bluuebunny/crossref_metadata_2025 huggingface dataset:
Easy Care Finishing of Knitted Cotton Fabric in Presence of a Reactive-type Antibacterial Agent
Authors: Abo-Shosha M.H. , Hashem A.M. , El-Hosamy M.B. , El-Nagar A.H.
Published: October 2008

Antibacterial easy care finishing of knitted cotton fabric is achieved by incorporation of Sanitized® T99-19, as a reactive antibacterial agent, in the easy care finishing formulation. Finishing is carried out using different types of softeners and catalysts as well as concentrations of reagents, curing time and temperature. In addition to Sanitized® T99-19, optimal finishing formulation, that can provide the fabric good antibacterial (against Staphylococcus aureus and Pseudomonas aeruginosa) and hydrophilic properties by the pad (100% wet pick-up)-dry (100°C per 5 min)-cure (160°C per 3 min) method can be summarized as follows: `Arkofix ®NG-ET crosslinker (75g/L), ZnSO4 (7.5 g/L), Siligen ® TX2490 softener (20 g/L), acetic acid (1 g/L) and a nonionic wetting agent (2 g/L)'. Finishing the fabric with this formulation in presence of 5 g/L of Sanitized® T99-19 results in decreasing its whiteness index, surface roughness, air permeability, and breaking extension about 5, 4, 7.5, 1, and 19%, respectively, and enhances its dry crease recovery angle about 19%. Analysis of variance of data obtained is carried out at P-value ≤ 0.05. Fabric finished using recipe I (Sanitized® T99-19 alone), recipe II (Sanitized® T99-19 with Siligen ® TX2490) or recipe III (Sanitized® T99-19 and Siligen ® TX2490 with Arkofix® NG-ET) manifests inhibition clear zones towards Staphylococcus aureus and Pseudomonas aeruginosa a bacteria, as a result of the physically bound portion of `dimethyl-tetradecyl-[3(trimethoxysilane-propyl] ammonium chloride (active ingredient of Sanitized® T99-19) and/or its adduct with Arkofix® NG-ET' that leaches out of the fabric. However, this portion cannot tolerate repeated laundering up to 10 cycles. Finishing the fabric using Sanitized® T99-19 at a concentration of 5 g/L can acquire the fabric very high values of reduction in bacterial count even after 25 washing cycles, regardless of treatment recipe. Below 5 g/L in recipe III, the fabric fails to manifest total reduction in bacterial count after 10 washing cycles. Reduction in bacterial count is remarkably improved by increasing the concentration from 5 to 10 g/L in recipe III, regardless of washing cycles.
Calculation and Design of Parameters for Four-step 3D Braided Preform with Complex Rectangular Cross Sections
Authors: Wei Zhang  , Xin Ding  , Yuling Li
Published: October 2008

The complex rectangular configuration refers to the geometrical shape jointed by two or more rectangles together. The calculation and design of parameters for 3D braided preform with simple rectangular cross-section are not suitable for those with complex rectangular cross-section because there are special microstructures in complex shaped preform. According to the unit cell models of 3D braided preform with complex rectangular cross-section, the method for computing the amount and volume of each unit cell is presented, the equation for calculating the fiber volume fraction is derived, and the relationships between preform parameters are developed. Based on the equations and relationships established, the procedure for designing the numbers of yarns arrangement is presented from preform dimensions, yarns linear density, fiber density, and fiber volume fraction. A preform with complex rectangular cross-section is designed and produced. The procedure for designing is supported by experimental results.
Summer Visits Nezahualcoyotl
Authors: Gleason Judith
Published: October 2008

Although the pre-Hispanic poet and statesman Nezahualcoyotl (1402 to 1472) continues to be a "cultural icon" in Mexico, apparently nobody north of the border has ever heard of him! Relying on John Curl's fine translations of his work, the author set out to remedy the situation by fancifully summering in the relaxed company of a supernatural connoisseur: Xochipilli. What follows is a topical essay highlighting the poet's uneasy political situation contravened by mastery of perceptual and metaphorical conventions of the Nahuatl idiom in which he improvised his renowned recitations.
Integration-Responsiveness and Knowledge-Management Perspectives on the MNC
Authors: Kasper Helmut , Lehrer Mark , Mühlbacher Jürgen , Müller Barbara
Published: October 2008

This interview-based study of eight multinational corporations (MNCs) in five industries investigates varying patterns of cross-site knowledge sharing associated with MNCs pursuing global, multidomestic, and transnational strategies. The study revealed considerable polarization in knowledge-sharing practices between MNCs implementing transnational and global strategies, with cross-site knowledge sharing being of very high intensity among the former and quite minimal among the latter. MNCs pursuing global, multidomestic, and transnational strategies each tended to share qualitatively different kinds of knowledge as well. The relationship between MNC strategy and intrafirm knowledge sharing is encapsulated in a framework that bridges two hitherto largely separate research streams: the integration-responsiveness framework and knowledge-management studies of the MNC.
The Line and the Animorph or `Travel Is More than Just A to B'
Authors: Sobchack Vivian
Published: October 2008

One of the elements that separates live-action, photoreal cinema from animation is the line, a conceptual meta-object that has no existence other than as an idea or a graphic representation. Lines are not essential to photoreal cinema. Using five animated television advertisements for Hilton Hotels made by German animator Raimund Krumme, the essay raises some of the paradoxes inherent in the single, two-dimensional, animated graphic line as both an abstract geometric construct and an eccentric visualization of energy and entropy. What Krumme's animations emphasize (even if in the service of an advertising campaign) is that, never a `thing', the line in motion intends and marks its own differánce and is always more lived and contingent than its geometry would suggest.
The Politics of Media in Stan Vanderbeek's Poemfields
Authors: Bartlett Mark
Published: October 2008

This article provides a context for understanding the series of computer-animated films — Poemfields — that Vanderbeek made at Bell Labs between 1966 and 1969, using the first moving image programming language, Bflix, invented by Bell computer scientist, Ken Knowlton. Through an analysis of these works, the author shows how Vanderbeek's politics were deeply and consciously socialist in orientation, how he aimed at nothing less than changing social consciousness through a radical conception of the then emerging information and communication technologies, and how computerized animation as it was emerging at that moment was central to both of these aims.
Extracinematic Animation: Gregory Barsamian in Conversation with Suzanne Buchan
Authors: Barsamian Gregory
Published: October 2008

Gregory Barsamian's strobe-lit kinetic sculptures create an experience that places observers in a perceptual paradox that oscillates between the illusion of animated cinema and the phenomenal presence of real objects that share the viewer's physical presence in space and time. The conversation reveals Barsamian's working methods, his aesthetic and philosophical influences and intentions and his artistic relationship with animated illusion.
Enhancing the in vivo expansion of adoptively transferred EBV-specific CTL with lymphodepleting CD45 monoclonal antibodies in NPC patients
Authors: Louis Chrystal U. , Straathof Karin , Bollard Catherine M. , Gerken Claudia , Huls M. Helen , Gresik M. Victoria , Wu Meng-Fen , Weiss Heidi L. , Gee Adrian P. , Brenner Malcolm K. , Rooney Cliona M. , Heslop Helen E. , Gottschalk Stephen
Published: October 2008

Treatment of Epstein-Barr virus (EBV)–positive nasopharyngeal carcinoma (NPC) with EBV-specific cytotoxic T cells (EBV-specific CTL) has been promising, producing clinical responses. However, infused EBV-specific CTL did not expand in vivo, likely limiting their antitumor activity. Lymphodepleting patients with chemotherapy before T-cell transfer enhances in vivo T-cell expansion, but results in nonspecific destruction of the resident immune system and can have significant toxicity. To evaluate if monoclonal antibodies (mAbs) can produce a more selective lymphodepletion, we conducted a clinical study in which NPC patients received a pair of lymphodepleting mAbs targeted to the CD45 antigen (CD45 mAbs) before EBV-specific CTL infusion. Eight patients with recurrent NPC received CD45 mAbs followed by escalating doses of auto-logous EBV-specific CTL. Infusion of CD45 mAbs resulted in transient lymphopenia in all patients and an increase in interleukin-15 (IL-15) levels in 6 out 8 patients. All patients had an increase in their peripheral blood frequency of EBV-specific T cells after CTL infusion. Three patients with a persistent increase had clinical benefits including 1 complete response (> 24 months) and 2 with stable disease (for 12 and 15 months). Lymphodepleting mAbs prior CTL transfer may represent an alternative to chemotherapy to enhance expansion of infused CTL. This study is registered at http://www.clinialtrials.gov as NCT00608257.
Imaging spontaneous tumorigenesis: inflammation precedes development of peripheral NK tumors
Authors: Rauch Dan , Gross Shimon , Harding John , Niewiesk Stefan , Lairmore Michael , Piwnica-Worms David , Ratner Lee
Published: October 2008

Early events in tumor development are spontaneous, microscopic, and affected by the microenvironment. We developed a mouse model of spontaneous lymphoma in which malignant transformation is coupled with light emission that can be detected noninvasively using bioluminescent imaging. The human T-cell leukemia virus (HTLV) type 1 transcriptional transactivator Tax is an oncogene sufficient to produce lymphoma in transgenic animal models. Using the granzyme B promoter to restrict Tax expression to the mature natural killer (NK)/T-cell compartment, we have reproduced many elements of HTLV-associated adult T-cell leukemia/lymphoma. Tax activates signaling cascades associated with transformation, inflammation, and tumorigenesis. Here, we report that Tax-mediated activation of luciferase in long terminal repeat-luciferase (LTR-LUC) mice serves as a reporter for imaging these processes in vivo. Using bioluminescent imaging (BLI), we discovered that microscopic intraepithelial lesions precede the onset of peripheral subcutaneous tumors, tumorigenesis progresses through early reversible stages, and Tax is sufficient for inducing tumors. Based on these findings, we propose that Tax expression in activated lymphocytes initiates a cascade of events that leads to NK/T cell recruitment, activation, and transformation. The use of BLI expands our ability to interrogate the role of Tax in tumorigenesis in vivo and has made the association of inflammation with tumor initiation amenable for study.
Abnormal spatial diffusion of Ca2+ in F508del-CFTR airway epithelial cells
Authors: Antigny Fabrice , Norez Caroline , Cantereau Anne , Becq Frédéric , Vandebrouck Clarisse
Published: October 2008

Background

In airway epithelial cells, calcium mobilization can be elicited by selective autocrine and/or paracrine activation of apical or basolateral membrane heterotrimeric G protein-coupled receptors linked to phospholipase C (PLC) stimulation, which generates inositol 1,4,5-trisphosphate (IP3) and 1,2-diacylglycerol (DAG) and induces Ca2+release from endoplasmic reticulum (ER) stores.

Methods

In the present study, we monitored the cytosolic Ca2+transients using the UV light photolysis technique to uncage caged Ca2+or caged IP3into the cytosol of loaded airway epithelial cells of cystic fibrosis (CF) and non-CF origin. We compared in these cells the types of Ca2+receptors present in the ER, and measured their Ca2+dependent activity before and after correction of F508del-CFTR abnormal trafficking either by low temperature or by the pharmacological corrector miglustat (N-butyldeoxynojirimycin).

Results

We showed reduction of the inositol 1,4,5-trisphosphate receptors (IP3R) dependent-Ca2+response following both correcting treatments compared to uncorrected cells in such a way that Ca2+responses (CF+treatmentvswild-type cells) were normalized. This normalization of the Ca2+rate does not affect the activity of Ca2+-dependent chloride channel in miglustat-treated CF cells. Using two inhibitors of IP3R1, we observed a decrease of the implication of IP3R1 in the Ca2+response in CF corrected cells. We observed a similar Ca2+mobilization between CF-KM4 cells and CFTR-cDNA transfected CF cells (CF-KM4-reverted). When we restored the F508del-CFTR trafficking in CFTR-reverted cells, the specific IP3R activity was also reduced to a similar level as in non CF cells. At the structural level, the ER morphology of CF cells was highly condensed around the nucleus while in non CF cells or corrected CF cells the ER was extended at the totality of cell.

Conclusion

These results suggest reversal of the IP3R dysfunction in F508del-CFTR epithelial cells by correction of the abnormal trafficking of F508del-CFTR in cystic fibrosis cells. Moreover, using CFTR cDNA-transfected CF cells, we demonstrated that abnormal increase of IP3R Ca2+release in CF human epithelial cells could be the consequence of F508del-CFTR retention in ER compartment.
Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene
Authors: Rautenberg Anja , Filatov Dmitry , Svennblad Bodil , Heidari Nahid , Oxelman Bengt
Published: October 2008

Background

Increasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (SlX1/Y1) show conflicting phylogenies within Silene (Caryophyllaceae). SlX1 and SlY1 are sex-linked genes on the sex chromosomes of dioecious members of Silene sect. Elisanthe.

Results

We sequenced the homologues of the SlX1/Y1 genes in several Sileneae species. We demonstrate that different parts of the SlX1/Y1 region give different phylogenetic signals. The major discrepancy is that Silene vulgaris and S. sect. Conoimorpha (S. conica and relatives) exchange positions. To determine whether gene duplication followed by recombination (an intralineage process) may explain the phylogenetic conflict in the Silene SlX1/Y1 gene, we use a novel probabilistic, multiple primer-pair PCR approach. We did not find any evidence supporting gene duplication/loss as explanation to the phylogenetic conflict.

Conclusion

The phylogenetic conflict in the Silene SlX1/Y1 gene cannot be explained by paralogy or artefacts, such as in vitro recombination during PCR. The support for the conflict is strong enough to exclude methodological or stochastic errors as likely sources. Instead, the phylogenetic incongruence may have been caused by recombination of two divergent alleles following ancient interspecific hybridization or incomplete lineage sorting. These events probably took place several million years ago. This example clearly demonstrates that different parts of the genome may have different evolutionary histories and stresses the importance of using multiple genes in reconstruction of taxonomic relationships.
Functional analysis of the group A streptococcal luxS/AI-2 system in metabolism, adaptation to stress and interaction with host cells
Authors: Siller Maria , Janapatla Rajendra P , Pirzada Zaid A , Hassler Christine , Zinkl Daniela , Charpentier Emmanuelle
Published: October 2008

Background

The luxS/AI-2 signaling pathway has been reported to interfere with important physiological and pathogenic functions in a variety of bacteria. In the present study, we investigated the functional role of the streptococcal luxS/AI-2 system in metabolism and diverse aspects of pathogenicity including the adaptation of the organism to stress conditions using two serotypes of Streptococcus pyogenes, M1 and M19.

Results

Exposing wild-type and isogenic luxS-deficient strains to sulfur-limited media suggested a limited role for luxS in streptococcal activated methyl cycle metabolism. Interestingly, loss of luxS led to an increased acid tolerance in both serotypes. Accordingly, luxS expression and AI-2 production were reduced at lower pH, thus linking the luxS/AI-2 system to stress adaptation in S. pyogenes. luxS expression and AI-2 production also decreased when cells were grown in RPMI medium supplemented with 10% serum, considered to be a host environment-mimicking medium. Furthermore, interaction analysis with epithelial cells and macrophages showed a clear advantage of the luxS-deficient mutants to be internalized and survive intracellularly in the host cells compared to the wild-type parents. In addition, our data revealed that luxS influences the expression of two virulence-associated factors, the fasX regulatory RNA and the virulence gene sibA (psp).

Conclusion

Here, we suggest that the group A streptococcal luxS/AI-2 system is not only involved in the regulation of virulence factor expression but in addition low level of luxS expression seems to provide an advantage for bacterial survival in conditions that can be encountered during infections.
Involvement of a phospholipase C in the hemolytic activity of a clinical strain of Pseudomonas fluorescens
Authors: Rossignol Gaelle , Merieau Annabelle , Guerillon Josette , Veron Wilfried , Lesouhaitier Olivier , Feuilloley Marc GJ , Orange Nicole
Published: October 2008

Background

Pseudomonas fluorescens is a ubiquitous Gram-negative bacterium frequently encountered in hospitals as a contaminant of injectable material and surfaces. This psychrotrophic bacterium, commonly described as unable to grow at temperatures above 32°C, is now considered non pathogenic. We studied a recently identified clinical strain of P. fluorescens biovar I, MFN1032, which is considered to cause human lung infection and can grow at 37°C in laboratory conditions.

Results

We found that MFN1032 secreted extracellular factors with a lytic potential at least as high as that of MF37, a psychrotrophic strain of P. fluorescens or the mesophilic opportunistic pathogen, Pseudomonas aeruginosa PAO1. We demonstrated the direct, and indirect – through increases in biosurfactant release – involvement of a phospholipase C in the hemolytic activity of this bacterium. Sequence analysis assigned this phospholipase C to a new group of phospholipases C different from those produced by P. aeruginosa. We show that changes in PlcC production have pleiotropic effects and that plcC overexpression and plcC extinction increase MFN1032 toxicity and colonization, respectively.

Conclusion

This study provides the first demonstration that a PLC is involved in the secreted hemolytic activity of a clinical strain of Pseudomonas fluorescens. Moreover, this phospholipase C seems to belong to a complex biological network associated with the biosurfactant production.
Prognostic parameters for recurrence of papillary thyroid microcarcinoma
Authors: Kim Tae Yong , Hong Suck Joon , Kim Jung Min , Gu Kim Won , Gong Gyungyub , Ryu Jin Sook , Kim Won Bae , Yun Sung-Cheol , Shong Young Kee
Published: October 2008

Background

Papillary thyroid microcarcinoma (PTMC) is defined as a papillary thyroid carcinoma less than or equal to 1.0 cm in size. Independent prognostic factors for clinical recurrence of PTMC have not been clearly delineated.

Methods

Clinicopathological parameters predicting PTMC recurrence were determined by retrospective analysis of 307 patients.

Results

Of the 293 patients eligible for analysis, 14 (5%) had recurrence during a median follow-up time of 65 months. Recurrence was observed in 8 of 166 patients (0.5%) treated with total or near-total thyroidectomy; gender (P = 0.02) and presence of lateral cervical node metastases at initial surgery (P = 0.01) were associated with recurrence. Six of the 127 patients (0.5%) treated with hemi- or subtotal thyroidectomy experience recurrences, but no significant prognostic factor for recurrence was identified. Multivariate Cox-regression analysis showed that gender and cervical lymph node metastasis were significant variables

Conclusion

PTMC showed very diverse disease extent and could not be regarded as indolent, relatively benign disease based on the primary tumor size. The extent of surgery should be based on prognostic parameters, such as gender and lateral neck node metastasis, in patients with PTMC.
Recombinant amyloid beta-peptide production by coexpression with an affibody ligand
Authors: Macao Bertil , Hoyer Wolfgang , Sandberg Anders , Brorsson Ann-Christin , Dobson Christopher M , Härd Torleif
Published: October 2008

Background

Oligomeric and fibrillar aggregates of the amyloid β-peptide (Aβ) have been implicated in the pathogenesis of Alzheimer's disease (AD). The characterization of Aβ assemblies is essential for the elucidation of the mechanisms of Aβ neurotoxicity, but requires large quantities of pure peptide. Here we describe a novel approach to the recombinant production of Aβ. The method is based on the coexpression of the affibody protein ZAβ3, a selected affinity ligand derived from the Z domain three-helix bundle scaffold. ZAβ3 binds to the amyloidogenic central and C-terminal part of Aβ with nanomolar affinity and consequently inhibits aggregation.

Results

Coexpression of ZAβ3 affords the overexpression of both major Aβ isoforms, Aβ(1–40) and Aβ(1–42), yielding 4 or 3 mg, respectively, of pure 15N-labeled peptide per liter of culture. The method does not rely on a protein-fusion or -tag and thus does not require a cleavage reaction. The purified peptides were characterized by NMR, circular dichroism, SDS-PAGE and size exclusion chromatography, and their aggregation propensities were assessed by thioflavin T fluorescence and electron microscopy. The data coincide with those reported previously for monomeric, largely unstructured Aβ. ZAβ3 coexpression moreover permits the recombinant production of Aβ(1–42) carrying the Arctic (E22G) mutation, which causes early onset familial AD. Aβ(1–42)E22G is obtained in predominantly monomeric form and suitable, e.g., for NMR studies.

Conclusion

The coexpression of an engineered aggregation-inhibiting binding protein offers a novel route to the recombinant production of amyloidogenic Aβ peptides that can be advantageously employed to study the molecular basis of AD. The presented expression system is the first for which expression and purification of the aggregation-prone Arctic variant (E22G) of Aβ(1–42) is reported.
Lung responses to secondary endotoxin challenge in rats exposed to pig barn air
Authors: Charavaryamath Chandrashekhar , Keet Taryn , Aulakh Gurpreet K , Townsend Hugh GG , Singh Baljit
Published: October 2008

Background

Swine barn air contains endotoxin and many other noxious agents. Single or multiple exposures to pig barn air induces lung inflammation and loss of lung function. However, we do not know the effect of exposure to pig barn air on inflammatory response in the lungs following a secondary infection. Therefore, we tested a hypothesis that single or multiple exposures to barn air will result in exaggerated lung inflammation in response to a secondary insult withEscherichia coliLPS (E. coliLPS).

Methods

We exposed Sprague-Dawley rats to ambient (N = 12) or swine barn air (N = 24) for one or five days and then half (N = 6/group) of these rats received intravenousE. coliLPS challenge, observed for six hours and then euthanized to collect lung tissues for histology, immunohistochemistry and ELISA to assess lung inflammation.

Results

Compared to controls, histological signs of lung inflammation were evident in barn exposed rat lungs. Rats exposed to barn air for one or five days and challenged withE. coliLPS showed increased recruitment of granulocytes compared to those exposed only to the barn. Control, one and five day barn exposed rats that were challenged withE. coliLPS showed higher levels of IL-1β in the lungs compared to respective groups not challenged withE. coliLPS. The levels of TNF-α in the lungs did not differ among any of the groups. Control rats withoutE. coliLPS challenge showed higher levels of TGF-β2 compared to controls challenged withE. coliLPS.

Conclusion

These results show that lungs of rats exposed to pig barn air retain the ability to respond toE. coliLPS challenge.
A case of polymyositis associated with papillary thyroid cancer: a case report
Authors: Kalliabakos Dimitrios , Pappas Apostolos , Lagoudianakis Emmanuel , Papadima Artemisia , Chrysikos John , Basagiannis Christos , Tsakoumagou Maria , Skanelli Yasemi , Manouras Andreas
Published: October 2008

Differentiated thyroid cancer is rarely associated with paraneoplastic events. Polymyositis, an autoimmune inflammatory myopathy, can be manifested as a paraneoplastic syndrome (PS). We report a case of a young woman who developed progressive proximal muscle weakness one and a half year after a total thyroidectomy for papillary thyroid cancer. Clinical features, laboratory results and muscle biopsy led us to the diagnosis of polymyositis, possibly related to her previous malignancy. A search for recurrence of the thyroid carcinoma or other underlying malignancy was fruitless. The patient improved slowly but almost completely after about 6 months of immunosupressive therapy, which she is still receiving.
Prospects of Rehabilitation for Elderly Schizophrenics
Authors: Lyketsos G. C. , Richardson S. C. , Aritzi S. K. , Lyketsos C. G.
Published: October 2008

The psychopathology and disabilities of a group of institutionalised elderly schizophrenics were compared with those of a group of non-schizophrenic elderly, and with younger schizophrenics reported in a parallel study and in the literature. Elderly schizophrenics showed significantly more psychopathology and disability than the non-schizophrenic elderly; however, they exhibited less psychopathology than younger schizophrenics. Disability among elderly schizophrenics was not correlated with chronicity of institutionalisation or psychopathology. There was a suggestion that disability among elderly schizophrenics may be due to organic deterioration.
Clinical Assessment and Performance Tasks in Depression: a Comparison of Amitriptyline and Trazodone
Authors: Botros W. A. , Ankier S. I. , Priest R. G. , McManus I. C. , Steinert J. , Samir Z. Y.
Published: October 2008

Depression, anxiety and psychomotor performance were assessed in 20 depressed patients during double-blind treatment with amitriptyline or trazodone. There was no difference in onset of antidepressant or anxiolytic action. No decrement or improvement on computerised tasks was found. Dry mouth was significantly more frequent and severe with amitriptyline.
The Abstract Data and Communication Library
Authors: Gabriel Edgar , Feki Saber , Benkert Katharina , Chaarawi Mohamad
Published: October 2008

Medical Doctors are increasingly incorporating simulation tools into their day-to-day work in hospitals and medical centers. The software packages used in these environments face tremendous reliability requirements and have to deal with restrictions with respect to the turn around time of a simulation, in order for the results to be useful. However, reaching performance goals for these applications is complicated by the wide range of hardware and software environments used in hospitals, making hardware dependent optimizations difficult. The Abstract Data and Communication Library (ADCL) helps to meet performance requirements by optimizing the communication operations for large scale simulations at runtime, adapting to the current hardware and software environment. ADCL provides for each communication pattern a large number of implementations and incorporates a runtime selection logic in order to choose the implementation leading to the highest performance of the application on the current platform.
Message-Passing Implementation of the Data Diffusion Communication Model in Fast Multipole Methods: Large Scale Biomolecular Simulations
Authors: Kurzak Jakub , Pettitt B. Montgomery
Published: October 2008

Biomolecular simulations require increasingly efficient parallel codes. We present an efficient communication algorithm for irregular problems exhibiting an all-to-many communication pattern. The algorithm is developed using message passing on distributed memory machines and assumes explicit knowledge of the interconnection topology. The algorithm maximizes locality of interprocessor communication by adopting to an arbitrary interconnection topology and at the same time takes multiprocessor nodes into account. The solution is incorporated into our implementation of the fast multipole method with periodic boundary conditions used for molecular dynamics simulations, but we believe it generalizes to many algorithms demonstrating an all-to-many communication pattern. We show that an irregular algorithm can be forced to behave like a systolic algorithm.
Semi-Automated Segmentation of Excised Atherosclerotic Plaque Tissue Components by K-Means Clustering Techniques
Authors: Karmonik Christof
Published: October 2008

With the increasing amount of medical imaging data available through advances in imaging hardware, automated pattern classification will gain more importance in the near future. This study highlights technical considerations of cluster-based k-means pattern classification techniques applied to the segmentation of major tissue components in multi-contrast magnetic resonance images (mcMRI) of excised atherosclerotic plaque tissue. The stability of the k-means algorithm was assessed by varying the initial positions of the cluster centroids and the values of the convergence criterion. Variations of the criterion function with the number of clusters were explored. The segmentation results of the k-means clustering algorithm were compared to two color- classification algorithms, the first based on dynamic programming and principal analysis, and the second based on color-bi-partitioning. While the standard k-means algorithm was found to provide a robust method for the unsupervised classification of major components in mcMR images acquired of atherosclerotic plaque tissue under clinical conditions, the Two color-classification algorithms provided less accurate classification when compared with histological data.
The role of the putative 3′ end processing endonuclease Ysh1p in mRNA and snoRNA synthesis
Authors: Garas Monika , Dichtl Bernhard , Keller Walter
Published: October 2008

Pre-mRNA 3′ end formation is tightly linked to upstream and downstream events of eukaryotic mRNA synthesis. The two-step reaction involves endonucleolytic cleavage of the primary transcript followed by poly(A) addition to the upstream cleavage product. To further characterize the putative 3′ end processing endonuclease Ysh1p/Brr5p, we isolated and analyzed a number of new temperature- and cold-sensitive mutant alleles. We show that Ysh1p plays a crucial role in 3′ end formation and in RNA polymerase II (RNAP II) transcription termination on mRNA genes. In addition, we observed a range of additional functional deficiencies inysh1mutant strains, which were partially allele-specific. Interestingly, snoRNA 3′ end formation and RNAP II termination were defective on specific snoRNAs in the cold-sensitiveysh1-12strain. Moreover, we observed the accumulation of several mRNAs including theNRD1transcript in this mutant. We provide evidence thatNRD1autoregulation is associated with endonucleolytic cleavage and that this process may involve Ysh1p. In addition, theysh1-12strain displayed defects in RNA splicing indicating that a functional link may exist between intron removal and 3′ end formation in yeast. These observations suggest that Ysh1p has multiple roles in RNA synthesis and processing.
In-situ Fatigue Damage Investigations in Welded Metallic Components by Infrared Techniques
Authors: Medgenberg Justus , Ummenhofer Thomas
Published: October 2008

The paper reviews the state of the art of thermal damage assessment in metals and proposes a specialized form of lock-in thermography as an efficient tool for the quantification of early fatigue damage phenomena in welded steel structures in the regime of mid- to high-cycle fatigue. It can be proved that advanced thermographic techniques are sensitive to early damage phenomena in the weld toe. They provide a new experimental mean for in-situ investigation of early inhomogeneous fatigue damage phenomena as mesoplasticity and fatigue cracks. The results demonstrate that non-contacting full field temperature measurements using highly sensitive infrared technology can be applied successfully to detect localized fatigue damage at around 10 % to 20 % of the total fatigue lifetime of the tested specimens. The applied method is based on the separation of thermoelastic and thermoplastic temperature effects which cause characteristic local temperature signatures. In contrast to other well-known approaches—as, e.g., measuring the rise of mean temperature during fatigue loading—the applied method offers a very high spatial resolution and resolves extremely localized phenomena. The methodology can be applied to monitor the fatigue process during conventional fatigue testing. The additional effort for the specimen preparation and the installation of the testing setup is minimal.
Quantitative Trait Locus Mapping Can Benefit From Segregation Distortion
Authors: Xu Shizhong
Published: October 2008

Segregation distortion is a phenomenon that has been observed in many experimental systems. How segregation distortion among markers arises and its impact on mapping studies are the focus of this work. Segregation distortion of markers can be considered to arise from segregation distortion loci (SDL). I develop a theory of segregation distortion and show that the presence of only a few SDL can cause the entire chromosome to distort from Mendelian segregation. Segregation distortion is detrimental to the power of detecting quantitative trait loci (QTL) with dominance effects, but it is not always a detriment to QTL mapping for additive effects. When segregation distortion of a locus is a random event, the SDL is beneficial to QTL mapping ∼44% of the time. If SDL are present and ignored, power loss can be substantial. A dense marker map can be used to ameliorate the situation, and if dense marker information is incorporated, power loss is minimal. However, other situations are less benign. A method that can simultaneously map QTL and SDL is discussed, maximizing both use of mapping resources and use by agricultural and evolutionary biologists.
Drosophila Hold'em Is Required for a Subset of Meiotic Crossovers and Interacts With the DNA Repair Endonuclease Complex Subunits MEI-9 and ERCC1
Authors: Joyce Eric F , Tanneti S Nikhila , McKim Kim S
Published: October 2008

Three Drosophila proteins, ERCC1, MUS312, and MEI-9, function in a complex proposed to resolve double-Holliday-junction intermediates into crossovers during meiosis. We report here the characterization of hold'em (hdm), whose protein product belongs to a single-strand-DNA-binding superfamily of proteins. Mutations in hdm result in reduced meiotic crossover formation and sensitivity to the DNA-damaging agent methyl methanesulfonate. Furthermore, HDM physically interacts with both MEI-9 and ERCC1 in a yeast two-hybrid assay. We conclude that HDM, MEI-9, MUS312, and ERCC1 form a complex that resolves meiotic recombination intermediates into crossovers.
Drosophila PCH2 Is Required for a Pachytene Checkpoint That Monitors Double-Strand-Break-Independent Events Leading to Meiotic Crossover Formation
Authors: Joyce Eric F , McKim Kim S
Published: October 2008

During meiosis, programmed DNA double-strand breaks (DSBs) are repaired to create at least one crossover per chromosome arm. Crossovers mature into chiasmata, which hold and orient the homologous chromosomes on the meiotic spindle to ensure proper segregation at meiosis I. This process is usually monitored by one or more checkpoints that ensure that DSBs are repaired prior to the meiotic divisions. We show here that mutations in Drosophila genes required to process DSBs into crossovers delay two important steps in meiotic progression: a chromatin-remodeling process associated with DSB formation and the final steps of oocyte selection. Consistent with the hypothesis that a checkpoint has been activated, the delays in meiotic progression are suppressed by a mutation in the Drosophila homolog of pch2. The PCH2-dependent delays also require proteins thought to regulate the number and distribution of crossovers, suggesting that this checkpoint monitors events leading to crossover formation. Surprisingly, two lines of evidence suggest that the PCH2-dependent checkpoint does not reflect the accumulation of unprocessed recombination intermediates: the delays in meiotic progression do not depend on DSB formation or on mei-41, the Drosophila ATR homolog, which is required for the checkpoint response to unrepaired DSBs. We propose that the sites and/or conditions required to promote crossovers are established independently of DSB formation early in meiotic prophase. Furthermore, the PCH2-dependent checkpoint is activated by these events and pachytene progression is delayed until the DSB repair complexes required to generate crossovers are assembled. Interestingly, PCH2-dependent delays in prophase may allow additional crossovers to form.
Drosophila and Vertebrate Casein Kinase Iδ Exhibits Evolutionary Conservation of Circadian Function
Authors: Fan Jin-Yuan , Preuss Fabian , Muskus Michael J , Bjes Edward S , Price Jeffrey L
Published: October 2008

Mutations lowering the kinase activity of Drosophila Doubletime (DBT) and vertebrate casein kinase Iε/δ (CKIε/δ) produce long-period, short-period, and arrhythmic circadian rhythms. Since most ckI short-period mutants have been isolated in mammals, while the long-period mutants have been found mostly in Drosophila, lowered kinase activity may have opposite consequences in flies and vertebrates, because of differences between the kinases or their circadian mechanisms. However, the results of this article establish that the Drosophila dbt mutations have similar effects on period (PER) protein phosphorylation by the fly and vertebrate enzymes in vitro and that Drosophila DBT has an inhibitory C-terminal domain and exhibits autophosphorylation, as does vertebrate CKIε/δ. Moreover, expression of either Drosophila DBT or the vertebrate CKIδ kinase carrying the Drosophila dbtS or vertebrate tau mutations in all circadian cells leads to short-period circadian rhythms. By contrast, vertebrate CKIδ carrying the dbtL mutation does not lengthen circadian rhythms, while Drosophila DBTL does. Different effects of the dbtS and tau mutations on the oscillations of PER phosphorylation suggest that the mutations shorten the circadian period differently. The results demonstrate a high degree of evolutionary conservation of fly and vertebrate CKIδ and of the functions affected by their period-shortening mutations.
Evaluation of Replacement Feeds for the Fry Feed Kyowa for Larval Walleyes
Authors: Johnson J Alan , Summerfelt Robert C , Clayton Richard D
Published: October 2008

Because Fry Feed Kyowa (FFK) was the standard and the only commercially manufactured starter feed suitable for intensive culture of larval walleyes Sander vitreus, it became imperative to evaluate other commercial feeds after FFK importation to the USA was banned to prevent the spread of bovine spongiform encephalopathy. A project was undertaken at the Rathbun Fish Culture Research Facility (Rathbun), Moravia, Iowa, and Iowa State University (ISU), Ames, using a single-factor experimental design with Lansy and Epac feeds (INVE Aquaculture, Inc., Ogden, Utah) and Gemma feed (Skretting, Vancouver, British Columbia). Walleyes were cultured at both sites from 3 to 28 d posthatch to evaluate the feeds. Performance indicators included presence of feed in gut, gas bladder inflation, survival, total length (mm), weight (mg), growth rate, and incidence of deformities. At both sites, survival was 2.6–3.6 times greater for fish given Gemma than for fish given the INVE feeds; the difference was significant at Rathbun but not at ISU. Length, weight, and growth rate at both sites were also significantly greater for Gemma-fed walleyes than for INVE-fed fish. Weight advantage produced by Gemma was 192% at ISU and 534% at Rathbon. Performance measures of fish given Gemma were similar to those of fish fed FFK in previous years.
Red King Crab Mating Success, Sex Ratio, Spatial Distribution, and Abundance Estimates as Artifacts of Survey Timing in Bristol Bay, Alaska
Authors: Dew C. Braxton
Published: October 2008

The Bristol Bay, Alaska, fishery for red king crab Paralithodes camtschaticus is a male-only fishery. A safeguard against male overfishing is the requirement that at least 8.4 million successfully mated, newly fertilized females be present on the grounds each year; otherwise no harvest is permitted. Estimation of the number of mated females in the population is complicated by the timing of the Bering Sea trawl survey, which in most years moves through Bristol Bay before red king crab spawning is complete. From 1977 through 2000, an average of 22% (range, 0–87%) of the broodstock remained unmated at the time of the May–June survey. Eighty-nine percent of the observed annual variation in the proportion of unmated crabs was explained by water temperature and the date of the survey. Thus, the degree of mating success shown by each year's survey, although influenced by male availability, is predominantly an artifact of temperature and survey timing. Also, red king crabs tend to spawn in untrawlable nearshore waters, increasing the difficulty of obtaining unbiased estimates of abundance from sampling an open population. Because the proportion of mature females that emigrate each year to the nearshore spawning grounds is greater than that of males, the sex ratio within the sampled region of a survey conducted during spawning is biased toward males. This bias masks one of the more obvious signs of male overharvest—a male-depauperate sex ratio. Finally, a survey conducted during spawning cannot provide an accurate mapping of the spatial distribution of the postspawning broodstock returning from inshore spawning grounds to incubate their newly fertilized eggs during the next 10–12 months. A time–temperature model indicated that delaying the Bristol Bay red king crab survey until the end of June would ameliorate the problems caused by sampling an open population engaged in spawning.
Exploring the Use of a Size-Based Egg-per-Recruit Model for the Red Abalone Fishery in California
Authors: Leaf Robert T. , Rogers-Bennett Laura , Jiao Yan
Published: October 2008

Eggs-per-recruit (EPR) models are widely used for management of invertebrate fisheries to provide guidance to managers about the magnitude of egg production for a given level of instantaneous annual fishing mortality (F). We constructed a deterministic size-based EPR model that utilizes size-specific natural mortality rates and egg production for red abalone Haliotis rufescens in California. We analyzed the sensitivity of the model to alterations in biological parameters, modeled the effect of incidental mortality of sublegal individuals on EPR, and modeled the effects of various management actions, including incorporation of a slot size limit, incorporation of a harvest refugium, and alternative legal minimum size limits. Model results were more sensitive to alterations in growth parameters and lower mortality estimates than to changes in upper mortality estimates or fecundity parameters. When F increased from 0.0 to 0.1 per year, EPR exhibited a large decline from 100% to 70%. Only the incorporation of a harvest refugium and an increase in the minimum size limit produced increases in the percent of maximum EPR. Implementing a slot limit of 152.4–203.2 mm maximum shell length (MSL) decreased the EPR value, indicating the importance of egg production by red abalone that are smaller than the current minimum size limit of 177.8 mm MSL. Because of the sensitivity of model predictions to changes in certain biological parameters, we recommend caution when applying EPR models to management, particularly for regions without spatially explicit parameter values. Despite this sensitivity, EPR models provide a heuristic framework for exploring the potential impacts of proposed fishery management strategies (e.g., harvest refugia), establishing biological reference points, examining how spatial and temporal variability in biological parameters affects egg production, and providing a guide for prioritizing research to improve data quality used for red abalone management.
Relationships between Reach-Scale Habitat Variables and Biotic Integrity Score, Brook Trout Density, and Brown Trout Density in Wisconsin Streams
Authors: Fayram Andrew H. , Mitro Matthew G.
Published: October 2008

Trout density and biotic integrity scores are central metrics used to guide trout stream management actions. However, it is unclear whether reach-scale habitat characteristics affect trout density and biotic integrity in a similar fashion. To determine the relative strength of relationships between reach-scale habitat characteristics and important biological metrics, we used artificial neural network models to examine the relationships between 11 reach-scale habitat variables and (1) catch per effort (CPE) for brook trout Salvelinus fontinalis, (2) CPE for brown trout Salmo trutta, and (3) coldwater fish index of biotic integrity (IBI) scores. The trout CPE models generally included habitat features related to physical characteristics; the IBI model generally included physical characteristics as well as those related to water quality. The brook trout CPE model included sinuosity and percent pool area. The brown trout CPE model included gradient and cover. The coldwater IBI model included gradient, percent fine sediments, buffer width, and width : depth ratio. Habitat restoration efforts that seek to maximize brook trout CPE, brown trout CPE, or IBI may benefit from consideration of habitat variables associated with each metric. We also performed quantile regression to evaluate whether any one of the three response metrics of interest was limiting to any of the other variables. Conditions that control IBI scores may also limit brook trout and brown trout densities; 90th-percentile regressions between brook trout or brown trout CPE and IBI score were significant. Although our findings suggest that IBI scores and trout densities can often be increased simultaneously, the fact that different habitat variables were included in each model suggests that the most appropriate habitat restoration efforts may also differ depending on the management goal.
Survival of the Faucet Snail after Chemical Disinfection, pH extremes, and Heated Water Bath Treatments
Authors: Mitchell Andrew J. , Cole Rebecca A.
Published: October 2008

The faucet snail Bithynia tentaculata, a nonindigenous aquatic snail from Eurasia, was introduced into Lake Michigan in 1871 and has spread to the mid-Atlantic states, the Great Lakes region, Montana, and most recently, the Mississippi River. The faucet snail serves as intermediate host for several trematodes that have caused large-scale mortality among water birds, primarily in the Great Lakes region and Montana. It is important to limit the spread of the faucet snail; small fisheries equipment can serve as a method of snail distribution. Treatments with chemical disinfection, pH extremes, and heated water baths were tested to determine their effectiveness as a disinfectant for small fisheries equipment. Two treatments eliminated all test snails: (1) a 24-h exposure to Hydrothol 191 at a concentration of at least 20 mg/L and (2) a treatment with 50°C heated water for 1 min or longer. Faucet snails were highly resistant to ethanol, NaCl, formalin, Lysol, potassium permanganate, copper sulfate, Baquacil, Virkon, household bleach, and pH extremes (as low as 1 and as high as 13).