension method has been applied in the field of conceptual design for mechanical products. This method has important significance to resolve the bottleneck problem of theory studying and engineering realizing of intelligent CAD.
Accuracy of the Three-Room Simulation of a Ten-Room Large House Fire
Authors: Kim Hyeong-Jin , Lilley David G.
Published: June 2008

Calculations (with a 10-room and a simpler 3-room simulation of the large house fire) of temperature and smoke levels in several rooms of a structural fire are possible with the CFAST computer code. The accuracy and applicability of the results is greatly enhanced though the comparison of the calculations with experimental data. Experimental work thereby assists in understanding fire behavior in structural fires. Temperature measurements at different locations during a house fire provide necessary data for the development of mathematical models, which attempt to simulate the fire on a computer. In this paper, a large 170 square meter single-level house was subject to a complete experimental burn, with temperature measurements and fire observations during the entire burn, and subsequent modeling via a detailed 10-room simulation and a simpler 3-room simulation. The CFAST (Consolidated Model of Fire Growth and Smoke Transport) computer code is used to calculate temperatures and smoke levels in the various rooms of the house during the burn (with 10 different rooms). Four fire scenarios are considered in the simulation, with increasing realism regarding the actual fire specification. A simpler calculation (with 3 different rooms) has also done to see if the similar results would be shown with the 10-room simulation. It was found that results for smoke temperature and smoke layer heights were very similar, leading to the conclusion that a 3-room simulation of a 10-room building gives adequate modeling capability of the real structural fire. Computation results give the expected trends (deduced from local point temperature measurements) of initial temperature surge and decay, peak and leveling off temperatures, especially with respect to the northwest bedroom with a closed door. The effect of whether a door of a room would have been open was investigated computationally, with results illustrating far more dangerous smoke temperature and smoke level in the room when its door is open.
Modal Spectral Element for the Transverse Vibrations of Axially Moving Wide-Band Strips
Authors: Lee Usik , Kim Joohong
Published: June 2008

The use of frequency-dependent spectral element matrix (or dynamic stiffness matrix) in structural dynamics is known to provide very accurate solutions, while reducing the number of degrees-of-freedom to resolve the computational and cost problems. Thus, in the present paper, the modal spectral element is formulated for thin plates moving with constant speed under a uniform in-plane axial tension. The concept of Kantorovich method is used to formulate the modal spectral element matrix in frequency-domain. The present modal spectral element is then evaluated by comparing its solutions with exact analytical solutions and FEM solutions. The effects of the moving speed and the in-plane tension on the dynamic characteristics of a moving plate are numerically investigated.
Parametric Modeling Method for Truss Structures
Authors: Wang Hongqing , Rosen David W.
Published: June 2008

This paper presents a parametric modeling method to create truss structures to enhance a part’s mechanical and/or dynamic properties. The main idea behind this method is to replace thick part sections with thinner sections that are reinforced by truss structure. Computational methods are presented to create truss structures that conform to a part’s shape. The methods utilize Bezier surfaces to approximate the part surface and to create the truss structure. Truss topologies can be created for a two-dimensional truss, a three-dimensional truss for single volume and a three-dimensional truss for multiple volumes. The decomposition of the part surfaces, the construction of approximating Bezier surfaces, and solid modeling of the truss structures are also shown. An example is presented to demonstrate the utility of conformal truss structures for a large part from the aerospace industry.
Shape Instance Generation From Domain Distributed Vague Models
Authors: Rusa´k Zolta´n , Horva´th Imre , Kuczogi Gyo¨rgy , Akar Evren
Published: June 2008

Representing the possible shapes of a cluster of objects by a variation domain, vague discrete modeling is a powerful method for describing non-nominal shapes. A vague discrete model (VDM) is vague in the sense that multiple objects are represented by one domain model, and that multiple shape instances can be generated based on certain instantiation rules. The vaguely defined particles contained in a VDM provide a discrete representation that supports multi-resolution manipulation of shapes. This paper presents the latest results related to deriving instance shapes from a given VDM. The problem here is that a VDM may contain multiple regions, which have to be instantiated individually and the generated parts have to be unified in order to get an instance of a complex shape. First the paper gives a concise overview of vague discrete modeling. It introduces the concept as well as the process of rule-based instantiation of shapes from a VDM. It proposes simple, compound and constrained instantiation techniques for treating the various cases. To map the application field-dependent instantiation rules to explicit mathematical terms, the concept of effect function is applied. The discontinuous set of particle clouds received after instantiation are geometrically connected by fuzzy transition functions. The first experiences show that the vague discrete modeling extended with rule-based instantiation has a great potential to support intuitive shape conceptualization, especially in collaborative virtual design environments.
A Study on Optimum Topology of Plate Structure Using Coordinate Transformation by Conformal Mapping
Authors: Kitayama Satoshi , Yamakawa Hiroshi
Published: June 2008

This paper presents a new method to determine an optimum topology of plate structure using coordinate transformation by conformal mapping. We have already proposed a method to determine an optimum topology of planar structure using coordinate transformation by conformal mapping. In that study first we defined simple design domain in which analysis and optimization were performed easily. We calculated optimum topology in this simple design domain. Then we applied coordinate transformation by conformal mapping to optimum topology calculated in simple design domain, and obtained some optimum topologies in complex design domain. We also showed that the invariants of stresses which were the sum and difference of principal stress satisfied Laplace equation and relationshi p between fluid mechanics and electromagnetic could be valid in the theory of elasticity. In this study we clarify two invariants of bending moments satisfy Laplace equation under a certain condition. We note the similarity between Airy stress function of 2-D elastic body and deflection of plate, and will show that the two invariants of bending moments which are the sum and difference of principal bending moments satisfy Laplace equation using this similarity. As a result we will show that corresponding relationship between fluid mechanics, electromagnetic and elasticity may be valid in the theory of plate. Then by using this relationship, we proposed a new method to determine optimum topology using coordinate transformation by conformal mapping. Our proposed method will be useful to determine optimum topology easily in complex design domain. Through numerical examples, we can examine the effectiveness of the proposed method.
Automated Design Synthesis for Micro-Electro-Mechanical Systems (MEMS)
Authors: Zhou Ningning , Agogino Alice , Pister Kristofer S. J.
Published: June 2008

This paper proposes a general architecture for using evolutionary algorithms to achieve MEMS design synthesis. Functional MEMS devices are designed by combining parameterized basic MEMS building blocks together using Multi-objective Genetic Algorithms (MOGAs) to produce a pareto optimal set of feasible designs. The iterative design synthesis loop is implemented by combining MOGAs with the SUGAR MEMS simulation tool. Given a high-level description of the device’s desired behavior, both the topology and sizing are generated. The topology or physical configuration includes the number and types of basic building blocks and their connectivity. The sizing of the designs entails assigning numerical values to parameterized building blocks. A sample from the pareto optimal set of designs is presented for a meandering resonator example, along with convergence plots.
Model Reduction in Structural Analysis Using a Multiresolution Analysis
Authors: Chellappa Sudarsanam , Diaz Alejandro R.
Published: June 2008

A method is presented to reduce the size of models used in analysis of elastic systems. The reduction is accomplished using a multiresolution analysis applied to elasticity operators to average fine scale properties and behavior while limiting loss of information. In discretized form, the method results in smaller matrices that can be used as building blocks to construct larger systems. The principal application envisioned is in design problems involving complex structural systems, such as crash-worthiness design, where very intensive computations demand computational efficiency.
Interactive Product Design Selection With an Implicit Value Function
Authors: Maddulapalli K. , Azarm S. , Boyars A.
Published: June 2008

We present an automated method to aid a Decision Maker (DM) in selecting the ‘most preferred’ from a set of design alternatives. The method assumes that the DM’s preferences reflect an implicit value function that is quasi-concave. The method is iterative, using three approaches in sequence to eliminate lower-value alternatives at each trial design. The method is interactive, with the DM stating preferences in the form of attribute tradeoffs at each trial design. We present an approach for finding a new trial design at each iteration. We provide an example, the design selection for a cordless electric drill, to demonstrate the method.
Adaptive Experimental Design Applied to Ergonomics Testing Procedure
Authors: Sasena Michael , Parkinson Matthew , Goovaerts Pierre , Papalambros Panos , Reed Matthew
Published: June 2008

Nonlinear constrained optimization algorithms are widely utilized in artifact design. Certain algorithms also lend themselves well to design of experiments (DOE). Adaptive design refers to experimental design where determining where to sample next is influenced by information from previous experiments. We present a constrained optimization algorithm known as superEGO (a variant of the EGO algorithm of Schonlau, Welch and Jones) that is able to create adaptive designs effectively. Its ability to allow easily for a variety of sampling criteria and to incorporate constraint information accurately makes it well suited to the needs of adaptive design. The approach is demonstrated on a human reach experiment where the selection of sampling points adapts successfully to the stature and perception of the individual test subject. Results from the initial study indicate that superEGO is able to create experimental designs that yield more accurate models using fewer points than the original testing procedure.