bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of coral reefs using herbivory/nutrient assays and indicator groups of benthic primary producers: a critical synthesis, proposed protocols, and critique of management strategies
Authors: Littler Mark M. , Littler Diane S. 
Published: August 2006

Abstract
Rapid assessment protocols for determining and monitoring the status of any given coral reef are provided and include measuring: (a) standing stocks of functional indicator groups, (b) herbivore populations, (c) water‐column nutrient levels, (d) tissue C:N:P ratios, (e) algal physiological‐response assays, and (f) herbivory assays. These measurements can reveal quantitative tipping‐point levels beyond which resilience to undesirable phase shifts begins to become critically reduced. Universal tipping‐point approximations are reviewed for inorganic nutrients, and posited for the first time for herbivory.
The relative roles of top‐down and bottom‐up controls in determining benthic community structure and the health of coral reefs are especially important management concerns. This paper specifically addresses the top‐down effects of herbivory and bottom‐up effects of nutrient enrichment on critical indicator groups, i.e. reef‐building corals, crustose coralline algae, dense turf algae and frondose macroalgae.
A predominance of (a) massive corals and calcareous coralline algae relative to frondose macroalgae and algal turfs indicates a healthy spatially heterogeneous condition reflecting low nutrients and high herbivory. An abundance of (b) frondose macroalgae illustrates the least desirable condition of elevated nutrient levels and reduced herbivory, possibly reflecting pollution in concert with destructive herbivore fishing practices. High coverage of (c) coralline algae suggests healthy high herbivory levels, but problems with elevated nutrients that are inhibitory to some corals. Domination by (d) dense turf algae indicates desirably low nutrient levels, but an inadequate herbivory component.
The fast growth and turnover rates of fleshy algae compared to other reef organisms highlight their value as early warning indicators of reef degradation.
From a management perspective, levels of herbivory and nutrients rank among the most useful quantitative indicators of coral reef resilience; whereas, the degree of degradation and mortality are inferred from the above functional indicator groups of benthic primary producers.
Published in 2006 by John Wiley & Sons, Ltd.
Vancomycin Analogues Containing Monosaccharides Exhibit Improved Antibiotic Activity: A Combined One‐Pot Enzymatic Glycosylation and Chemical Diversification Strategy
Authors: Thayer Desiree A. , Wong Chi‐Huey 
Published: August 2006

AbstractMany natural products contain carbohydrate moieties that contribute to their biological activity. Manipulation of the carbohydrate domain of natural products through multiple glycosylations to identify new derivatives with novel biological activities has been a difficult and impractical process. We report a practical one‐pot enzymatic approach with regeneration of cosubstrates to synthesize analogues of vancomycin that contain an N‐alkyl glucosamine, which exhibited marked improvement in antibiotic activity against a vancomycin‐resistant strain of Enterococcus.
A Brief Review on Software Developments for Group Sequential and Adaptive Designs
Authors: Wassmer Gernot , Vandemeulebroecke Marc 
Published: August 2006

AbstractIn this paper the currently available software we know for group sequential and adaptive designs is briefly reviewed. Stand‐alone packages as well as modules within software packages or programming languages exist. New software developments for adaptive designs enable the user to perform data dependent design adaptations while controlling the Type I error rate. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An Adaptive Hierarchical Test Procedure for Selecting Safe and Efficient Treatments
Authors: König Franz , Bauer Peter , Brannath Werner 
Published: August 2006

AbstractWe consider the situation where during a multiple treatment (dose) control comparison high doses are truncated because of lack of safety and low doses are truncated because of lack of efficacy, e.g., by decisions of a data safety monitoring committee in multiple interim looks. We investigate the properties of a hierarchical test procedure for the efficacy outcome in the set of doses carried on until the end of the trial, starting with the highest selected dose group to be compared with the placebo at the full level α. Left truncation, i.e., dropping doses in a sequence starting with the lowest dose, does not inflate the type I error rate. It is shown that right truncation does not inflate the type I error if efficacy and toxicity are positively related and dose selection is based on monotone functions of the safety data. A positive relation is given e.g. in the case where the efficacy and toxicity data are normally distributed with a positive pairwise correlation. A positive relation also applies if the probability for an adverse event is increasing with a normally distributed efficacy outcome. The properties of such truncation procedures are investigated by simulations. There is a conflict between achieving a small number of unsafely treated patients and a high power to detect safe and efficient doses. We also investigated a procedure to increase power where a reallocation of the sample size to the truncated treatments and the control remaining at the following stages is performed. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
How Practical are Adaptive Designs Likely to be for Confirmatory Trials?
Authors: Gould A. Lawrence 
Published: August 2006

AbstractThis is a discussion of the following papers appearing in this special issue on adaptive designs: ‘Confirmatory Seamless Phase II/III Clinical trials with Hypotheses Selection at Interim: General Concepts’ by Frank Bretz, Heinz Schmidli, Franz König, Amy Racine and Willi Maurer; and ‘Confirmatory Seamless Phase II/III Clinical Trials with Hypotheses Selection at Interim: Applications and Practical Considerations’ by Heinz Schmidli, Frank Bretz, Amy Racine and Willi Maurer. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Confirmatory Seamless Phase II/III Clinical Trials with Hypotheses Selection at Interim: Opportunities and Limitations
Authors: Jennison Christopher , Turnbull Bruce W. 
Published: August 2006

AbstractThis is a discussion of the following two papers in this special issue on adaptive designs: ‘Confirmatory seamless phase II/III clinical trials with hypotheses selection at interim: General concepts’ by Frank Bretz, Heinz Schmidli, Franz König, Amy Racine and Willi Maurer, and ‘Confirmatory seamless phase II/III clinical trials with hypotheses selection at interim: Applications and practical considerations’ by Heinz Schmidli, Frank Bretz, Amy Racine and Willi Maurer. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Adaptive vs. Group Sequential Self‐designing Trials
Authors: Mehrotra Devan V. , Fan Xiaoyin (Frank) 
Published: August 2006

AbstractThis is a discussion of the paper. ‘Repeated Confidence Intervals in Self‐Designing Clinical Trials and Switching between Non‐Inferiority and Superinferiority’ by Joachim Hartung and Guido Knapp, appearing in this special issue on adaptive designs. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Polarized infrared microspectroscopy of single spruce fibers: Hydrogen bonding in wood polymers
Authors: Schmidt Martin , Gierlinger Notburga , Schade Ulrich , Rogge Tilmann , Grunze Michael 
Published: August 2006

AbstractWe studied wood polymers in their native composite structure using mechanically isolated single spruce (Picea abies [L.] Karst.) fibers. Dichroic infrared spectra of fibers placed in a custom‐built microfluidic cuvette were acquired in air, in liquid (heavy) water, and in liquid dimethylacetamide using a novel combination of synchrotron‐based Fourier transform infrared microspectroscopy with polarization modulation. Differences were observed in the O–H stretching frequency region of the spruce spectra upon changing the ambient conditions. Analysis of these spectral variations provides information on hydrogen bonding, orientation, and accessibility of structural units of the wood polymers in the spruce cell walls. Our in situ approach contributes to a further understanding of the structural details of wood polymers in their native setting. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 546–555, 2006This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
An exclusion mechanism in ion exchange chromatography
Authors: Harinarayan C. , Mueller J. , Ljunglöf A. , Fahrner R. , Van Alstine J. , van Reis R. 
Published: August 2006

AbstractProtein dynamic binding capacities on ion exchange resins are typically expected to decrease with increasing conductivity and decreasing protein charge. There are, however, conditions where capacity increases with increasing conductivity and decreasing protein charge. Capacity measurements on two different commercial ion exchange resins with three different monoclonal antibodies at various pH and conductivities exhibited two domains. In the first domain, the capacity unexpectedly increased with increasing conductivity and decreasing protein charge. The second domain exhibited traditional behavior. A mechanism to explain the first domain is postulated; proteins initially bind to the outer pore regions and electrostatically hinder subsequent protein transport. Such a mechanism is supported by protein capacity and confocal microscopy studies whose results suggest how knowledge of the two types of IEX behavior can be leveraged in optimizing resins and processes. © 2006 Wiley Periodicals, Inc.
Poly(lactic‐co‐glycolic acid) hollow fibre membranes for use as a tissue engineering scaffold
Authors: Ellis Marianne J. , Chaudhuri Julian B. 
Published: August 2006

AbstractMass transfer limitations of scaffolds are currently hindering the development of 3‐dimensional, clinically viable, tissue engineered constructs. We have developed a poly(lactide‐co‐glycolide) (PLGA) hollow fibre membrane scaffold that will provide support for cell culture, allow psuedovascularisation in vitro and provide channels for angiogenesis in vivo. We produced PDLLGA flat sheet membranes using 1, 4‐dioxane and 1‐methyl‐2‐pyrrolidinone (NMP) as solvents and water as the nonsolvent, and hollow fibre membranes, using NMP and water, by dry/wet‐ and wet‐spinning. The resulting fibres had an outer diameter of 700 μm and an inner diameter of 250 μm with 0.2–1.0 μm pores on the culture surface. It was shown that varying the air gap and temperature when spinning changed the morphology of the fibres. The introduction of a 50 mm air gap caused a dense skin of 5 μm thick to form, compared to a skin of 0.5 μm thick without an air gap. Spinning at 40°C produced fibres with a more open central section in the wall that contained more, larger macrovoids compared to fibres spun at 20°C. Culture of the immortalised osteogenic cell line 560pZIPv.neo (pZIP) was carried out on the PDLLGA flat sheets in static culture and in a PDLLGA hollow fibre bioreactor under counter‐current flow conditions. Attachment and proliferation was statistically similar to tissue culture polystyrene on the flat sheets and was also successful in the hollow fibre bioreactor. The PDLLGA hollow fibres are a promising scaffold to address the size limitations currently seen in tissue engineered constructs. Biotechnol. Bioeng. 2007;96: 177–187. © 2006 Wiley Periodicals, Inc.
Genetic inactivation of the APC gene contributes to the malignant progression of sporadic hepatocellular carcinoma: A case report
Authors: Katoh Hiroto , Shibata Tatsuhiro , Kokubu Akiko , Ojima Hidenori , Kosuge Tomoo , Kanai Yae , Hirohashi Setsuo 
Published: August 2006

AbstractAlthough activated Wnt/β‐catenin pathway is considered to be one of the main driving forces of hepatocarcinogenesis, no somatic mutations of the adenomatous polyposis coli (APC) gene have been found in sporadic hepatocellular carcinoma (HCC) to date. Here we present a case of a sporadic nodule‐in‐nodule‐type HCC that provides the first evidence that biallelic genetic inactivation of the APC gene contributed to the development of the tumor. High‐density array‐based comparative genomic hybridization (aCGH) was performed to clarify genome‐wide chromosomal structural alteration profiles of both early and advanced components of this nodule‐in‐nodule HCC. aCGH analysis revealed a chromosomal loss of the APC gene locus only in the inner advanced component of this tumor. Direct sequencing of the remaining allele revealed a nonsense mutation at codon 682 in the Armadillo repeats, resulting in a truncated protein that lacked all of the β‐catenin‐binding motifs. Nonsense mutations at this location are rare among other types of cancer. In conclusion, combined with an immunohistochemical analysis of the β‐catenin protein, this case provides the first evidence that genetic inactivation of the APC gene can play a significant role in the progression of sporadic HCC, probably by activating the Wnt/β‐catenin pathway. © 2006 Wiley‐Liss, Inc.
Comprehensive assessment of DNA copy number alterations in human prostate cancers using Affymetrix 100K SNP mapping array
Authors: Liu Wennuan , Chang Baoli , Sauvageot Jurga , Dimitrov Latchezar , Gielzak Marta , Li Tao , Yan Guifang , Sun Jishan , Sun Jielin , Adams Tamara S. , Turner Aubrey R. , Kim Jin Woo , Meyers Deborah A. , Zheng Siqun Lilly , Isaacs William B. , Xu Jianfeng 
Published: August 2006

AbstractAlthough multiple recurrent chromosomal alterations have been identified in prostate cancer cells, the specific genes driving the apparent selection of these changes remain largely unknown. In part, this uncertainty is due to the limited resolution of the techniques used to detect these alterations. In this study, we applied a high‐resolution genome‐wide method, Affymetrix 100K SNP mapping array, to screen for somatic DNA copy number (CN) alterations among 22 pairs of samples from primary prostate cancers and matched nonmalignant tissues. We detected 355 recurrent deletions and 223 recurrent gains, many of which were novel. As expected, the sizes of novel alterations tend to be smaller. Importantly, among tumors with increasing grade, Gleason sum 6, 7, and 8, we found a significant trend of larger number of alterations in the tumors with higher grade. Overall, gains are significantly more likely to occur within genes (74%) than are deletions (49%). However, when we looked at the most frequent CN alterations, defined as those in ≥4 subjects, we observed that both gains (85%) and deletions (57%) occur preferentially within genes. An example of a novel, recurrent alteration observed in this study was a deletion between the ERG and TMPRSS2 genes on chromosome 21, presumably related to the recently identified fusion transcripts from these two genes. Results from this study provide a basis for a systematic and comprehensive cataloging of CN alterations associated with grades of prostate cancer, and the subsequent identification of specific genes that associated with initiation and progression of the disease. This article contains supplementary material available via the Internet at http://www.interscience.wiley.com/jpages/1045‐2257/suppmat. © 2006 Wiley‐Liss, Inc.
Microbial induction of CARD15 expression in intestinal epithelial cells via toll‐like receptor 5 triggers an antibacterial response loop
Authors: Begue B. , Dumant C. , Bambou J.C. , Beaulieu J.F. , Chamaillard M. , Hugot J.P. , Goulet O. , Schmitz J. , Philpott D.J. , Cerf‐Bensussan N. , Ruemmele F.M. 
Published: August 2006

AbstractWith the discovery of CARD15 as susceptibility gene for Crohn's disease (CD) a first link to a potential defect in the innate immune system was made. In this work we aimed to analyze enterocyte NOD2/CARD15 expression and regulation in response to bacterial motifs and the consequences of the most common CD‐specific CARD15 mutation on antibacterial responses of normal intestinal epithelial cells (IEC). Under normal conditions, IEC lines and ileal enterocytes did not express NOD2/CARD15 mRNA or protein, contrary to IEC derived from inflammatory CD sections. In vitro analyses revealed that the simple contact with non‐pathogenic commensal E. Coli K12 was sufficient to induced NOD2/CARD15 mRNA and protein in human IEC (HIEC). We identified bacterial flagellin interacting with TLR5 as major motif in this regulation of NOD2/CARD15. E. Coli mutants not expressing flagellin (ΔFliC) failed to induce CARD15. Similarly, in HIEC transfected with a plasmid encoding dominant negative TLR5, no CARD15 induction was observed after K12 contact. Isolated TLR2 or TLR4 stimulation had no or only a marginal effect on NOD2/CARD15 expression. NOD2/CARD15 negative HIEC were unresponsive to muramyl dipeptide (MDP), but once NOD2/CARD15 was induced, HIEC and Caco2 cells responded to intra or extracellular MDP presentation with the activation of the NFkB pathway. IEC transfected with the Crohn‐specific CARD15 mutant (F3020insC, FS) failed to activate NFkB after MDP‐challenge, in contrast to CARD15WT IEC. In response to MDP, IEC induced a massive antibacterial peptide (ABP) response, seen in the apical release of CCL20. This was completely abolished in IEC carrying CARD15FS. These data suggest a critical role of NOD2/CARD15 in the bacterial clearance of the intestinal epithelium while CD‐specific mutated NOD2/CARD15 causes an impaired epithelial barrier. J. Cell. Physiol. 209: 241–252, 2006. © 2006 Wiley‐Liss, Inc.
Transcriptional and proteolytic regulation of the insulin‐like growth factor‐I system of equine articular chondrocytes by recombinant equine interleukin‐1β
Authors: Porter Ryan M. , Akers R. Michael , Howard Rick D. , Forsten‐Williams Kimberly 
Published: August 2006

AbstractInterleukin‐1 (IL‐1) and insulin‐like growth factor‐I (IGF‐I), which have opposing effects on matrix metabolism within articular cartilage, are thought to play prominent roles in the pathogenesis of osteoarthritis. To better understand the link between these anabolic (IGF‐I) and catabolic (IL‐1) stimuli, we examined exogenous IL‐1 regulation of the IGF‐I signaling system of articular chondrocytes (ACs). Equine ACs from non‐arthritic stifle joints were expanded in monolayer culture, encapsulated for 10 days in alginate beads, and stimulated as high‐density monolayers with recombinant equine IL‐1β (0, 1, 10 ng/ml) for 48 h. IL‐1β enhanced expression of IGF‐IR levels, as determined by both [125I]‐IGF‐I binding studies and Western blotting, while reducing the concentration of endogenous IGF‐I detected in conditioned media by radioimmunoassay. Western ligand blotting revealed that chondrocytes primarily secreted IGF binding proteins (IGFBPs) with molecular weights of 28–30 and 32–34 kDa, which were identified as IGFBPs 5 and 2, respectively, and that IL‐1β treatment diminished IGFBP‐2, the prominent homolog in conditioned media. Northern blot analysis suggested IL‐1β regulation of IGF‐I and, to some extent, IGF‐IR was mediated by transcription; however, the cytokine did not affect IGFBP‐2 expression. To test for evidence of proteolysis by matrix metalloproteinases (MMPs), additional cultures were co‐incubated with inhibitors for MMPs 2/9, 3, and 8. IGFBP‐2 suppression was partially reversed by gelatinase (MMP‐2/9) inhibition. In summary, these findings further delineate the role of IL‐1 as a key regulator of the IGF‐I system within articular cartilage, demonstrating that regulation occurs through both direct (transcriptional) and indirect (proteolytic) mechanisms. J. Cell. Physiol. 209: 542–550, 2006. © 2006 Wiley‐Liss, Inc.
PAK4 and αPIX determine podosome size and number in macrophages through localized actin regulation
Authors: Gringel Alexandra , Walz Daniel , Rosenberger Georg , Minden Audrey , Kutsche Kerstin , Kopp Petra , Linder Stefan 
Published: August 2006

AbstractPodosomes are actin‐rich adhesion structures typical for monocytic cells and are implicated in migration and invasion. Major modes of podosome regulation include RhoGTPase signaling and actin regulatory pathways. However, it is not clearly understood how these signals induce highly localized changes in podosome formation and dynamics. Here, we show that the RhoGTPase effector PAK4, a member of the p21 associated kinase family, and its regulator αPIX (PAK‐interacting exchange factor), are central to podosome formation in primary human macrophages. Immunofluorescence, biochemical and microarray data indicate that PAK4 acts as physiological regulator of podosomes in this system. Accordingly, transfection of a specific shRNA, as well as expression of PAK4 truncation mutants, resulted in reduced numbers of podosomes per cell. Moreover, expression of kinase active or inactive PAK4 mutants enhanced or reduced the size of individual podosomes, respectively, indicating a modulatory influence of PAK4 kinase activity on podosome size. Similar to the results gained with PAK4, cellular/overexpressed PIX was shown to be closely associated with podosomes. Moreover, both overexpression of αPIX wt and a mutant lacking the SH3 domain led to coalescence of podosomes. In sum, we propose that PAK4 and αPIX can induce highly localized changes in actin dynamics and thereby regulate size and number of podosomes in primary human macrophages. J. Cell. Physiol. 209: 568–579, 2006. © 2006 Wiley‐Liss, Inc.
Proton spectroscopy provides accurate pathology on biopsy and in vivo
Authors: Mountford Carolyn , Lean Cynthia , Malycha Peter , Russell Peter 
Published: August 2006

AbstractIn the last 25 years, MR spectroscopy (MRS) has moved from being a basic research tool into routine clinical use. The spectroscopy method reports on those chemicals that are mobile on the MR time scale. Many of these chemicals reflect specific pathological processes but are complicated by the fact that many chemicals change at one time. There are currently two clinical applications for spectroscopy. The first is in the pathology laboratory, where it can be an adjunct to, and in some cases replacement, for difficult pathologies like Barrett's esophagus and follicular adenoma of the thyroid. The spectroscopy method on a breast biopsy can also report on prognostic indicators, including the potential for spread, from information present in the primary tumor alone. The second application for spectroscopy is in vivo to provide a preoperative diagnosis and this is now achievable for several organs including the prostate. The development of spectroscopy for clinical purposes has relied heavily on the serially‐sectioned histopathology to confirm the high accuracy of the method. The combination of in vivo MRI, in vivo MRS, and ex vivo MRS on biopsy samples offers a modality of very high accuracy for preoperative diagnosis and provision of prognostic information for human cancers. J. Magn. Reson. Imaging 2006. © 2006 Wiley‐Liss, Inc.
Artifacts and pitfalls in diffusion MRI
Authors: Le Bihan Denis , Poupon Cyril , Amadon Alexis , Lethimonnier Franck 
Published: August 2006

AbstractAlthough over the last 20 years diffusion MRI has become an established technique with a great impact on health care and neurosciences, like any other MRI technique it remains subject to artifacts and pitfalls. In addition to common MRI artifacts, there are specific problems that one may encounter when using MRI scanner gradient hardware for diffusion MRI, especially in terms of eddy currents and sensitivity to motion. In this article we review those artifacts and pitfalls on a qualitative basis, and introduce possible strategies that have been developed to mitigate or overcome them. J. Magn. Reson. Imaging 2006. © 2006 Wiley‐Liss, Inc.