bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational consequences of protein glycosylation: Preparation of O‐mannosyl serine and threonine building blocks, and their incorporation into glycopeptide sequences derived from α‐dystroglycan
Authors: Liu Mian , Borgert Andrew , Barany George , Live David 
Published: September 2007

AbstractWith the goal to investigate the structural impact of O‐mannosyl glycosylation on α‐dystroglycan, a glycoprotein that has an important role in the extracellular organization of muscle, glycopeptides derived from its mucin‐like sequence have been prepared by solid‐phase peptide synthesis. Two approaches have been explored to obtain needed mannosylated serine and threonine building blocks. With the α‐carboxyl group unprotected, and with tetraaceto‐1‐fluoro‐α‐D‐mannose as the sugar donor, the desired α‐O‐mannosyl‐Fmoc‐Ser/Thr formed, along with mannosyl ester isomers and the species with mannose attached to both hydroxyl and carboxyl functions. Relevant mechanistic questions and stability issues were elucidated. Alternatively, building blocks were made with the α‐carboxyl protected/activated as the pentafluorophenyl (Pfp) ester. Glycopeptides synthesized herein contained 5–9 residues, and featured one, two, and four consecutive Ser and/or Thr residues O‐glycosylated with mannose. Circular dichroism (CD) spectra for Man‐containing glycopeptides recorded in water show them to be not well ordered. For one of the α‐dystroglycan‐derived sequences, the comparative conformational consequences of glycosylation by either Man or GalNAc have been examined by CD and NMR, with both methods showing a more organized structure when GalNAc is present. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 358–368, 2008.This 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
Clinicopathological significance of fibrous tissue around fixed recurrent rectal cancer in the pelvis
Authors: Uehara K , Shimoda T , Nakanishi Y , Taniguchi H , Akasu T , Fujita S , Yamamoto S , Moriya Y 
Published: September 2007

Abstract

Background
Fibrous tissue around a locally recurrent rectal tumour is an interesting histological feature, but its clinicopathological significance has not been investigated.

Methods
This retrospective study examined clinicopathological findings in 48 patients who underwent curative total pelvic exenteration with distal sacrectomy (TPES) between 1992 and 2004. Data were analysed with respect to fibrosis around the recurrent tumour, categorized into one of three groups: no fibrosis (f0), partial fibrosis (f1) or circumferential fibrosis (f2).

Results
Ten, 17 and 21 patients had f0, f1 and f2 fibrosis respectively, with 5-year survival of none, four and eight patients respectively. The overall survival of patients with circumferential fibrosis was significantly better than that in patients with no fibrosis (P = 0·003). Univariable analysis showed that a high level of sacrectomy (P = 0·036), absence of lymphatic invasion (P = 0·031) and circumferential fibrosis (P = 0·039) were significantly associated with better overall survival. In multivariable analysis, circumferential fibrosis (P = 0·031) and low serum carcinoembryonic antigen levels (P = 0·044) were independent factors for a favourable outcome.

Conclusion
The outcome of patients with locally recurrent rectal cancer after curative TPES appears to be better when circumferential fibrosis is present around the tumour.
Effect of collagen turnover and matrix metalloproteinase activity on healing of venous leg ulcers
Authors: Meyer F J , Burnand K G , Abisi S , TeKoppele J M , van Els B , Smith A 
Published: September 2007

Abstract

Background
The presence of fibrous tissue in poorly healing venous leg ulcers suggests abnormal collagen metabolism. The aim was to determine whether there were differences in collagen turnover and matrix metalloproteinase (MMP) activity between ulcers that healed, those that did not heal and normal skin.

Methods
Biopsies were taken from the ulcers of 12 patients whose venous ulcers went on to heal and 15 patients whose ulcers failed to heal despite 12 months of compression bandaging. Biopsies were taken from 15 normal controls. Collagen turnover (collagen III N-terminal propeptide (PIIINP) and degraded collagen), and total MMP, MMP-1 and MMP-3 activities were measured.

Results
PIIINP and degraded collagen levels were higher in ulcers that healed compared with lesions that failed to heal (P = 0·005 and P &lt; 0·001 respectively) and normal skin (P = 0·003 and P &lt; 0·001). MMP-1 activity was also higher in healing ulcers than resistant ulcers (P &lt; 0·001) and normal skin (P &lt; 0·001). Significantly more total MMP activity was present in all ulcers than in normal skin (P &lt; 0·001), but there was no difference in total MMP (and MMP-3 activity) between ulcers that healed and those that did not.

Conclusion
Rapidly healing venous leg ulcers had increased collagen turnover and MMP-1 activity, which appeared to differentiate them from those that failed to heal within 12 months.
Multicentre randomized clinical trial of mechanical bowel preparation in elective colonic resection (Br J Surg 2007; 94: 689–695)
Authors: Noble E J , Daniels I R 
Published: September 2007

Abstract
The Editors welcome topical correspondence from readers relating to articles published in the Journal. Responses should be sent electronically via the BJS website (www.bjs.co.uk). All letters will be reviewed and, if approved,appear on the website. A selection of these will be edited and published in the Journal. Letters must be no more than 250 words in length.
An alignment‐free methodology for modelling field‐based 3D‐structure activity relationships using inductive logic programming
Authors: Buttingsrud Bård , King Ross Donald , Alsberg Bjørn Kåre 
Published: September 2007

AbstractTraditional 3D‐quantitative structure–activity relationship (QSAR)/structure–activity relationship (SAR) methodologies are sensitive to the quality of an alignment step which is required to make molecular structures comparable. Even though many methods have been proposed to solve this problem, they often result in a loss of model interpretability. The requirement of alignment is a restriction imposed by traditional regression methods due to their failure to represent relations between data objects directly. Inductive logic programming (ILP) is a class of machine‐learning methods able to describe relational data directly. We propose a new methodology which is aimed at using the richness in molecular interaction fields (MIFs) without being restricted by any alignment procedure. A set of MIFs is computed and further compressed by finding their minima corresponding to the sites of strongest interaction between a molecule and the applied test probe. ILP uses these minima to build easily interpretable rules about activity expressed as pharmacophore rules in the powerful language of first‐order logic. We use a set of previously published inhibitors of factor Xa of the benzamidine family to discuss the problems, requirements and advantages of the new methodology. Copyright © 2007 John Wiley & Sons, Ltd.
Sequential design of mixture experiments for the development of new products
Authors: Muteki Koji , MacGregor John F. 
Published: September 2007

AbstractThis paper presents a new sequential approach to mixture DOE that simultaneously selects new materials and ratios in which to combine them with the objective of achieving a set of specified final product properties. In each sequentially designed experiment the approach selects new materials and formulation ratios through an optimization based on mixture‐property partial least square (PLS) models that account for similarities among the properties of different materials (Muteki et al. 1, 2). The approach is useful for the case where one has existing experiments some of which may not be too far from those required for the desired new product. The sequential DOE methodo logy is demonstrated on an industrial polymer blending problem. Copyright © 2007 John Wiley & Sons, Ltd.
Identification of genes involved in radiation‐induced G1 arrest
Authors: Musumarra Giuseppe , Trovato‐Salinaro Angela , Scirè Salvatore , Foti Anna , Barresi Vincenza , Fortuna Cosimo Gianluca , Strazzulla Giovanni , Condorelli Daniele Filippo 
Published: September 2007

AbstractThe advent of microarray gene expression technology permits the simultaneous analysis of the levels of expression of thousands of genes and provides large dataset requiring multivariate analysis tools. Multiple genetic factors may modulate the occurrence and magnitude of the arrest in the G1 phase of the cell cycle following exposure to ionizing radiation in human tumour cell lines. The ability to G1 arrest after exposure to gamma rays and the global gene expression profile, evaluated by cDNA microarray technology, have been reported for the National Cancer Institute (NCI) 60 tumour cell lines panel. The sensitivity of the tumour cell lines to radiations represents an activity fingerprinting that can be correlated by partial least squares (PLS) to the transcriptional profiles of the same cell lines. VIP values obtained by the PLS method are able to detect transcripts relevant to the radiation‐induced G1 arrest. High VIP values were obtained for the basal levels of transcripts such as p21/Waf1/Cip1 and MDM2, that are well known for their roles in G1 arrest after irradiation. Novel functional relationships suggested by high VIP values can be investigated experimentally. As an example, in the present study, we report that the transcript for the FLJ11046 protein is induced dose‐dependently by gamma‐irradiation in a cell line with mutated p53, but not in cell lines with wild‐type p53. Moreover specific silencing of FLJ11046 transcript by RNA interference technology results in a block of cell growth. Copyright © 2007 John Wiley & Sons, Ltd.
Ligand‐Activated Lithium‐Mediated Zincation of N‐Phenylpyrrole
Authors: Seggio Anne , Lannou Marie‐Isabelle , Chevallier Floris , Nobuto Daisuke , Uchiyama Masanobu , Golhen Stéphane , Roisnel Thierry , Mongin Florence 
Published: September 2007

AbstractMetalation of N‐phenylpyrrole by using an in situ mixture of ZnCl2⋅TMEDA (0.5 equiv; TMEDA=N,N,N′,N′‐tetramethylethylenediamine) and LiTMP (1.5 equiv; TMP=2,2,6,6‐tetramethylpiperidino) was optimized. The reaction carried out at room temperature in THF resulted in incomplete metalation (56 % conversion) and selectivity (mixture of 2‐iodo and 2,2′‐diiodo derivatives in an 86:14 ratio after trapping with iodine). By using diethyl ether (DEE), toluene, or hexane instead of THF, low conversions of 17, 38, or 23 % were observed, respectively, but the formation of the diiodide was avoided. When hexane was used as solvent, strong lithium‐complexing ligands such as [12]crown‐4 and N,N′‐dimethylpropylideneurea (DMPU) inhibited the reaction whereas more (hemi)labile ligands (TMEDA>THF≈DME) favored it. This result shows that a temporary accessibility of lithium to interact with the rest of the base and/or the substrate is a prerequisite for an efficient metalation. A 75 % yield of 2‐iodo‐N‐phenylpyrrole was obtained after reaction with the base in the presence of five equivalents of TMEDA for two hours at room temperature, and subsequent trapping with iodine. We were able to successfully replace the spare TMP with a less expensive butyl group.
Non‐Cytotoxic, Bifunctional EuIII and TbIII Luminescent Macrocyclic Complexes for Luminescence Resonant Energy‐Transfer Experiments
Authors: Ferrand Anne‐Claire , Imbert Daniel , Chauvin Anne‐Sophie , Vandevyver Caroline D. B. , Bünzli Jean‐Claude G. 
Published: September 2007

AbstractA new macrocyclic ligand, L3, has been synthesised, based on the cyclen framework grafted with three phenacyl light‐harvesting groups and a C5‐alkyl chain bearing a carboxylic acid function as a potential linker for biological material. Acidity constants are determined by spectrophotometric titrations, as well as conditional stability constants for the resulting 1:1 complexes with trivalent lanthanide ions. The complexes have stabilities comparable to 1,4,7,10‐tetrakis(carbamoylmethyl)‐1,4,7,10‐tetraazacyclododecane (dtma) complexes, with pLn≈12–13. Photophysical properties of the ligand and of the EuL3 and TbL3 complexes have been determined for both microcrystalline samples and solutions in water and acetonitrile. They point to the metal ion being present in an environment with axial symmetry derived from the C4 point group. The hydration number determined for TbL3 decreases with increasing pH value and becomes fractional at pH 7.5, which points to an equilibrium between two differently solvated species and probably to the participation of the deprotonated carboxylic acid chain in the complexation. The quantum yields in water (1.9 % for EuIII, 3.4 % for TbIII) are smaller than those for complexes with the symmetrically substituted parent macrocycle, but efficient luminescence resonant energy transfer (LRET) was observed when Cy5 dye was added to the solutions. Finally, the influence of the TbL3 complex on cell viability is tested on both malignant (5D10 mouse hybridoma, Jurkat human T leukaemia, MCF‐7 human breast carcinoma) and non‐malignant (Hacat human keratinocyte) cell lines. Cell viability after 24 h incubation at 37 °C with 500 μM TbL3 was >90 % for all cell lines, except Jurkat (>70 %). All of these properties make LnL3 complexes interesting potential probes for bioanalyses.
Caldesmon is necessary for maintaining the actin and intermediate filaments in cultured bladder smooth muscle cells
Authors: Deng Maoxian , Mohanan Sunish , Polyak Erzsebet , Chacko Samuel 
Published: September 2007

AbstractCaldesmon (CaD), a component of microfilaments in all cells and thin filaments in smooth muscle cells, is known to bind to actin, tropomyosin, calmodulin, and myosin and to inhibit actin‐activated ATP hydrolysis by smooth muscle myosin. Thus, it is believed to regulate smooth muscle contraction, cell motility and the cytoskeletal structure. Using bladder smooth muscle cell cultures and RNA interference (RNAi) technique, we show that the organization of actin into microfilaments in the cytoskeleton is diminished by siRNA‐mediated CaD silencing. CaD silencing significantly decreased the amount of polymerized actin (F‐actin), but the expression of actin was not altered. Additionally, we find that CaD is associated with 10 nm intermediate‐sized filaments (IF) and in vitro binding assay reveals that it binds to vimentin and desmin proteins. Assembly of vimentin and desmin into IF is also affected by CaD silencing, although their expression is not significantly altered when CaD is silenced. Electronmicroscopic analyses of the siRNA‐treated cells showed the presence of myosin filaments and a few surrounding actin filaments, but the distribution of microfilament bundles was sparse. Interestingly, the decrease in CaD expression had no effect on tubulin expression and distribution of microtubules in these cells. These results demonstrate that CaD is necessary for the maintenance of actin microfilaments and intermediate‐sized filaments in the cytoskeletal structure. This finding raises the possibility that the cytoskeletal structure in smooth muscle is affected when CaD expression is altered, as in smooth muscle de‐differentiation and hypertrophy seen in certain pathological conditions. Cell Motil. Cytoskeleton 2007. © 2007 Wiley‐Liss, Inc.
Movement of stress fibers away from focal adhesions identifies focal adhesions as sites of stress fiber assembly in stationary cells
Authors: Endlich Nicole , Otey Carol A. , Kriz Wilhelm , Endlich Karlhans 
Published: September 2007

AbstractForce generated in contractile actin filament bundles (stress fibers—SFs) is transmitted to the extracellular matrix (ECM) via linker proteins and transmembrane integrins at focal adhesions (FAs). Though it has long been known that actin is rapidly exchanged in FAs, the connection between SFs and FAs has not been studied in detail. We introduced fiduciary marks on SFs by expressing GFP‐palladin or GFP‐α‐actinin‐1, which are both FA and dense body proteins, and by pattern bleaching of GFP‐actin. Following fiduciary marks on SFs over time by time‐lapse fluorescence microscopy, we detected assembly of SFs at FAs in stationary cells resulting in movement of SFs away from FAs with a velocity of 0.2–0.4 μm/min. Visualization of FAs in GFP‐palladin/DsRed‐paxillin double transfected cells showed that SF elongation was not accompanied by a change in FA length. SF elongation at FAs depended on actin polymerization and force as demonstrated by inhibitors of actin polymerization (cytochalasin D, jasplakinolide) and inhibitors of myosin‐dependent contraction (blebbistatin, Y‐27632), respectively. Our finding of SF assembly at FAs has important implications for SF formation, force transmission, and tension distribution within the actin cytoskeletal network of stationary cells. Cell Motil. Cytoskeleton 2007. © 2007 Wiley‐Liss, Inc.
Challenges and recommendations for advancing the state‐of‐the‐science of quality of life assessment in symptom management trials
Authors: Buchanan David R. , O'Mara Ann M. , Kelaghan Joseph W. , Sgambati Maria , McCaskill‐Stevens Worta , Minasian Lori 
Published: September 2007

AbstractMajor findings are presented from a workshop on Quality of Life Assessment in Cancer Symptom Management Trials, sponsored by the National Cancer Institute. Data‐driven research reports focused on 3 topics, 1) the rationale and utility of health‐related quality of life (HRQOL) assessment, 2) conceptual models, and 3) measurement and design issues. Recommendations for including HRQOL assessment cited the potential value of: capturing additional treatment effects (eg, fatigue + depression); describing the patient experience; predicting patient prognosis; identifying potential adverse effects; observing interactions among symptoms; calculating quality adjusted survival and cost‐effectiveness; and generating new hypotheses. Recommendations for developing more fully developed conceptual models focused on maintaining clear distinctions among symptoms, function, summary measures of HRQOL, and global HRQOL assessments; identifying symptom clusters; pursuing hypotheses about whether clustering is better explained as symptom‐related or as patient‐related (genetic predispositions); and gaining a better understanding of the dynamic and reciprocal influences of symptoms on each other. With respect to measurement and design issues, because different HRQOL measures cover different domains with various degrees of sensitivity, there is a need to select measures that are carefully tailored to the study's hypotheses. Finally, there is a growing appreciation that trials must be powered to test for effects on secondary endpoints. Cancer 2007. Published 2007 by the American Cancer Society.
Analysis of risk factors for distant metastases in squamous cell carcinoma of the oral cavity
Authors: Liao Chun‐Ta , Wang Hung‐Ming , Chang Joseph Tung‐Chieh , Ng Shu‐Hang , Hsueh Chuen , Lee Li‐Yu , Lin Chih‐Hung , Chen I‐How , Huang Shiang‐Fu , Yen Tzu‐Chen 
Published: September 2007

AbstractBACKGROUND.The number of patients with oral cavity squamous cell carcinoma (OSCC) is increasing. Because the characteristics of patients with OSCC who develop distant metastases (DM) remain uncertain, the authors analyzed potential risk factors.METHODS.For this report, the authors retrospectively reviewed data from 889 consecutive patients with OSCC who underwent radical surgery from January 1996 to November 2004. Patients were divided into 2 groups according to whether they had either achieved locoregional control (Group A; n = 678 patients) or developed a locoregional recurrence (Group B; n = 211 patients). Cox proportional‐hazards models were used to identify independent predictors of the 5‐year DM rate.RESULTS.In the entire study cohort, the 5‐year DM rate was 9.6% (6.6% for Group A and 21.4% for Group B). In Group A, the number of positive lymph nodes (≥5; P = .009) and the presence of extracapsular spread (ECS) (P < .001) were independent risk factors for DM. In Group B, the presence of ECS (P = .008), poor differentiation (P = .040), pathological stage ≥III (P = .036), and the presence of neck recurrence (P = .001) were independent prognosticators.CONCLUSIONS.The current results indicated that different risk factor categories according to locoregional control may be used to facilitate the selection of appropriate management for patients with OSCC after they undergo radical surgery. Cancer 2007. © 2007 American Cancer Society.
Practical time‐gated luminescence flow cytometry. I: Concepts
Authors: Jin Dayong , Connally Russell , Piper James 
Published: September 2007

AbstractThe method of time‐gated detection of long‐lifetime (1–2,000 μs) luminescence‐labeled microorganisms following rapid excitation pulses has proved highly efficient in suppressing nontarget autofluorescence (<0.1 μs), scatterings, and other prompt stray light (Hemmila and Mukkala, Crit Rev Clin Lab Sci 2001;38:441–519). The application of such techniques to flow cytometry is highly attractive but there are significant challenges in implementing pulsed operation mode to rapid continuous flowing sample to achieve high cell analysis rates (Leif R, Vallarino L, Rare‐earth chelates as fluorescent markers in cell separation and analysis, In: Cell Separation Science and Technology, ACS Symposium Series 464, American Chemical Society, 1991, pp 41–58; Condrau et al., Cytometry 1994;16:187–194; Condrau et al., Cytometry 1994;16:195–205; Shapiro HM, Improving signals from labels: Amplification and other techniques, In: Practical Flow Cytometry, 4th ed., Wiley, New York, 2002, p 345). We present here practical approaches for achieving high cell analysis rates at 100% detection efficiency, using time‐gated luminescence (TGL) flow cytometry. In particular, we report that new‐generation UV LEDs are practical sources in TGL flow cytometry.Spatial effects of long‐lived luminescence from the target fluorophore in a fast‐flowing sample stream have been investigated; excitation and detection requirements in TGL flow cytometry were theoretically analyzed; two practical approaches, a triggered model and a continuous flow‐section model, were considered as a function of flow speed, sizes and relative positions of the excitation/detection spots, label lifetime, excitation pulse duration/intensity, and detection duration. A particular configuration using LED excitation to detect europium dye‐labeled targets in such a system has been modeled in detail.In the triggered model, TGL mode is confined to a low repetition rate (<1 kHz) and engaged only while a target particle is present in the excitation zone. In the flow‐section model, TGL mode is engaged continuously at high repetition rates to permit much higher cell arrival rates. The detection of 5.7‐μm europium calibration beads in a UV LED‐excited TGL flow cytometer has been shown to be feasible with a calculated signal‐to‐background ratio up to 11:1. © 2007 International Society for Analytical Cytology
Data transmission over analog TV broadcasting
Authors: Koukourlis Christos S. 
Published: September 2007

AbstractThe implementation of a contemporary method that enables the transmission of digital information at a rate of 2 Mbps over TV signal using the existing broadcasting infrastructure is described. Detailed information on the prototype hardware is given along with experimental results that prove the validity of the proposed method. Finally, a concept for including the method to the existing TV broadcasting network is proposed. Copyright © 2007 John Wiley & Sons, Ltd.