bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic evaluation of pathways associated with dexamethasone‐mediated apoptosis and resistance in multiple myeloma
Authors: Rees‐Unwin Karen S. , Craven Rachel A. , Davenport Emma , Hanrahan Sarah , Totty Nicholas F. , Dring Ann M. , Banks Rosamonde E. , J.Morgan Gareth , Davies Faith E.
Published: October 2007

We have used global protein expression analysis to characterize the pathways of dexamethasone‐mediated apoptosis and resistance in myeloma. Analysis of MM.1S cells by two‐dimensional polyacrylamide gel electrophoresis (2D‐PAGE) identified a series of proteins that were up‐ and downregulated following dexamethasone treatment. Downregulated proteins included proteins involved in cell survival and proliferation, whereas upregulated proteins were involved in post‐translational modification, protein folding and trafficking. A comparison with published gene expression studies identified FK binding protein 5 (FKBP5) (also known as FKBP51), a key regulatory component of the Hsp90‐steroid‐receptor complex to be increased at the mRNA and protein level postdexamethasone exposure. Quantitative real time polymerase chain reaction and 2D‐PAGE analysis of the dexamethasone resistant cell line MM.1R demonstrated no increase in FKBP5, consistent with its association with dexamethasone‐mediated apoptosis. Western blot analysis of FKBP5 and other members of the Hsp90‐receptor complex showed an increase in FKBP5 whilst FKBP4 (also known as FKBP52) and Hsp90 expression remained constant. No changes were observed in MM.1R. In conclusion, we demonstrated that following steroid receptor signalling, the cell carries out a number of adaptive responses prior to cell death. Interfering with these adaptive responses may enhance the myeloma killing effect of dexamethasone.
High activity 90Y‐ibritumomab tiuxetan (Zevalin®) with peripheral blood progenitor cells support in patients with refractory/resistant B‐cell non‐Hodgkin lymphomas
Authors: Ferrucci Pier F. , Vanazzi Anna , Grana Chiara M. , Cremonesi Marta , Bartolomei Mirco , Chinol Marco , Ferrari Mahila , Radice Davide , Papi Stefano , Martinelli Giovanni , Paganelli Giovanni
Published: October 2007

Radioimmunotherapy (RIT) is an alternative approach in the treatment of resistant/refractory B‐cell non‐Hodgkin lymphoma (NHL). We performed a feasibility and toxicity pilot study of escalating activity of 90Y‐ibritumomab tiuxetan followed by autologous stem cell transplantation (ASCT). Three activity levels were fixed – 30 MBq/kg (0·8 mCi/kg), 45 MBq/kg (1·2 mCi/kg) and 56 MBq/kg (1·5 mCi/kg) – and 13 patients enrolled. One week before treatment all patients underwent dosimetry. ASCT was performed 13 d after Zevalin® administration. Treatment was well tolerated and all patients engrafted promptly. No differences in terms of haematological toxicities were observed among the three levels, apart from a delayed platelet recovery in heavily pretreated patients receiving 56 MBq/kg. Non‐haematologic toxicity was mainly related to infections and liver toxicity. One patient died 4 months after treatment because of hepatitis C virus reactivation. One patient developed a myelodysplastic syndrome 2 years after treatment. In conclusion, high‐activity Zevalin® with ASCT is feasible and could be safely delivered in elderly and heavily pretreated NHL patients, including those who previously received high‐dose chemotherapy and ASCT. Maximum tolerated dose was not clearly defined according to dosimetry and clinical toxicities, and further studies are needed to confirm the toxicity profile and evaluate efficacy.
Bacille–Calmette–Guerin vaccination and the development of allergic disease in children: a randomized, prospective, single‐blind study
Authors: Steenhuis T. J. , Van Aalderen W. M. C. , Bloksma N. , Nijkamp F. P. , Van Der Laag J. , Van Loveren H. , Rijkers G. T. , Kuis W. , Hoekstra M. O.
Published: October 2007

Background
The increase in the prevalence of allergic diseases in countries with a so‐called western lifestyle may be due to a decrease in exposure to infectious agents in early life.

Objective
To establish the effect of Bacille–Calmette–Guerin (BCG) vaccination in 6‐week‐old high‐risk infants in a prospective single‐blind, randomized, placebo‐controlled trial on the prevalence of allergic disease at the age of 4 and 18 months.

Methods
Subjects were 121 predominantly Caucasian high‐risk newborns, having either a mother, or both a father and at least one sibling with past or present allergic disease. BCG or placebo was administered at the age of 6 weeks, and repeated once when both a post‐vaccination scar and a positive TB skin test were absent at the age of 4 months.

Results
At the age of 18 months, the prevalence of allergic disease was not significantly different between the two groups. A trend towards less eczema (P=0.07) and significantly less use of medication for eczema was shown in the BCG group compared with the placebo group (P=0.04).

Conclusion
A single (or once repeated) BCG vaccination in 6‐week‐old high‐risk Caucasian infants was not associated with a 50% reduction in the prevalence of allergic disease. However, there could be a smaller beneficial effect of BCG, especially because a trend towards less eczema and significantly less use of medication for eczema was shown. For definite proof, a larger study should be carried out.
Serum total and high molecular weight adiponectin levels are correlated with the severity of diabetic retinopathy and nephropathy
Authors: Kato Kenichi , Osawa Haruhiko , Ochi Masaaki , Kusunoki Yukiko , Ebisui Osamu , Ohno Keizo , Ohashi Jun , Shimizu Ikki , Fujii Yasuhisa , Tanimoto Mitsune , Makino Hideichi
Published: October 2007

Objective  Adiponectin is secreted specifically from adipocytes, and improves insulin sensitivity. Of its isoforms, the high molecular weight (HMW) complex is thought to be the most active. The aim of this study was to determine the relationship between serum total or HMW adiponectin and diabetic microangiopathy.

Design, patients and measurements  We analysed 198 Japanese patients with type 2 diabetes mellitus (T2DM) whose fasting serum samples were available. Serum total adiponectin and HMW adiponectin were measured using an enzyme‐linked immunosorbent assay (ELISA).

Results  Serum total adiponectin was found to have increased in the advanced stages of diabetic retinopathy (mean ± SE, none, 6·9 ± 0·3; simple, 8·3 ± 1·0; preproliferative, 8·4 ± 0·8; proliferative, 12 ± 1·1 mg/l; anovaP = 0·0004) and nephropathy (stage I, 7·0 ± 0·3; II, 7·7 ± 0·5; III, 9·5 ± 0·9; IV, 16 ± 4·5 mg/l, P < 0·0001). Similarly, serum HMW adiponectin had increased in the advanced stages of retinopathy (3·7 ± 0·2, 4·6 ± 0·5, 4·6 ± 0·6 and 6·9 ± 0·8 mg/l, respectively, P = 0·0005) and nephropathy (3·7 ± 0·2, 4·3 ± 0·4, 5·3 ± 0·7 and 7·9 ± 2·2 mg/l, respectively, P = 0·0007). Neither serum total nor HMW adiponectin was correlated with neuropathy. The HMW/total adiponectin ratio was not correlated with microangiopathy. Multiple regression analysis revealed that serum total and HMW adiponectin were independent factors for retinopathy stage (P = 0·0055 and P = 0·0027, respectively) and nephropathy stage (P = 0·0003 and P = 0·0018, respectively), when adjusted for age, gender, body mass index (BMI) and the duration of T2DM. This correlation remained significant when serum creatinine (or estimated glomerular filtration rate) and hypertension were added as independent variables. Treatment with thiazolidinediones (TZDs) did not affect these findings.

Conclusions  Serum total adiponectin and HMW adiponectin were found to be positively correlated with the severity of retinopathy and nephropathy but not with neuropathy in T2DM.
Three years prospective investigation of anterior pituitary function after traumatic brain injury: a pilot study
Authors: Tanriverdi Fatih , Ulutabanca Halil , Unluhizarci Kursad , Selcuklu Ahmet , Casanueva Felipe F. , Kelestimur Fahrettin
Published: October 2007

Objective   It has been recently demonstrated that traumatic brain injury (TBI)‐mediated hypopituitarism could be more frequent than previously known. However, most of the previous data were obtained from retrospective studies, and the natural history of the hypopituitarism due to TBI is still unclear. So far no study has been reported in which the pituitary function of the same patients has been investigated more than 1 year after TBI. Therefore, we report the results of 3 years prospective follow‐up of anterior pituitary function in patients with mild, moderate and severe TBI.

Patients and design   Thirty patients (25 males, 5 females; age 37·2 ± 2·4 years) with TBI were included in the study. Pituitary function was evaluated at 1 and 3 years after TBI.

Results   After individual evaluation of GH deficiency from 1 year to 3 years after TBI, 7 of 13 (53·8%) GH‐deficient patients at 1st year recovered after 3 years of TBI, and GH deficiency detected at 3 years in one patient was new onset. Additionally, five of six (83·3%) ACTH‐deficient patients at 1st year recovered after 3 years of TBI, and ACTH deficiency detected at 3 years in one patient was new onset.

Conclusions   GH deficiency is the most common pituitary deficit 1 and 3 years after TBI. In patients with mild and moderate TBI, pituitary function improves over time in a considerable number of patients, but it may also worsen rarely over the 3‐year period. In patients with severe TBI, ACTH and GH deficiencies at 1st year evaluation persist at 3rd year.
Factors influencing spontaneous mobilization of CD34+ and CD133+ progenitor cells after myocardial infarction
Authors: Turan R. G. , Brehm M. , Koestering M. , Tobias Z. , Bartsch T. , Steiner S. , Picard F. , Ebner P. , Schannwell C. M. , Strauer B. E.
Published: October 2007

Background  Bone marrow‐derived circulating progenitor cells (BM‐CPCs) are mobilized into adult peripheral blood (PB) during acute myocardial infarction (AMI) and may contribute to the regeneration of infarcted myocardium. The purpose of the present study is to determine whether mobilization of BM‐CPCs into PB depends on cardiovascular risk factors (CVRFs), age of patients, infarct associated inflammatory markers, and left ventricular function after AMI.

Materials and methods  Peripheral blood concentrations of CD34/45+ and CD133/45+ BM‐CPCs were measured by flow cytometry in 44 patients after AMI and in 16 subjects with atypical chest pain acting as controls.

Results  Mobilization of CD34/45+ and CD133/45+ BM‐CPCs on day 1 after AMI showed significant negative correlation with age, the number of CVRFs, infarct size, creatine phosphokinase peak in bivariate as well as in multivariate analyses. We additionally found a positive correlation of CD34/45+ and CD133/45+ BM‐CPCs mobilization on day 1 after AMI with global ejection fraction (EF) in bivariate analysis but could not confirm this in multivariate analysis. Elevated of C‐reactive protein (CRP) and leukocyte levels on day 1 after AMI were significantly associated with decreased concentrations of CD34/45+ BM‐CPCs. The concentrations of CD34/45+ and CD133/45+ BM‐CPCs significantly increased in AMI patients, with the peak on day 7 as compared to the control group.

Conclusions  The mobilization of CD34/45+ and CD133/45+ BM‐CPCs into the PB depends on many factors, i.e. the number of CVRFs, age, infarct size and inflammatory markers of patients. Most importantly, the severity of the circulatory dysfunction and the amount of necrotic myocardial tissue are the main determinants. Moreover, this spontaneous mobilization of BM‐CPCs may serve as a very important surrogate for infarct size as well as for global EF and it may determine the regenerative potency after AMI.
HMG CoA reductase inhibition and left ventricular mass in hypertrophic cardiomyopathy: a randomized placebo‐controlled pilot study
Authors: Bauersachs J. , Störk S. , Kung M. , Waller C. , Fidler F. , Hoyer C. , Frantz S. , Weidemann F. , Ertl G. , Angermann C. E.
Published: October 2007

Background  Statins reduce cardiomyocyte hypertrophy in animal models of hypertrophic cardiomyopathy, aortic banding and heart failure after myocardial infarction. We investigated the effect of the hydroxymethylglutaryl coenzyme A reductase inhibitor atorvastatin on left ventricular (LV) mass in patients with hypertrophic cardiomyopathy in a randomized placebo‐controlled double‐blind pilot study.

Materials and methods  Patients with hypertrophic cardiomyopathy were randomized to be treated once daily by atorvastatin 80 mg or placebo for nine months. LV mass was assessed by serial cardiac magnetic resonance imaging. LV systolic and diastolic function was determined by echocardiography. Markers of collagen metabolism and inflammation were also assessed.

Results  Out of 78 screened patients with hypertrophic cardiomyopathy 28 (2 × 14) patients were eligible for randomization. Eleven patients in each group completed the study with cardiac magnetic resonance imaging assessments meeting the evaluation standards at baseline and at follow‐up. Low‐density lipoprotein cholesterol levels in the atorvastatin group decreased from 3·24 ± 1·14 mmol L−1 (125 ± 44 mg dL−1) at baseline to 1·37 ± 0·49 mmol L−1 (53 ± 19 mg dL−1) at follow‐up (P < 0·001), but were unchanged in the placebo group. Baseline LV mass was 228 ± 51 g in the placebo and 232 ± 67 g in the atorvastatin group. The primary endpoint of change in LV mass from baseline to follow‐up was 2 ± 10% in the atorvastatin group versus 0 ± 13% in the placebo group (P = NS). Parameters of LV volumes and diameters, systolic and diastolic function, and markers of collagen metabolism were also unchanged in both groups.

Conclusion  In patients with hypertrophic cardiomyopathy, this randomized placebo‐controlled double‐blind pilot study did not demonstrate an effect of 9‐month treatment with atorvastatin 80 mg on LV mass reduction.
Uptake and metabolism of nitrate in mycorrhizal plants as affected by water availability and N concentration in soil
Authors: Azcón R. , Rodríguez R. , Amora‐Lazcano E. , Ambrosano E.
Published: October 2007

We compare the effect of arbuscular mycorrhizal (AM) colonization and PO4−3 fertilization on nitrate assimilation, plant growth and proline content in lettuce plants growing under well‐watered (−0.04 MPa) or drought (−0.17 MPa) conditions. We also tested how AM‐colonization and PO4−3 fertilization influenced N uptake (15N) and the percentage of N derived from the fertilizer (% NdfF) by plants under a concentration gradient of N in soil. Growth of mycorrhizal plants was comparable with that of P‐fertilized plants only under well‐watered conditions. Shoot nitrogen content, proline and nitrate reductase activity were greater in AM than in P‐fertilized plants under drought. The addition of 100 μg g−1 P to the soil did not replace the AM effect under drought. Under well‐watered conditions, AM plants showed similar (at 3 mmol N), greater (at 6 mmol N) or lesser (at 9 mmol N) %NdfF than P‐fertilized plants. Comparing a control (without AM inoculation) to AM plants, differences in % NdfF ranged from 138% (3 mmol N) to 22.6% (6 mmol N) whereas no differences were found at 9 mmol N. In comparison with P fertilization, mycorrhizal effects on %NdfF were only evident at the lowest N levels, which indicated a regulatory mechanism for N uptake in AM plants affected by N availability in the soil. At the highest N level, P‐fertilized plants showed the greatest %NdfF. In conclusion, AM symbiosis is important for N acquisition and N fertilizer utilization but this beneficial mycorrhizal effect on N nutrition is reduced under large quantities of N fertilizer.
PAH release from tar‐oil contaminated soil material in response to forced environmental gradients: implications for contaminant transport
Authors: Wehrer M. , Totsche K. U.
Published: October 2007

Laboratory test systems are frequently used to assess the release of pollutants from contaminated sites. To infer behaviour in the field, all factors that control the release of such pollutants should be considered in the experiment. We carried out column experiments with varying boundary conditions under saturated flow to identify the processes governing the release and to evaluate the effect of environmental conditions on several polycyclic aromatic hydrocarbons (PAHs). We compared the results with groundwater concentrations monitored in the field. The contaminated soil material originated from a former tar‐processing site. The effluent was analysed in response to forced variations in flow velocity, residence time, ionic strength and temperature. Interruptions to the flow had no effect on concentrations, which were close to those predicted by Raoult’s law. We conclude that release of PAHs is controlled by equilibrium dissolution according to Raoult’s law at moderate ionic strength. Diminishing the ionic strength by a pulse of pure water, however, results in a marked increase in the concentrations of exported PAHs. We attribute this to PAHs being bound to mobile particles. The effect was larger in the column percolated with fast flow, suggesting that the release of carriers is controlled by shear stress. An increase of temperature by 10 K resulted in marked increases in concentrations of the PAHs in the outflow between 6 and 160%. Concentrations in the groundwater correlate well with those in the outflow from the columns with similar ionic strength and temperature. We were able to identify the processes governing the release of PAHs under various conditions and to explain the concentrations observed in the field. The study illustrates that column outflow experiments, which support decisions in risk assessment, must be designed appropriately.
Ammonium uptake and mineralization in prairie streams: chamber incubation and short‐term nutrient addition experiments
Authors: O'BRIEN JONATHAN M. , DODDS WALTER K.
Published: October 2007

1. We used two separate approaches to estimate ambient ammonium cycling in the north and south branches of Kings Creek, a prairie stream. Chamber experiments were conducted to determine ammonium uptake and mineralization rates associated with epilithic biofilms and filamentous algae collected from the streams. A series of short‐term whole‐stream ammonium addition experiments were also conducted to estimate the rate of uptake at ambient stream concentrations, based on the relationship between ammonium concentrations and uptake rates.

2. Chamber experiments were scaled up to whole‐stream levels, resulting in ambient gross uptake estimates of 0.08 μg−2 s−1for the north branch and 0.16 μg−2 s−1for the south branch. The substrata‐specific estimates of mineralization were higher than uptake in both streams.

3. Substrata‐specific measurements indicated that ammonium uptake is higher in riffle habitats than in pools habitats. The results of the short‐term ammonium addition experiments support these findings.

4. Short‐term ammonium addition experiments show that uptake rates saturate with increasing ammonium concentrations. The observed saturation of uptake rates is consistent with a Michaelis–Menten relationship.

5. Scaled estimates of uptake from the chamber experiments were similar to estimates of ambient ammonium uptake based on the whole‐stream experiments, and were comparable with previous estimates of ammonium uptake and mineralization made by using stable isotope tracer methods in Kings Creek.
Acidity versus habitat structure as regulators of littoral microcrustacean assemblages
Authors: WALSENG BJØRN , YAN NORMAN D. , PAWSON TREVOR W. , SKARPAAS OLAV
Published: October 2007

1. Emergence traps were set overnight on the sediment surface to sample the littoral microcrustaceans of 22 Canadian Shield lakes that ranged in pH from 4.56 to 6.92. Traps were randomly allocated in quintuplicate in both wave‐washed sandy habitats where pipewort (Eriocaulon septangulare) was the dominant macrophyte (termed pipewort habitats), and more protected habitats dominated by floating‐leaved macrophytes (termed floating‐leaved habitats).

2. In total, 50 cladoceran and 22 copepod species were found, with 16–45 species in each lake. Lakes that had never acidified exhibited a more diverse fauna than lakes that had acidified.

3. There were only minor differences between the numbers of species found in floating‐leaved versus pipewort habitats except for one lake. Non‐chydorid cladoceran, chydorids and copepods constituted 45%, 26% and 29% of the total number of individuals, respectively.

4. Based on presence/absence, dominance scores and frequency of occurrences of species, the microcrustacean faunal composition was similar in the two habitats. A detrended correspondence analysis confirmed that there was no separation between the two main types of habitat, and that pH was the parameter most strongly correlated with the dominant microcrustacean compositional gradient among lakes.
Review of quality of life: menorrhagia in women with or without inherited bleeding disorders
Authors: SHANKAR M. , CHI C. , KADIR R. A.
Published: October 2007

Summary.  The objectives of this study were to identify the impact of menorrhagia on the health‐related quality of life (HRQOL) of women in general and those with inherited bleeding disorders and to identify the commonly used tools in assessing quality of life. A review of studies evaluating quality of life in women suffering from menorrhagia was conducted. Data sources used included electronic databases Medline and Embase. Reference lists and bibliographies of the relevant papers and books were hand‐searched for additional studies. Eighteen of the 53 studies identified measured quality of life prior to treatment of menorrhagia. Ten of the studies used a validated measure of quality of life. Five studies involving a total of 1171 women with menorrhagia in general and using SF‐36 were considered for further review. The mean SF‐36 scores in women with menorrhagia were worse in all the eight scales when compared with normative scores from a general population of women. Three studies, involving 187 women, assessed the quality of life in women with menorrhagia and inherited bleeding disorders. None of these studies used a validated HRQOL score making it difficult for comparison. However, all reported poorer scores in study women compared to the controls. In conclusion, HRQOL is adversely affected in women with menorrhagia in general and in those with inherited bleeding disorders. HRQOL evaluation is useful in the management of women with menorrhagia for assessment of treatment efficacy.
Blockade of endogenous B7‐H1 suppresses antibacterial protection after primary Listeria monocytogenes infection
Authors: Seo Su‐Kil , Jeong Hye‐Young , Park Sae‐Gwang , Lee Soo‐Woong , Choi Il‐Whan , Chen Lieping , Choi Inhak
Published: October 2007

B7‐H1 (also known as CD274 and PD‐L1) is a cosignalling molecule regulating T‐cell immunity positively or negatively in vivo. However, little is known about the role of endogenous B7‐H1 in bacterial infection. We found that B7‐H1 expression was up‐regulated in various cell populations including CD4+ and CD8+ T cells, natural killer (NK) cells and macrophages following Listeria monocytogenes infection. Administration of the antagonistic B7‐H1 monoclonal antibody resulted in a significant increase in mortality in mice infected with a lethal dose of L. monocytogenes compared with mice given the control immunoglobulin. In vivo blockade of B7‐H1 greatly inhibited the production of tumour necrosis factor (TNF)‐α and nitric oxide, key effector molecules responsible for intracellular killing by macrophages. B7‐H1 blockade also suppressed the expression of granzyme B and interferon (IFN)‐γ by NK cells. Interestingly, blocking of endogenous B7‐H1 selectively inhibited CD8+ T cells rather than CD4+ T cells in response to L. monocytogenes infection, as evidenced by the reduction of IFN‐γ production and the expression of effector surface markers including CD62Lint/low and CD44high in CD8+ T cells from mice given anti‐B7‐H1 monoclonal antibody. In addition, we found that the proliferation of listeriolysin‐O (LLO)‐specific and IFN‐γ‐producing L. monocytogenes‐reactive CD8+ T cells was significantly decreased not only in the effector phase but also in the memory phase in the presence of anti‐B7‐H1 antibody. Our findings thus suggest that endogenous B7‐H1 can provide positive costimulatory signals for innate and adaptive immunity leading to protection against intracellular bacterial infection.
Tumour necrosis factor‐α‐mediated human polymeric immunoglobulin receptor expression is regulated by both mitogen‐activated protein kinase and phosphatidylinositol‐3‐kinase in HT‐29 cell line
Authors: Takenouchi‐Ohkubo N. , Moro I. , Mukae S. , Kaneko Y. , Komiyama K.
Published: October 2007

Human polymeric immunoglobulin receptor (pIgR) is present on the surface of glandular epithelium, and it plays a crucial role in the mucosal immune defence. pIgR expression in HT‐29 cells is up‐regulated by one of the proinflammatory cytokines, tumour necrosis factor (TNF)‐α. However, the mechanism used by the TNF‐α‐mediated signalling pathway has not been examined exclusively. To elucidate this mechanism in detail, HT‐29 cells were cotreated with TNF‐α and mitogen‐activated protein kinase kinase (MAPKK, also called MEK1) inhibitor, PD98059, and the amount of free secretory component (SC) secreted into the culture medium was measured. The amount of free SC stimulated by TNF‐α was increased by addition of PD98059. This up‐regulation occurred at the transcriptional level. The amount of SC was also up‐regulated by addition of TNF‐α with U0126, an inhibitor of MEK1 and MEK2. Nuclear factor (NF)‐κB activity and NF‐κB binding to the κB2 site localized upstream of the pIgR gene did not change after coincubation of HT‐29 cells with TNF‐α and PD98059. The expression level of pIgR by TNF‐α was decreased by LY294002, an inhibitor of phosphatidylinositol‐3‐kinase (PI3K), at the transcriptional level. Extracellular signal‐regulated kinase (ERK)1/2 phosphorylation and NF‐κB binding to the κB2 site were not affected by LY294002 treatment. These data suggest that TNF‐α‐mediated pIgR expression is negatively regulated by ERK pathway, which is independent of NF‐κB. In addition, decrease of SC production by Ly294002 suggests that the presence of PI3K mediated regulation of SC production.
Characterization of suppressive oligodeoxynucleotides that inhibit Toll‐like receptor‐9‐mediated activation of innate immunity
Authors: Peter Mirjam , Bode Konrad , Lipford Grayson B. , Eberle Florian , Heeg Klaus , Dalpke Alexander H.
Published: October 2007

Synthetic oligodeoxynucleotides containing unmethylated CpG sequences (CpG‐ODNs) stimulate Toll‐like receptor‐9 (TLR‐9), thereby activating innate immunity. Stimulatory CpG‐ODNs have been shown to be valuable in modifying immune responses in allergy, infection and cancer. Recently, it has been reported that the stimulation of TLR‐9 by endogenous DNA might contribute to the pathogenesis of autoimmune diseases. We here report the identification of a suppressive, guanosine‐rich ODN (G‐ODN) that inhibited the activation of TLR‐9 by stimulatory CpG‐ODNs. The G‐ODN was suppressive in murine macrophages and dendritic cells as well as in human plasmacytoid dendritic cells in vitro. G‐ODN blocked the secretion of tumour necrosis factor‐α (TNF‐α) and interleukin‐12p40 and interfered with the up‐regulation of major histocompatibility complex (MHC) class II and costimulatory molecules. G‐ODN was inhibitory even at a molar ratio of 1 : 10 (G‐ODN:CpG‐ODN) and when administered up to 7 hr after stimulation with CpG. G‐ODN specifically inhibited TLR‐9 but not other TLRs. Inhibition was dependent on a string of five guanosines. G‐ODN was also inhibitory in an in vivo model of CpG/galactosamin (GalN) lethal shock. G‐ODN interfered with upstream TLR‐9 signalling. However, by extensive analysis we can exclude that G‐ODN acts at the stage of cellular uptake. G‐ODN therefore represents a class of suppressive ODNs that could be of therapeutic use in situations with pathologic TLR‐9 activation, as has been proposed for certain autoimmune diseases.
A new method for estimating visitation rates of cryptic animals via repeated surveys of indirect signs
Authors: Gruber Bernd , Reineking Björn , Calabrese Justin M , Kranz Andreas , Poledníková Katerina , Poledník Luká , Klenke Reinhard , Valentin Anett , Henle Klaus
Published: October 2007

Visitation rate is a measure of the frequency with which animals visit specific locations of interest. This information is crucial for various problems in the conservation and management of animal species, e.g. to determine the risk wildlife poses to human managed resources or the predation risks of nests. An important assessment tool, especially for cryptic animals, is to count indirect signs of presence, such as tracks or faeces.

Here we propose a maximum likelihood‐based method that uses information on the age of tracks or signs, and we show that existing visitation rate/probability estimators are special cases of this more general approach.

Using simulated data, we compared the performance of the new visitation rate estimator to three other estimators, including the most commonly used estimator. These estimators make use of either fresh, aged or total signs, whereas our approach uses information simultaneously on both fresh and aged signs. The new estimator is, on average, in excess of three times more accurate than the next best estimator. Moreover, the new approach is very flexible and can be applied for sampling regimens with irregular time intervals between sampling.

We demonstrate the application of the method to field data by estimating the visitation rate of Eurasian otters (Lutra lutra) to a commercial fish pond. To facilitate the use of this method, we provide an easy‐to‐use Excel workbook and give recommendations on the most efficient sampling regimens.

Synthesis and applications. Visitation rate is an important quantity that can be estimated by repetitive sampling of indirect signs. We demonstrate the advantage of incorporating information explicitly on the age of signs over existing approaches. The new estimator can be applied to any species for which it is possible to discriminate between aged and new signs or tracks, and should be widely applicable in ecology and conservation biology.
Mangrove forest distributions and dynamics (1975–2005) of the tsunami‐affected region of Asia†
Authors: Giri C. , Zhu Z. , Tieszen L. L. , Singh A. , Gillette S. , Kelmelis J. A.
Published: October 2007

Aim  We aimed to estimate the present extent of tsunami‐affected mangrove forests and determine the rates and causes of deforestation from 1975 to 2005.

Location  Our study region covers the tsunami‐affected coastal areas of Indonesia, Malaysia, Thailand, Burma (Myanmar), Bangladesh, India and Sri Lanka in Asia.

Methods  We interpreted time‐series Landsat data using a hybrid supervised and unsupervised classification approach. Landsat data were geometrically corrected to an accuracy of plus‐or‐minus half a pixel, an accuracy necessary for change analysis. Each image was normalized for solar irradiance by converting digital number values to the top‐of‐the atmosphere reflectance. Ground truth data and existing maps and data bases were used to select training samples and also for iterative labelling. We used a post‐classification change detection approach. Results were validated with the help of local experts and/or high‐resolution commercial satellite data.

Results  The region lost 12% of its mangrove forests from 1975 to 2005, to a present extent of c. 1,670,000 ha. Rates and causes of deforestation varied both spatially and temporally. Annual deforestation was highest in Burma (c. 1%) and lowest in Sri Lanka (0.1%). In contrast, mangrove forests in India and Bangladesh remained unchanged or gained a small percentage. Net deforestation peaked at 137,000 ha during 1990–2000, increasing from 97,000 ha during 1975–90, and declining to 14,000 ha during 2000–05. The major causes of deforestation were agricultural expansion (81%), aquaculture (12%) and urban development (2%).

Main conclusions  We assessed and monitored mangrove forests in the tsunami‐affected region of Asia using the historical archive of Landsat data. We also measured the rates of change and determined possible causes. The results of our study can be used to better understand the role of mangrove forests in saving lives and property from natural disasters such as the Indian Ocean tsunami, and to identify possible areas for conservation, restoration and rehabilitation.
Close anthropogenic control of Fagus sylvatica establishment and expansion in a Swedish protected landscape – implications for forest history and conservation
Authors: Lindbladh Matts , Niklasson Mats , Karlsson Matts , Björkman Leif , Churski Marcin
Published: October 2007

Aim   The dominant forces behind the expansion of Fagus sylvatica (beech) in northern Europe during the late Holocene have been much debated. Palaeoecological analyses were performed for a biodiversity hotspot reserve in order to study the processes behind the local establishment of Fagus, as well as the historical vegetational development in relation to present‐day biodiversity and conservation.

Location  Biskopstorp Forest Reserve in south‐west Sweden.

Methods  Pollen and charcoal were analysed from three small‐hollow sites in the reserve. Two of the investigated wetlands were located adjacent to old‐growth stands of Fagus, and the third was located near a stand of old Quercus.

Results  The 2500‐year record shows that Fagus was first established around the two Fagus old‐growth sites, c. ad 900 and 1200, respectively, and that this was followed by an expansion around ad 1600. During the establishment phase, and more so in the expansion phase, there were simultaneous increases in types of pollen indicative of human activity. These indicators are also frequent throughout the record from the Quercus site, but here Fagus never became common.

Main conclusions  The dynamics behind the establishment and expansion of Fagus in the reserve seems to have been influenced to a large degree by human activity, for example selective cutting, human‐induced fires, and agriculture. Fagus became established in the reserve more than 1000 years after it became established regionally, making climate less probable as the dominant force behind the species’ stand‐scale establishment. The spreading of Fagus across southern Scandinavia has previously been shown to be a patchy process in time and space. Our study suggests that this patchiness is evident also at a small spatial scale (a few kilometres). At the Quercus site, relatively high amounts of pollen from the field layer throughout the record indicate open conditions that probably favoured Quercus. The degree of human impact at this site was probably too high to allow the expansion of Fagus. With the long‐term perspective provided by our study it was possible to identify the last 200–300 years as an unrepresentative period with respect to tree species composition and forest dynamics. The large increase of Picea locally and regionally over the last several hundred years, combined with dramatic levels of human impact, have altered the tree composition and forest dynamics to such an extent that active management is necessary in order to maintain biodiversity in the reserve.
Bone mass in young adults with Down syndrome
Authors: Guijarro M. , Valero C. , Paule B. , Gonzalez‐Macias J. , Riancho J. A.
Published: October 2007

Background  Down syndrome (DS) is a frequent cause of intellectual disability. With the increasing life expectancy of these patients, concerns have been raised about the risk of osteoporosis. In fact, several investigators have reported a reduced bone mass in DS. However, the results may be confounded by comorbid diseases, and differences in lifestyle habits and body size. Therefore, we planned to determine anthropometric and lifestyle factors influencing bone mineral density (BMD) in young adults with DS.

Methods  Thirty‐nine patients with DS (mean age 26 years) and 78 controls were studied. Areal BMD was measured by dual x‐ray decsitometry (DXA); volumetric BMD at the lumbar spine and femoral neck was estimated with published formulae.

Results  DS patients had lower areal BMD than controls at all regions (spine, hip and total body). Height and projected bone area were also lower. There were no differences between both groups regarding estimated volumetric BMD at the femoral neck. However, spine volumetric BMD was also lower in DS than controls. In multivariate analysis, DS, male sex, little physical activity and low sunlight exposure were associated with lower spine volumetric BMD; on the other hand, fat mass and sunlight exposure were associated with femoral neck volumetric BMD.

Conclusion  This study shows that patients with DS had a reduced areal BMD, but it is in part a consequence of the reduced body size, particularly at the femoral neck. Physical activity and sunlight exposure are associated to volumetric BMD and should be stimulated in order to maintain an adequate bone mass in these patients.
Deletion of the OPHN1 gene detected by aCGH
Authors: Madrigal I. , Rodríguez‐Revenga L. , Badenas C. , Sánchez A. , Milà M.
Published: October 2007

Background  The oligophrenin 1 gene (OPHN1) is an Rho‐GTPase‐activating protein involved in the regulation of the G‐protein cycle required for dendritic spine morphogenesis. Mutations in this gene are implicated in X‐linked mental retardation (XLMR).

Methods  We report a deletion spanning exons 21 and 22 of the OPHN1 gene identified by a tiling path X‐chromosome array comparative genomic hybridization (CGH) and multiplex ligation‐dependent probe amplification, confirmed by polymerase chain reaction (PCR), in a family with four males with intellectual disabilities.

Results  Patients harbouring mutations in this gene share the same clinical manifestations reinforcing the idea of a syndromic XLMR. The most important neurological findings are cerebellar hypoplasia and ventriculomegaly.

Conclusions  We recommend screening of the OPHN1 gene in male patients with XLMR and cerebellar anomalies. This case highlights the value of high‐resolution techniques as Multiplex Ligation Probe Amplification (MLPA) and CGH array for a better characterization of copy number changes and suggests that MLPA technology may be very useful for an initial screening of small deletions and duplications in XLMR patients.
SEM investigation of interfacial dislocations in nickel‐base superalloys
Authors: EPISHIN ALEXANDER , LINK THOMAS , NOLZE GERT
Published: October 2007

A new technique for investigation of interfacial dislocations in nickel‐base superalloys by scanning electron microscopy is presented. At high temperatures the pressure of interfacial dislocations against the γ/γ′‐interface causes grooves. This ‘fingerprint of the dislocation network’ is visualized by deep selective etching, which removes the γ′‐phase down to the γ/γ′‐interface. Compared with transmission electron microscopy, the proposed method has important advantages: observation of large sample areas, no superposition of dislocations lying in different specimen depths, possibility of three‐dimensional view of dislocation configurations, information about the dislocation mobility, reduced time for preparation and visualization. The method can be applied for multiphase materials where the interface is grooved by interfacial dislocations.
In vivo dynamic light scattering microscopy of tumour blood vessels
Authors: KALCHENKO V. , PREISE D. , BAYEWITCH M. , FINE I. , BURD K. , HARMELIN ALON
Published: October 2007

We present a study investigating the use of dynamic light scattering microscopy based on the temporal laser speckle's contrast that is produced over time by red blood cells (RBCs) flowing inside tumour blood vessels. The proposed noninvasive methodology is capable of producing high‐resolution images of tumour vasculature. The technique is effective at producing images from tissue at a significant depth, as well as potentially having the ability to monitor tumour perfusion. An advantage of this methodology is that it has improved depth penetration compared with conventional imaging techniques (such as reflected‐light microscopy), and one can avoid the use of any fluorescent or artificial chemicals for labeling. This is advantageous since labeling materials can affect imaging and animal welfare with respect to experiments that require continuous and repetitive monitoring.
Characterization of spectral FRET imaging microscopy for monitoring nuclear protein interactions
Authors: CHEN YE , MAULDIN JOSHUA P. , DAY RICHARD N. , PERIASAMY AMMASI
Published: October 2007

The spectral processed Förster resonance energy transfer (psFRET) imaging method provides an effective and fast method for measuring protein–protein interactions in living specimens. The commercially available linear unmixing algorithms efficiently remove the contribution of donor spectral bleedthrough to the FRET signal. However, the acceptor contribution to spectral bleedthrough in the FRET image cannot be similarly removed, since the acceptor spectrum is identical to the FRET spectrum. Here, we describe the development of a computer algorithm that measures and removes the contaminating ASBT signal in the sFRET image. The new method is characterized in living cells that expressed FRET standards in which the donor and acceptor fluorescent proteins are tethered by amino acid linkers of specific lengths. The method is then used to detect the homo‐dimerization of a transcription factor in the nucleus of living cells, and then to measure the interactions of that protein with a second transcription factor.
Resolving the geometry of biomolecules imaged by cryo electron tomography
Authors: BONGINI L. , FANELLI D. , SVENSSON S. , GEDDA M. , PIAZZA F. , SKOGLUND U.
Published: October 2007

In this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics through automatized protocols. The first method performs a Brownian dynamics evolution of a simplified molecular model into a fictitious force field generated by the tomograms. This procedure enables us to dock the simplified model into the experimental profiles. The second uses a fuzzy framework to delineate the subparts of the proteins and subsequently determine their interdomain relations. The two methods are discussed and their complementarities highlighted with reference to the case of the immonoglobulin antibody. Both artificial maps, constructed from immunoglobulin G entries in the Protein Data Bank and real tomograms are analyzed. Robustness issues and agreement with previously reported measurements are discussed.
Image enhancement for increased dot‐counting efficiency in FISH
Authors: SHAH SHISHIR
Published: October 2007

Background: The most commonly used molecular cytogenetic technique is fluorescence in situ hybridization (FISH). It has been widely applied in many areas of diagnosis and research, including pre‐natal and post‐natal screening of chromosomal aberrations, pre‐implantation genetic diagnosis, cancer cytogenetics, gene mapping, molecular pathology and developmental molecular biology. The analysis of FISH images consists of detecting fluorescent dots, after which the number of dots per cell can be counted or their relative positions can be measured. A major impediment in the analysis of FISH specimens is signal (dot) quality, which is influenced by the hybridization efficiency and/or the sensitivity of the camera that records the images.

Method: In this paper, we present an approach to improve the efficiency of detecting fluorescent signals in FISH images by recovering the radiance map of the camera. This allows us to generate a high‐dynamic‐range image wherein an extended range of the sample radiance captured by the camera can be visualized at distinct intensity values. The resulting higher‐order numeric complexity of the transformed image is adjusted (or simplified) by examining the intensity distribution in each of the three colour channels (red, green and blue), and remapping the intensity values to generate a high‐contrast image with a lower‐order (compressed) dynamic range. The remapping is based on a criterion that optimizes the detection of the hybridized signals, allowing attenuation of saturated intensity values while amplifying low‐intensity signals.

Results: A simple dot‐counting algorithm is used to automatically process 2000 FISH images. The images are taken for lymphocytes from cultured blood specimens for cytogenetic testing. Images are manually analyzed by an expert to obtain ground truth for dot counts. A quantitative analysis is performed by comparing results of automated dot detection on images before and after enhancement with the developed algorithms. In addition, common errors in dot counting due to split dots, dust, poor segmentation and overlapping signals are analyzed and the robustness of the developed approach against these errors evaluated. It is observed that dot‐detection efficiency is increased by an average of 9% across all colour channels while reducing errors in missed and false dot counts.

Conclusions: Our proposed method and results demonstrate that dot‐counting specificity and sensitivity can be improved by pre‐processing and enhancing the image using the radiance curve of the camera and generating a high‐contrast, remapped high‐dynamic‐range image prior to using any algorithm for dot counting.
Morphology of polystyrene films deposited by RF plasma
Authors: HAÏDOPOULOS M. , MIRABELLA F. , HORGNIES M. , VOLCKE C. , THIRY P.A. , ROUXHET P. , PIREAUX J.‐J.
Published: October 2007

A new plasma reactor, set up with a large planar inductively coupled source, is used for the first time to deposit a polymer coating (pPS) from a styrene monomer. This work is devoted to the relationship between external plasma parameters and substrate topography, and pPS coating morphology, which is investigated by scanning electron microscopy and atomic force microscopy. Stainless steel, gold and glass surfaces are used as substrates. It is clearly demonstrated that the film morphology can be controlled by adjustment of RF input power, pressure. The analysis performed further reveals that the pPS film's characteristics strongly depend on the substrate topography and its electrical potential during the discharge. Finally, the plasma duration also strongly influences the morphology of the films. The morphologies obtained include smooth films without any specific feature, worm‐like structures, particles (nanometer‐ and micrometer‐sized) associated along preferential directions and randomly distributed particles (micrometer‐sized). The intrinsic topography of the substrate influences the film structure in the case of thin films (thickness lower than about 100 nm).

Polymerization is suggested to take place at the surface in contact with the discharge rather than in the gas phase. Nucleation and growth start preferentially on substrate defects such as polishing scratches.
Three‐dimensional point spread function model for line‐scanning confocal microscope with high‐aperture objective
Authors: DUSCH E. , DORVAL T. , VINCENT N. , WACHSMUTH M. , GENOVESIO A.
Published: October 2007

Point Spread Function (PSF) modelling is an important task in image formation analysis. In confocal microscopy, the exact PSF is rarely known, thus one has to rely on its approximation. An initial estimation is usually performed experimentally by measuring fluorescent beads or analytically by studying properties of the optical system. Yet, fluorescent line‐scanning confocal microscopes are not widespread; therefore, very few adapted models are available in the literature. In this paper, we propose an analytical PSF model for line‐scanning confocal microscopes. Validation is performed by measuring the error between our model and an experimental PSF measured with fluorescent beads, assumed to represent the real PSF. Comparison with existing models is also presented.