bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microengineered Surface Topography Facilitates Cell Grafting from a Prototype Hydrogel Wound Dressing with Antibacterial Capability
Authors: Smith Annie G. , Din Abbas , Denyer Morgan , Crowther Nicholas J. , Eagland Donald , Vowden Kath , Vowden Peter , Britland Stephen T. 
Published: September 2006

AbstractSkin wounds derive therapeutic benefit from redeployment of dermal tissues, whether as split‐thickness allo‐ and autografts or as biological dressings comprising cultured cells. However, the clinical outcome is strongly influenced by the techniques used for cell/tissue grafting and also the microbiological status of the wound. Here we report that microtopography incorporated into the surface of a novel polymeric material, derivatized with fibronectin to promote attachment and encourage motility, improved the efficiency of cell transfer onto de‐epithelialized human skin ex vivo. The microtopography had two functions, first as a conduit for migrating cells to cross between the vehicle and recipient surface and second to shield adherent cells from destruction by mechanical shearing during handling and application. Quantitative analysis showed that topographic projections (columns) rather than recesses (pits) in the hydrogel surface achieved the highest efficiency of cell transfer. In order to address the crucial relevance of microbiological contamination to the success of wound grafting, the effect of iodine on several common bacterial pathogens was examined using an XTT+CQ10 kinetic cell viability assay. Increasing concentrations of iodine initially stressed and after 0.5% v/v were subsequently bacteriocidal for Gram‐negative Pseudomonas aeruginosa and Escherichia coli and Gram‐positive Bacillus subtillis and Staphylococcus aureus. Slightly higher doses of iodine (approx 1–1.5% v/v) were required to kill HaCaT cells outright, but for both pro‐ and eukaryotes the major determinant of cytotoxicity was absolute dose rather than duration of exposure. Iodine delivered by the hydrogel at low concentration was bacteriostatic but not apparently cytotoxic to epithelial cells as measured by MTT end‐point cell viability assay. Zone of inhibition studies confirmed that bacteriocidal quantities of neomycin, phenol red, and silver could also be delivered using the same hydrogel. This research suggests that grafting cell‐based biological dressings to wounds using a topographically modified hydrogel dressing capable of simultaneous reducing the microbiological threat to a successful outcome may be a realistic clinical proposition.
Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass spectrometry
Authors: Eckel-Passow J. E. , Oberg A. L. , Therneau T. M. , Mason C. J. , Mahoney D. W. , Johnson K. L. , Olson J. E. , Bergen H. R. 
Published: September 2006

Abstract
Motivation: Using stable isotopes in global proteome scans, labeled molecules from one sample are pooled with unlabeled molecules from another sample and subsequently subjected to mass-spectral analysis. Stable-isotope methodologies make use of the fact that identical molecules of different stable-isotope compositions are differentiated in a mass spectrometer and are represented in a mass spectrum as distinct isotopic clusters with a known mass shift. We describe two multivariable linear regression models for 16O/18O stable-isotope labeled data that jointly model pairs of resolved isotopic clusters from the same peptide and quantify the abundance present in each of the two biological samples while concurrently accounting for peptide-specific incorporation rates of the heavy isotope. The abundance measure for each peptide from the two biological samples is then used in down-stream statistical analyses, e.g. differential expression analysis. Because the multivariable regression models are able to correct for the abundance of the labeled peptide that appear as an unlabeled peptide due to the inability to exchange the natural C-terminal oxygen for the heavy isotope, they are particularly advantageous for a two-step digestion/labeling procedure. We discuss how estimates from the regression model are used to quantify the variability of the estimated abundance measures for the paired samples. Although discussed in the context of 16O/18O stable-isotope labeled data, the multivariable regression models are generalizable to other stable-isotope labeled technologies.
Contact: eckel@mayo.edu
DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold
Authors: Dlakić Mensur 
Published: September 2006

Abstract
Two RNases, Dicer and Argonaute, are at the heart of the RNA interference (RNAi) molecular machinery responsible for gene silencing. Both RNases contain multiple domains, most of which have been characterized or have functions that can be predicted based on sequence comparisons. However, Dicers of higher eukaryotes contain the domain known as DUF283 which at present has no assigned role. Using sensitive profile–profile comparisons, we detected a divergent double-stranded RNA-binding domain coinciding with the DUF283 of Dicer. This finding has potential implications regarding the mechanistic role of Dicer in RNAi.
Contact: mdlakic@montana.edu
Supplementary information: Supplementary images are available at Bioinformatics online.
Synthetic biology—putting engineering into biology
Authors: Heinemann Matthias , Panke Sven 
Published: September 2006

Abstract
Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis—synthetic biology's system fabrication process—supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.
Contact: panke@ipe.mavt.ethz.ch
Modelling the effect of Nile perch predation and harvesting on fisheries dynamics of Lake Victoria
Authors: Mugisha J. Y. T. , Ddumba H. 
Published: September 2006

AbstractWe used a mathematical model to predict and explain the effect of harvesting combined with predation by the Nile perch on Nile tilapia. The model incorporates three developmental stages of each species. The findings show that uncontrolled human exploitation of the stock leads to loss of fish biodiversity in the lake. The results of the study also show that increasing harvesting rate of the mature Nile perch leads to stable stationary states of the system. However, increasing predation rates by Nile perch lead to unstable equilibria.
Living in the shadow of fear: adolescents’ lived experience of depression
Authors: Woodgate Roberta Lynn 
Published: September 2006

Aim.  This paper reports a phenomenological study whose aim was to gain an understanding of what it was like to be an adolescent living with depression.Background.  Depression is a significant mental health problem among adolescents. Identifying the meanings that adolescents assign to their experiences with depression is needed in order to develop interventions that will improve their care and quality of life.Method.  The study took place in a city in Western Canada. Fourteen adolescents (13·5 to 18 years) diagnosed with depression participated in individual open‐ended interviews and focus group interviews between July 2001 and June 2002. Field notes were recorded. Thematic statements that were representative of the adolescents’ lived experience were isolated from the interviews and field notes. Using all the phrases, sentence clusters and field notes, the data were then reduced until essential and incidental themes emerged.Findings.  ‘Living in the shadow of fear’ emerged as the essence of the adolescents’ experiences and ultimately defined what it was like to live with depression. The shadow of fear was associated not only with fear of a return of the ‘bad’ feelings related to their depression, but also to fear of not getting help, not surviving the ‘bad’ feelings, and fear of having to do all the ‘hard work’ in overcoming the ‘bad’ feelings. This essence was supported by four themes: ‘containing the shadow of fear’, ‘keeping the self alive’, ‘maintaining a sense of belonging in the world’ and ‘feeling valued as a human being’.Conclusions.  Adolescents with depression need adequate resources and support throughout the illness trajectory, including those periods when their depression is under control.
Late Quaternary history of Hippophaë rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variation
Authors: BARTISH IGOR V. , KADEREIT JOACHIM W. , COMES HANS PETER 
Published: September 2006

AbstractFossil pollen records indicate that Hippophaë rhamnoides (Sea Buckthorn) was widespread on late‐ and early postglacial raw soils throughout much of central and northern Europe, but that Early Holocene reforestation restricted populations to northern coastal habitats, or along mountain streams in the Alps, Pyrenees, and Carpathians. We used sequence variation at the nuclear chalcone synthase intron (Chsi), in conjunction with chloroplast DNA–restriction fragment length polymorphism data, to investigate the intraspecific phylogeny, phylogeographic structure, and expansion demographic history of this dioecious and wind‐pollinated shrub at its range‐wide scale in Europe and Asia Minor. Four major Chsi phylogroups of unresolved relationships were identified with estimated divergences ∼172 000 years ago. Large‐scale phylogeographic structures of nuclear and cytoplasmic markers were congruent in identifying (i) southeastern Europe as the most likely source of colonization into central Europe and Scandinavia, and (ii) the area just north of the Alps as a contact zone between populations from the Alps and the east/central European‐Scandinavian lineage. Coalescence‐based analyses (i.e. nested clade analysis and mismatch distributions) of Chsi variation were able to detect at least four major episodes of population growth, all within about the last 40 000 years. In particular, these analyses identified a nearly synchronized timing of population expansions in various parts of the species’ range in central‐eastern Europe/Asia Minor, most likely correlating with the Younger Dryas Stadial (∼13 000–11 600 years ago). It remains to be established whether the phylogeographic history of H. rhamnoides, and particularly its rapid response to the rapid environmental changes of the Younger Dryas cold snap, is unique to the species, or whether it is shared with other cold‐tolerant shrub (or grassland) species known from late‐glacial raw soils in Europe.
Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum
Authors: ZANE L. , MARCATO S. , BARGELLONI L. , BORTOLOTTO E. , PAPETTI C. , SIMONATO M. , VAROTTO V. , PATARNELLO T. 
Published: September 2006

AbstractThe Antarctic silverfish Pleuragramma antarcticum (Nototheniidae) is the most abundant pelagic fish inhabiting Antarctic waters. In this study we investigated, through partial sequencing of the D‐loop mitochondrial region, samples collected at four different locations in the Southern Ocean, three in the Atlantic and one in the Pacific sector. Sampling was replicated in two different years at two locations. Sequence analysis showed a remarkably high polymorphism, with 110 haplotypes over the 256 investigated specimens, and about 80% of haplotypes occurring only once. Neutrality tests indicated that all samples were not at mutation–drift equilibrium, and suggested a past population expansion. This result was supported by the presence of a star‐like topology in the D‐loop gene tree, and by results of mismatch distribution. The start of the expansion was dated, using a specifically calibrated clock, between 111 and 126 thousand years ago. This value corresponds to the start of the cooling period that led to the last glaciation peak, and is in close agreement with a recently suggested range expansion for pelagic Antarctic ecosystems. Analysis of molecular variation indicated a small, though highly significant, value of differentiation between samples. This result, together with the lack of association between clades and geographical locations, indicates a weak population structure for the species.
Prestorage leucoreduction improves several in vitro red cell storage parameters following gamma irradiation
Authors: Wagner S. J. , Myrup A. C. 
Published: September 2006

summary Gamma irradiation (GI) can prevent transfusion‐associated graft‐vs.‐host disease, result in a small decrement in 24‐h in vivo red blood cell (RBC) recovery and in a minor loss of maintenance of several in vitro parameters during routine storage. Results from studies by Davey et al. (Transfusion 1995, 35, 55S) demonstrated that the decrement in 24‐h recovery was not observed if units were first leucoreduced (LR), suggesting that RBC damage on leucocytes from GI was secondary to the effects of irradiation . In this study, we further investigated how leucoreduction affected eight in vitro storage parameters of gamma‐irradiated units by using a matched sample study design.Leucoreduction significantly reduced (P < 0·05) the deleterious effect of GI on adenosine triphosphate glucose levels, haemolysis and mean corpuscular volume (MCV) for AS‐3 units and significantly decreased (P < 0·05) the deleterious effect of GI on glucose levels, haemolysis and MCV for AS‐1 units. Leucoreduction did not influence (P >> 0·5) the enhanced potassium release associated with GI. Some, but not all, the observed RBC damage caused by GI appears to be secondary to the effect of irradiation on leucocytes. Based on the in vivo survival studies of Davey et al. and the results of this study, there is justification to consider performing additional survival studies to support extended storage of LR gamma‐irradiated RBC.
Second‐line treatment in invasive mould infections
Authors: Karthaus Meinolf , Cornely Oliver A. 
Published: September 2006

AbstractA prevalence of up to 30% of invasive fungal infections (IFI) has been reported from autopsy studies in patients treated for haematological malignancies. Despite substantial advances in the last decade, IFI are still associated with a mortality of up to more than 70%, in particular for those patients suffering from invasive aspergillosis. Some progress has been made in diagnostics with the advent of new non‐culture based tools and the improvement of imaging techniques. However, the response rates are about 40–60% in the first‐line treatment of IFI. Salvage therapy will be necessary for those being intolerant or refractory towards the respective first‐line antifungal. Following a long period of stagnation, there has been a considerable progress during the last five years in the treatment of refractory IFI. This review highlights the new treatment options for the salvage setting in the context of the state‐of‐the‐art management of IFI in cancer patients.
Pilot study of pegylated interferon‐alpha 2a in dialysis patients with chronic hepatitis C virus infection
Authors: CHAN TAK MAO , HO STEPHEN K N , TANG COLIN S O , TSE KAI CHUNG , LAM MAN FAI , LAI KAR NENG , YUNG SUSAN 
Published: September 2006

SUMMARY:Aim:  Pegylated interferon (PEG‐IFN) combined with ribavirin is recommended for the treatment of chronic hepatitis C virus (HCV) infection in patients without renal failure. The optimal treatment of hepatitis C in dialysis patients remains to be established. A high incidence of adverse effects has been observed with conventional interferon and PEG‐IFN alpha‐2b in dialysis patients.Methods:  We conducted a prospective study to investigate the tolerability and efficacy of PEG‐IFN alpha‐2a (135 µg weekly for 48 weeks) in six dialysis patients with chronic HCV infection.Results:  Two patients completed 48 weeks of treatment. Treatment was stopped in three patients (beyond 24 weeks) when they developed unrelated complications, and stopped in one patient due to failure of viral clearance. None required treatment discontinuation due to adverse effects, and PEG‐IFN alpha‐2a was subjectively well tolerated. Marrow suppression with mild anaemia, leucopenia, or thrombocytopenia remained common. Two patients (infected with genotypes 3a and 1b, respectively) had sustained virological response.Conclusions:  Results from this pilot study showed that PEG‐IFN alpha‐2a appeared relatively well tolerated in dialysis patients with chronic HCV infection, and about one‐third of patients could achieve sustained virological response.
Non diabetic renal disease in type 2 diabetes mellitus
Authors: SONI SACHIN S , GOWRISHANKAR SWARNALATA , KISHAN A GOPAL , RAMAN ANURADHA 
Published: September 2006

SUMMARY:Aim:  The aim of this analysis of renal biopsies in people with type 2 diabetes was to know the prevalence and nature of non‐diabetic renal disease (NDRD) and to note its correlation with the duration of diabetes, extent of proteinuria and presence or absence of retinopathy.Methods:   From January 2000 to December 2004, 160 people with type 2 diabetes with clinically suspected NDRD underwent renal biopsy reported by a single pathologist. The case records of these patients were retrospectively analysed. Based on the biopsy findings, patients were grouped as Group I, isolated NDRD; Group II, NDRD with underlying diabetic glomerulosclerosis; and Group III, isolated diabetic glomerulosclerosis. The relation of histology with clinical profile in each group was noted and statistically analysed using strata 6 software.Results:   Of the 160 patients studied, 118 were males and 42 were females (2.8:1). The average age was 51.35 years (30–79). Indications for renal biopsy included: nephrotic syndrome in 55 (34.37%), acute renal failure (ARF) in 49 (30.62%), rapidly progressive renal failure (RPRF) in 24 (15%), absent retinopathy in 19 (11.87%), haematuria in 10 (6.25%) and acute on chronic renal failure (CRF) in three (1.87%) patients. Group I included 68 patients (42.50%), Group II included 48 patients (30%) and Group III included 44 patients (27.50%). The mean duration of diabetes was 5.37, 10.12 and 6.86 years in Groups I, II and III respectively. The duration of diabetes was significantly less in Group I compared with Group II and III combined (5.37 vs 8.53; P < 0.001). Diabetic retinopathy was absent in 61 (38.13%) patients, of whom 41 (67.21%) had isolated NDRD. The most common NDRD were acute interstitial nephritis (18.1%), post infectious glomerulonephritis (17.24%), membranous nephropathy (11.20%) and focal segmental glomerulosclerosis (7.75%).Conclusions:  Prevalence of NDRD (either isolated or superimposed on underlying diabetic glomerulosclerosis) is very high in appropriate clinical settings. The shorter duration of diabetes and the absence of retinopathy, especially when associated with nephrotic proteinuria, strongly predict NDRD.
Increased preoperative serum C‐reactive protein level predicts a poor prognosis in patients with localized renal cell carcinoma
Authors: KOMAI YOSHINOBU , SAITO KAZUTAKA , SAKAI KUNIHIKO , MORIMOTO SHINJI 
Published: September 2006

OBJECTIVETo evaluate the value of the preoperative serum C‐reactive protein (CRP) level in the prognosis of patients with localized renal cell carcinoma (RCC).PATIENTS AND METHODSThe study comprised 101 patients who had a radical nephrectomy for localized RCC (pT1–3N0M0). An elevated CRP was defined as >0.5 mg/dL before surgery. Survival rates for each variant were calculated using the Kaplan–Meier method, with the difference between survival curves evaluated using the log‐rank test. Multivariate analysis was by Cox proportional hazard model; for all analyses the difference was considered significant when P < 0.05.RESULTSThe median (range) follow‐up was 55  (2–187) months; 26 patients (26%) had high CRP levels, and 12 (46%) of these and three (4.0%) of the remaining 75 died from disease. The 5‐ and 10‐year disease‐specific survival rates (75% and 30%, respectively) in patients with high CRP levels were significantly worse than those in patients with normal CRP levels (both 93%, P < 0.001). In other variants, preoperative haemoglobin concentration, pathological stage, grade, histological type and microvascular tumour invasion were also related to disease‐specific survival. By the Cox proportional hazards model, pathological stage and an elevated CRP were the most important prognostic factors for disease‐specific survival in patients with localized RCC (P = 0.008 and 0.012, respectively).CONCLUSIONThe preoperative CRP level was associated with poor survival in patients with localized RCC.
Pudendal nerve stimulation of a preparation of isolated guinea‐pig urethra
Authors: Walters Richard D. , McMurray Gordon , Brading Alison F. 
Published: September 2006

OBJECTIVETo assess the functional response of the urethral striated muscle to activation of its nerves, using a novel isolated organ‐bath preparation.MATERIALS AND METHODSThe urethra of the female guinea‐pig was chosen as a suitable model for investigation, as it is functionally and structurally similar to the human urethra. Female Dunkin–Hartley guinea‐pigs (400–500 g) were used; for the histochemical and immunohistochemical experiments, unfixed urethras were cryo‐sectioned (14 µm thick) and were stained using established methods. For in vitro experiments, whole urethras were suspended vertically, with pudendal nerves intact, for isometric tension and intraluminal pressure recording in a 40‐mL organ bath. Drugs were applied directly to the bathing solution.RESULTSIn the striated muscle layer of the urethra there was positive β‐NADPH‐diaphorase activity. In organ‐bath studies the pudendal nerve‐evoked contractions (0.2 ms pulses, 5 s trains, 70 V and 1–100 Hz) were abolished in the presence of tubocurarine (10−6m), and unaffected by guanethidine and atropine (both 10−6m). Pre‐incubation with sodium nitroprusside and SIN‐1 chloride significantly reduced the initial peak pressure responses (P < 0.05, anova for paired data) evoked by electrical field stimulation of the pudendal nerves at stimulus parameters of 0.2 ms pulses, 5 s trains, 70 V and 25 Hz.CONCLUSIONElectrically induced contractions were abolished by tubocurarine, confirming that the pudendal nerve innervates the striated muscle of the guinea‐pig external urethral sphincter via nicotinic receptors. β‐NADPH‐diaphorase histochemistry gave positive staining around guinea‐pig striated muscle cells and possibly identified neuromuscular junction sites staining positively for the nitric oxide synthase marker. Together with the results of the organ‐bath experiments, the results suggest that the striated muscle cells of the guinea‐pig urethra have the machinery to respond to nitric oxide.