bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated colorimetric determination of recombinant fungal laccase activity in fermentation sarples using syringaldazine as chromogenic substrate
Authors: Holm K. A. , Nielsen D. M. , Eriksen J.
Published: March 2007

An automated Cobas Fara method was developed determining the activity of recombinant M. thermophila laccase (rMtL). The chromogenic substrate used was syringaldazine. Under aerobic conditions, rMtL catalyses the oxidation of syringaldazine forming tetrametoxy‐azo bis methylene quinone. The developed violet colour was measured kinetically at 530 nm as an expression of the enzyme activity, rMtL is a very sensitive oxidoreductase, therefore many factors had to be carefully controlled in order to get a robust analytical assay. In order to stabilize rMtL, PEG 6000 was added to the enzyme dilution medium. Furthermore, Triton X‐I00 was included in the enzyme incubation solution.

The analytical as well as technical conditions have been optimized, resulting in a method with good precision, sensitivity and speed of analysis. The Michaelis‐Menten constant, Km, was determined to be 22μM syringaldazine. LOQ was determined to be 0.010 Uml-1, LOD to be 0.0002 Uml-1 The analytical range of the enzyme dilution curve was from 0.01 to 0.044 Uml-1 The repeatability was 1.9%, the reproducibility 3.1%. Testing the robustness of the method showed that the most sensible factors in the rMtL analysis in decreasing range were: incubation temperature, concentration of Triton X‐I00, molarity and pH of the incubation buffer, and finally the concentration of syringaldazine.
A submersible battery‐powered flowinjection (FI) sensor for the determinationof nitrate in estuarine and coastal waters
Authors: David Anthony R. J. , McCormack Trevor , Worsfold Paul J.
Published: March 2007

The design, construction and performance of a remotely deployed
submersible flow injection‐based nutrient (total oxidized nitrogen)
sensor are described. The sensor featured a custom‐built microcomputer
and a solid‐state, flow‐through spectrophotometric detector,
and the derivatization chemistry was based on in‐line coppercadmium
reduction of nitrate to nitrite, and diazotization with
N1NED and sulphanilamide. The limit of detection was
0.0014 mg l-1 NO3‐N and the linear range was 0.0014‐
0.77 mg l-1 with a 260 μl sample volume and a 20 mm path
length flow cell. Results from submersed deployments in the Tamar
estuary and North Sea are also reported.
Determination of μmol l-1 level of iron (III) innatural waters and total iron in drugs byflow injection spectrophotometry
Authors: Sahasrabuddhey B. , Mishra S. , Jain A. , Verma K. K.
Published: March 2007

The equilibrium problems, characterized by recurring end‐points,
involved in the reaction of iron (III) with iodide make the batch
iodometric determination of iron (III) unsuitable. Since the flow
injection determination does not require attainment of steady state
either for mixing of reagents or for the chemical reaction, the
iodometric determination has been accurately and precisely performed
using this technique in the present work. This method does
not require any special reagent, including chelating agents or those
which are loxic, and has a limit of detection of 0.2 μmol l-1
(11 μg l-1) of iron (III). The interference of fluoride has been
avoided by adding zirconyl nitrate to the test sample solution, and
of copper (II) by complex formation with 2‐mercaptobenzoxazole.
The method has been applied to determine iron (III) in natural
waters, and total iron in drugs.
An approach to control of bioreactors. Application of the gain–scheduling method
Authors: Alvarez Estrella , Riverol Carmen , Correa J. M. , Navaza J. M.
Published: March 2007

A control system based on a combination of the gain‐scheduling
control method and an adaptive PID controller was designed for
the production of xylose from hardwood hemicellulose using a
stirring tank reactor. Different operating conditions have been
considered for estimating the adjustable parameter (θ) to take into
account the changes of energy of the system. The performance of
the control system was studied first by numerical simulation, and
after implementation in the stirred tank reactor where the controller
actually works.
Optimization of an automated FI‐FT‐IR procedure for the determination ofo‐xylene, toluene and ethyl benzene in n‐hexane
Authors: Wells Ian , Worsfold Paul J.
Published: March 2007

The development and optimization of an automated flow injection
(FI) manifold coupled with a Fourier transform infrared (FT‐IR) detector for the determination of toluene, ethyl benzene and o‐oxylene in an n‐hexane matrix is described. FT‐IR parameters optimized were resolution and number of co‐added scans; FI parameters optimized were type of pump tubing, carrier flow rate and sample volume. ATR and transmission flow cells were compared for the determination of o‐xylene, the ATR cell was easier to use and gave better figures of merit, except for sensitivity, for which the transmission cell was twice as good. Multivariate calibration routines were applied to the FI‐FT‐IR data and the PLS1 algorithm gave relative root mean standard errors of crossvalidation (RRMSECVs) < 7% for all three analytes using
mean‐centred data and the first derivative for o‐xylene.
Flow‐injection sandwich ELISA for bioprocess monitoring
Authors: Rhee Jong Il , Hagedorn Jörg , Scheper Thomas , Schügerl Karl
Published: March 2007

A fully automated flow‐injection immunoassay based on sandwich enzyme‐linked immunosorbent assay (ELISA) is described for the model system: protein G‐sepharose, rabbit IgG and horseradish peroxidase (HRP)‐labelled protein A. After injecting rabbit IgG and HRP‐labelled protein A into a cartridge containing protein
G‐sepharose sequentially, a mixture of hydrogen peroxide and the redox indicator, 2.2′‐azino‐bis(3‐ethylbenzthiazoline‐6‐sulphonic acid) (ABTS) is passed through the cartridge. The HRP‐labelled protein A bound in the cartridge is directly proportional to the concentration of rabbit IgG. The colour variation of ABTS caused during the reaction between HRP and H202 in the cartridge is detected photometrically. The whole assay procedure is controlled and evaluated by a computer. Rabbit IgG and HRP‐labelled protein A are also detected by a fluorometer, which is
introduced into the flow system. In the flow‐injection sandwich ELISA, the slope of the calibration curve is 0.4491 in the range of 0 and 300 μg ml-1 rabbit IgG, while it is 0.1274 in the heterogeneous immunoassay. So the flow‐injection sandwich ELISA system is found to be more sensitive than a heterogeneous immunoassay for the monitoring of the model protein.
Soluble plasma-derived von Willebrand factor assembles to a haemostatically active filamentous network
Authors: Barg Alexej , Ossig Rainer , Goerge Tobias , Schillers Hermann , Oberleithner Hans , Schneider Stefan , Schneider Matthias
Published: March 2007

The large glycoprotein vonWillebrand factor (VWF) is involved in the initial haemostatic reaction mediating the interaction between platelets and the injured vessel wall. It has been demonstrated that unusually large VWF (ULVWF) multimers after being released from endothelium are capable of developing elongated membrane-anchored strings that are hyperactive to bind platelets. In the present study we investigated whether soluble plasma-derived VWF is competent to develop similar thrombotically active multimers. We demonstrated that soluble VWF multimers isolated from human plasma self-assemble to a network of fibers immobilized on a collagen matrix and are functionally active to bind platelets. Formation of these VWF fibers depends on shear flow, concentration of solubleVWF, and a suitable binding surface. Self-assembly of soluble VWF does not require the presence of cellular membrane ligands. The network of fibers is subjected to rapid degradation by proteolytic activity of plasma ADAMTS-13.Atomic force microscopy images elucidate the nanostructure of VWF fibers and illustrate self-association and -aggregation of several filamentous multimers. Together, these results suggest that circulatingVWF can contribute to a formation of hyperactive VWF fibers on exposed subendothelial collagen during vascular injury.
Plasma membrane Ca2+-ATPase associates with CLP36, α-actinin and actin in human platelets
Authors: Bozulic Larry , Malik Mohammad , Powell David , Nanez Adrian , Link Andrew , Ramos Kenneth , Dean William
Published: March 2007

The plasma membrane Ca2+-ATPase (PMCA) plays an essentialrole in maintaining low cytosolic Ca2+ in resting platelets. Earlier studies demonstrated that the 4b isoform of PMCA interacts viaits C-terminal end with the PDZ domains of membrane-associated guanylate kinase proteins. Activation of saponin-permeabilized platelets in the presence of a peptide composed of the lastten residues of the PMCA4b C-terminus leads to a significant decrease of PMCA associated with the cytoskeleton, suggesting that PDZ domain interactions play a role in tethering the pumpto the cytoskeleton. Here we present experiments conducted to evaluate the mechanism of this association. Co-immunoprecipitationassays coupled with liquid chromatography/tandemmass spectrometry analysis and immunoblotting were used to identify proteins that interact with PMCA in the resting platelet. Our results indicate that the only PDZ domain-containing proteinassociated with PMCA is the LIM family protein, CLP36. Glutathione-S-transferase pull-down from a platelet extractusing a fusion protein containing the C-terminal PDZ domainbinding motif of PMCA confirmed binding of CLP36 to PMCA. Gel filtration chromatography of detergent-solubilized plateletsdemonstrated the existence of a 1,000-kDa complex containingPMCA and CLP36, and in addition, α -actinin and actin. Immunoflourescencemicroscopy confirmed the co-localization ofPMCA with CLP36 in resting and activated platelets. Taken togetherthese results suggest that PMCA is localized in non-filamentousactin complexes in resting platelets by means of PDZdomain interactions and then associates with the actin cytoskeletonduring cytoskeletal rearrangement upon platelet activation. Thus, in addition to the reversible serine/threonine andtyrosine phosphorylation events previously described in humanplatelets, PMCA function may be regulated by interactions withanchoring and cytoskeletal proteins.
Active endothelin is an important vasoconstrictor in acute coronary thrombi
Authors: Adlbrecht Christopher , Bonderman Diana , Plass Christian , Jakowitsch Johannes , Beran Gilbert , Sperker Wolfgang , Siostrzonek Peter , Glogar Dietmar , Maurer Gerald , Lang Irene
Published: March 2007

Acute coronary syndrome is characterized by compromised blood flow at the epicardial and microvascular levels. We have previously shown that thrombectomy in ST-elevation myocardial infarction (STEMI) accelerates ST-segment resolution, possibly by preventing distal embolization. We hypothesized that thrombus constituents contribute to microcirculatory dysfunction. Therefore, we analyzed the molecular and cellular composition of acute coronary thrombi, and correlated vasoconstrictive mediators with the magnitude of ST-segment resolution within one hour of percutaneous coronary intervention (PCI). Fresh coronary thrombi were retrieved in 35 consecutive STEMI patients who were treated with the X-Sizer thrombectomy catheter, and thrombus cell counts and vasoconstrictor concentrations were assessed. Twelve-lead ECG recordings were analyzed prior to and one hour after PCI. Concentration of endothelin (ET) was 20.0 (7.9–52.2) fmol/ml in thrombus compared with 0.1 (0.1–0.3) fmol/ml in corresponding peripheral plasma (p<0.0001), representing a selective 280 (70.0–510.0)- fold enrichment, exceeding enrichment of noradrenaline, angiotensin II and serotonin. Human coronary thrombus homogenates exerted vasoconstriction of porcine coronary artery rings that was inhibited by the dual ET receptor blocker tezosentan. Extracted ET (r=0.523 p=0.026) and number of leukocytes (r=0.555 p=0.017) were correlated with the magnitude of STsegment resolution. In conclusion, the amount of active ET and white blood cells aspirated from STEMI target vessels correlated with improvement of territorial microcirculatory function as illustrated by enhanced ST-segment resolution.
Analysis of the novel factor X gene mutation Glu51Lys in two families with factor X-Riyadh anomaly
Authors: Wulff Karin , Abdel-Razeq Hikmat , Saud Khalida , Al-Gaili Fateh , Herrmann Falko , Al-Hilali Akram
Published: March 2007

Two families with 'factor X(FX)-Riyadh' have been identified (one of them related to the originally reported family). Affected members of both families exhibit prolongation in prothrombin time (PT) with normal partial thromboplastin time (PTT) and low assay levels of FX, when measured by PT-based assay. They do not have clinical bleeding diathesis, regardless of the PT prolongation. FX genes of the affected family members were analyzed by sequence analysis. A novel missense mutation in exon 4 of the FX gene, which causes the Glu51Lys substitution in the first epidermal growth factor-like domain of FX was found. The Glu51Lys mutation represents a type II mutation with low FX coagulant activity in the extrinsic pathway and normal FX antigen levels. This mutation may result in disruption of the predicted H-bonding between residue Glu51 of FX and the Asn199 residue of the tissue factor (TF) in the FX/TF/factorVIIa ternary complex, producing the phenotype 'FX deficiency Riyadh', with prolonged PT and normal PTT.
ABO blood group genotypes, plasma von Willebrand factor levels and loading of von Willebrand factor with A and B antigens
Authors: Morelli Vania , de Visser Marieke , van Tilburg Nico , Vos Hans , Eikenboom Jeroen , Rosendaal Frits , Bertina Rogier
Published: March 2007

ABO blood group is a genetic determinant of von Willebrand factor (VWF) levels. We investigated the effect of ABO genotypes on VWF and factor VIII (FVIII) levels and on the degree to which VWF is loaded with A- and B-antigens, expressed as normalized ratios, nA-ratio and nB-ratio, respectively, in the Leiden Thrombophilia Study, a large case-control study on venous thrombosis. We found that the ABO locus had an allele-specific, dosage dependent effect on VWF and FVIII levels and on the loading of VWF with A-antigen and B-antigen. The highest mean nA- and nB-ratios were found in A
1 A
1 and BB genotypes, respectively. Four A1 O carriers had four 43-bp repeats in the minisatellite region of theABO gene in stead of the expected one repeat. All had a reduced nA-ratio compared to A 1 O carriers with one repeat in their A1 allele. The amount of A – and B- antigens expressed onVWF (nA-ratio and nB-ratio) explained about 18% (R2) of the variation in VWF levels.
Critical temperature ranges of hypothermia-induced platelet activation: Possible implications for cooling patients in cardiac surgery
Authors: Breuer Melanie , Wendel Hans , Peter Karlheinz , Dietz Klaus , Ziemer Gerhard , Straub Andreas
Published: March 2007

Cooling of the patient is routinely applied in cardiac surgery to protect organs against ischemia. Hypothermia induces activation of platelets, but the effects of temperatures such as used during cardiac surgery are not well described. To investigate this in an in-vitro study heparinized whole blood was incubated at different temperatures (37°C, 34.5°C, 32°C, 29.5°C, 27°C, 24.5°C, 22°C, 19.5°C and 17°C).The effect of these temperatures on aggregation, P-selectin expression, GP IIb/IIIa activation and platelet microparticle (PMP) formation of unstimulated and ADP-stimulated platelets of 36 subjects was evaluated in flow cytometry. A four-parametric logistic model was fitted to depict the temperature effect on platelet parameters. Lower temperatures increased aggregates, P-selectin expression, and GP IIb/IIIa activation. The number of PMPs decreases with hypothermia. Additional experiments revealed a slight influence of heparin on platelet P-selectin expression but excluded an effect of this anticoagulant on the other evaluated parameters. Threshold temperatures, which mark 5% changes of platelet parameters compared to values at 37°C, were calculated. On ADP-stimulated platelets the thresholds for P-selectin expression and GP IIb/IIIa activation are 34.0°C and 36.4°C, respectively, and lie in the temperature range routinely applied in cardiac surgery. Hypothermia- induced platelet activation may develop in most patients undergoing cardiac surgery, possibly resulting in thromboembolic events, coagulation defects, and proinflammatory leukocyte bridging by P-selectin bearing platelets and PMPs. These findings suggest that pharmacological protection of platelets against hypothermia-induced damage may be beneficial during cardiac surgery.
The management of thrombosis in pregnancy: Role of low-molecular-weight heparin
Authors: Kher André , Nielsen Jorn , Bauersachs Rupert
Published: March 2007

Fatal pulmonary embolism remains the most common cause of mortality among pregnant women in many Western countries. The physiological changes of pregnancy produce a hypercoagulable state that increases the risk of venous thromboembolism (VTE).Women with inherited or acquired thrombophilias are at particularly high risk of VTE during pregnancy, and thromboprophylaxis may be advisable in some cases. Thrombophilia is also associated with complications of pregnancy, including fetal loss, pre-eclampsia, intra-uterine growth restriction, and placental abruption. The antithrombotic agents available for the prevention and treatment of VTE during pregnancy, and pregnancy complications, include unfractionated heparin (UFH), low-molecular-weight heparin (LMWH) and aspirin. Vitamin K antagonists are contra-indicated in pregnancy. Low-dose aspirin may have a role in the prevention of some pregnancy complications, although its safety in early and late pregnancy is uncertain. The efficacy and safety of LMWHs have been demonstrated for the prevention and treatment of VTE in pregnancy. These agents are increasingly being used in place of UFH, which is associated with a higher incidence of side effects compared with LMWH, in addition to the need for regular laboratory monitoring. Evidence is also emerging to support the use of LMWH in the prevention of recurrent fetal loss, although further trials are needed to explore the role of LMWHs in this indication and in the prevention of other complications of pregnacy.
Monocyte IL-10 produced in response to lipopolysaccharide modulates thrombin generation by inhibiting tissue factor expression and release of active tissue factor-bound microparticles
Authors: Poitevin Stéphane , Cochery-Nouvellon Eva , Dupont Annick , Nguyen Philippe
Published: March 2007

Lipopolysaccharide (LPS)-stimulated monocytes are known to have a procoagulant effect. This property is currently explained by the fact that monocytes, in response to LPS, can express tissue factor (TF) and undergo a process of membrane microvesiculation. Interleukin-10 (IL-10) has been shown to downregulate TF expression and inhibit procoagulant activity (PCA). In order to further characterize the inhibitory effect of IL-10 on LPS-induced PCA, we used the integrated system of analysis of kinetics of thrombin generation in normal plasma (thrombinography). For this, we developed an original method of elutriation allowing to obtain a highly purified monocyte preparation, under endotoxin-free conditions. Thrombin generation was measured using a highly sensitive and specific fluorogenic method which we adapted to inhibit the contact factor pathway. Results show that recombinant human IL-10 decreased the kinetics of thrombin generation in a dose-dependent manner. Furthermore, the inhibition of endogenous IL-10 released by monocytes in response to LPS is associated with an increase in the kinetics of thrombin generation. We demonstrated that this effect was a consequence of the up-regulation of TF expression and TF-bound microparticle release. In conclusion, we report that IL-10 can regulate thrombin generation in conditions close to physiology as allowed by thrombinography, and that endogenous IL-10 regulates TF expression and release of active TF-bound microparticles by a negative feed back loop through IL-10 receptor α
Fibronectin-binding proteins and clumping factor A in Staphylococcus aureus experimental endocarditis: FnBPA is sufficient to activate human endothelial cells
Authors: Heying Ruth , Gevel Joke , Que Yok-Ai , Moreillon Philippe , Beekhuizen Henry
Published: March 2007

Surface molecules of Staphylococcus aureus are involved in the colonization of vascular endothelium which is a crucial primary event in the pathogenesis of infective endocarditis (IE).The ability of these molecules to also launch endothelial procoagulant and proinflammatory responses, which characterize IE, is not known. In the present study we investigated the individual capacities of three prominent S. aureus surface molecules; fibronectinbinding protein A (FnBPA) and B (FnBPB) and clumping factor A (ClfA), to promote bacterial adherence to cultured human endothelial cells (ECs) and to activate phenotypic and functional changes in these ECs. Non-invasive surrogate bacterium Lactococcus lactis, which, by gene transfer, expressed staphylococcal FnBPA, FnBPB or ClfA molecules were used. Infection of ECs increased 50- to 100-fold with FnBPA- or FnBPB-positive recombinant lactococci. This coincided with EC activation, interleukin- 8 secretion and surface expression of ICAM-1 andVCAM-1 and concomitant monocyte adhesion. Infection with ClfA-positive lactococci did not activate EC. FnBPA-positive L. lactis also induced a prominent tissue factor-dependent endothelial coagulation response that was intensified by cell-bound monocytes. Thus S. aureus FnBPs, but not ClfA, confer invasiveness and pathogenicity to non-pathogenic L. lactis organisms indicating that bacterium-EC interactions mediated by these adhesins are sufficient to evoke inflammation as well as procoagulant activity at infected endovascular sites.
Remodeling of carotid arteries is associated with increased expression of thrombomodulin in a mouse transverse aortic constriction model
Authors: Hsieh Chung-Yu , Wang Danny , Chung Hsing-Chun , Liu Shu-Lin , Chao Ting-Hsing , Shi Guey-Yueh , Wu Hua-Lin , Li Yi-Heng
Published: March 2007

Thrombomodulin (TM) is an endothelial glycoprotein that functions as a thrombin cofactor in the activation of protein C. Recent evidence has revealed that TM has unique effects on cellular proliferation, adhesion, and inflammation. We examined TM expression in the arterial remodeling process with different shear conditions. Quantitative real-time reverse transcription- PCR (Q-PCR) revealed that shear stress (25 dyne/cm2 for 6 hours) induced a 2.6 ± 0.4 -fold increase inTM mRNA levels in endothelial cell culture. Adult FVB (Friend leukemia virus B strain) mice underwent transverse aortic constriction (TAC) between the right (RCA) and left carotid artery (LCA). Doppler (n = 8), morphometric (n = 8), and Q-PCR (n = 8 or 10) studies were performed on carotid arteries at different time points. The RCA lumen and media area increased. The LCA wall shear stress decreased after TAC. RCA wall shear stress increased at day 7 followed by a decrease to the baseline at day 28.TM mRNA level in the LCA was decreased by 61% at day 7 after TAC (0.39 ± 0.04; p<0.05 vs. baseline). It progressively returned to the baseline at day 14 (0.85 ± 0.12) and day 28 (1.48 ± 0.05; all p = NS). TM appeared in the media of the RCA;TM mRNA level in the RCA was increased by 11-fold at day 14 after TAC (11.0 ± 0.22) and progressively decreased at day 28 (5.34 ± 0.25, all p<0.05 vs. baseline). Our studies suggested that altered shear stress induced significantTM gene expression changes during the arterial remodeling process.
Mutational screening of six afibrinogenemic patients: Identification and characterization of four novel molecular defects
Authors: Monaldini Luca , Asselta Rosanna , Duga Stefano , Peyvandi Flora , Karimi Mehran , Malcovati Massimo , Tenchini Maria
Published: March 2007

Congenital afibrinogenemia (CAF) is a rare coagulation disorder characterized by very low or unmeasurable levels of functional and immunoreactive fibrinogen in plasma, associated with a hemorrhagic phenotype of variable severity. It is transmitted as an autosomal recessive trait (prevalence 1:1,000,000) and is invariantly associated with mutations affecting one of the three fibrinogen genes (FGA, FGB, and FGG, coding for Aα, Bβ, and γ chain, respectively). Fibrinogen is secreted by hepatocytes as a hexamer composed of two copies of each chain; the lack of one chain has been demonstrated to prevent its secretion. Most genetic defects causing afibrinogenemia are point mutations, where- as only three large deletions have been identified so far, all affecting the FGA gene. We here report the molecular characterization of six unrelated afibrinogenemic patients leading to the identification of eight different mutations, four hitherto unknown: a 4.1-Kb large deletion involving exon 1 of FGA (AC107385:g. 65682_69828del), two nonsense mutations (p.Trp229X in FGA and p.Trp266X in FGB), and an ins-del mutation (g.1787_ 1789del3ins12) in FGA. The molecular characterization of CAFcausing genetic defects increases our understanding on the genetic basis of this disease and might be helpful for prenatal screening
purposes, as also demonstrated during this study.
Community Attitudes Towards Discriminatory Practice Against People with Severe Mental Illness in Hong Kong
Authors: Chiu Marcus Y.L. , Chan Kenneth K.L.
Published: March 2007

Background: The existing literature on community attitudes towards people with severe mental illness (SMI) tends to be rather general and impressionistic, with apparently conflicting findings which have yet to be adequately understood.

Aims: This article undertakes to examine the community's level of tolerance towards discriminatory practice against people with SMI in three domains: family relations, employment and health care.

Methods: Structured interviews with a representative sample of 507 citizens were carried out using the computer-assisted telephone interview system (CATI).

Results: Our survey reveals some expected common misunderstandings about mental illness, with the older age group showing the greatest toleration towards discrimination. However, respondents showed a strong objection to discriminatory behaviour which people with SMI commonly face in health care and employment, whereas greater toleration towards discrimination was found in the family domain.

Conclusions: The coexistence of misunderstandings about mental illness and public rejection of discriminatory practice against people with SMI suggests that community attitudes are multi-dimensional and more amendable than expected. The findings of this study call for target-specific educational strategies for community education, as well as accompanying policy initiatives to end discriminatory practice, if people with SMI are to be truly taken as our fellow citizens.
Recovery from Mental Illness as an Emergent Concept and Practice in Australia and the UK
Authors: Ramon Shulamit , Healy Bill , Renouf Noel
Published: March 2007

The language of recovery is now widely used in mental health policy, services, and research. Yet the term has disparate antecedents, and is used in a variety of ways. Some of the history of the use of the term recovery is surveyed, with particular attention to the new meaning of the term, especially as identified by service users, supported and taken up to various degrees by research and in the professional literature. Policy and practice in two countries – Australia and the United Kingdom – are examined to determine the manner and extent to which the concept of recovery is evident. In its new meaning, the concept of recovery has the potential to bring about profound and needed changes in mental health theory and practice. It is being taken up differently in different settings. It is clear that – at least in Australia and the United Kingdom – there are promising new recovery models and practices that support recovery, but the widespread use of recovery language is not enough to ensure that the core principles of the recovery model are implemented.
Prevalence Of Depression And Correlates Of Depressive Symptoms For Residents In The Urban Part Of Jeju Island, Korea
Authors: Kim Moon-Doo , Hong Seong-Chul , Lee Chang-In , Kwak Young-Sook , Shin Tae-Kyun , Jang Yun-Hee , Oh Eun-Hee , Lee Ji-Woong , Jeon Bong-Hee , Hwang Seo-Eun
Published: March 2007

Aims: This study examined the prevalence of depression and depressive symptoms, and the correlates of depressive symptoms, and proposes some methods for reducing risk of depression in residents of the urban part of Jeju Island in Korea.

Methods: In all, 1050 residents were selected using multiphasic cluster sampling to represent each district. Of the 981 respondents, 413 were men and 568 were women. The Center for Epidemiologic Studies Depression Scale (CES-D) was used to evaluate depression (CES-D score over 25) and depressive symptoms (CES-D score over 21). Multiple logistic regression analysis was performed for comparisons.

Results: The prevalence of depression in males and females was comparable, at 9.47 and 11.36%, respectively. The prevalence of depressive symptoms in men was 15.01%, while in women the level rose to 18.37%. Those with high self-assessed level of stress scores were significantly more likely to have depressive symptoms than those with low self-assessed level of stress scores (odds ratio (OR) = 5.73 (95% confidence interval (95%CI), 1.29–25.36)). Residents at high risk of problem drinking (CAGE score over 3) were significantly more likely to have depressive symptoms than those with a CAGE score under 1 (OR = 3.43 95%CI, 1.77–6.66). Respondents who slept poorly had more depressive symptoms than respondents who slept well (OR = 2.11 95%CI, 1.37–3.23). Females were significantly more likely to have more depressive symptoms than males (OR = 1.70 95%CI, 1.08–2.68).

Conclusions: The prevalence of depression and depressive symptoms in urban Jeju Island is similar to that in a nation-wide sample. By providing intensive mental health services to those who have high stress levels, problem drinking, and poor health behavior, early detection of depressive symptoms in the community will be important for improving general health status.
Queering feminist technology studies
Authors: Landström Catharina
Published: March 2007

This article argues that the influence of heteronormativity on the conceptualization of women and technology in feminist constructivist technology studies creates serious problems for the analysis. This research aims to understand the coproduction of gender and technology in society, but does not approach the two elements in a symmetrical fashion. Hence, ethnographic studies can only exemplify how the gender of technology producers is reflected in the technology created. Masculine gender identity is stabilized as a cause for the masculinity of a technology that is shaped by social relationships. The criticism is fleshed out in a close examination of case study accounts of ethnographies among producers and users of technology. It is argued that a habitual reproduction of heteronormativity, present in the surrounding culture and in the technological communities studied, has prevented the adoption of approaches to the subject conducive to the objective of this feminist research. Acknowledging that destabilizing gender can undermine the critical thrust of feminist critique, the paper turns towards queer theory for ideas about how to produce criticism that does not rely on the stability of identity. The article closes with suggesting how a queer feminist approach could contribute to different readings of life with technology.
Strange bedfellows
Authors: Paasonen Susanna
Published: March 2007

Feminist debates on pornography have relied on articulations of affect, from anti-pornography rhetoric of grief, anger and disgust to anti-anti-pornography claims to enjoyment and pleasure. The complexity of reading, the interpenetration of affect and analysis, experience and interpretation tend to become effaced in arguments both for and against pornography. This article argues for the necessity of moving beyond the affective range of disgust versus pleasure in feminist studies of pornography. Drawing on theorizations of reading and affect, particularly Eve Kosofsky Sedgwick’s discussion of ‘paranoid’ and ‘reparative’ reading, it investigates the possibilities of analysing commercial email porn spam without reducing the outcome to the literal and the self-evident. This involves taking seriously the power of pornographic texts to move their readers, scholars included. Since affective encounters with porn are ambivalent and often contradictory, their status as basis of knowledge over pornography remains highly unstable.
Crime Dynamics at Lithuanian Borders
Authors: Ceccato Vânia
Published: March 2007

This article compares levels and patterns of offences in different parts of Lithuania with the aim of assessing whether border regions are more susceptible to crime than the rest of the country. The article focuses on identifying and explaining these patterns for selected categories of offences while taking account of contextual factors. Spatial statistical techniques and Geographic Information Systems underpin the methodology employed. Findings suggest that there are variations in the level and geography of offences between border regions and the rest of the country. Despite the fact that the highest average increases in recorded criminal offences were found in two border regions, non-border regions had a higher average increase in the 1990s. This partially explains why, out of the six selected offences, only assault shows an increase owing to the ‘border effect’. The proportion of the population living in urban areas is by far the most important covariate in explaining the regional variations in offence ratios.
Nelarabine induces complete remissions in adults with relapsed or refractory T-lineage acute lymphoblastic leukemia or lymphoblastic lymphoma: Cancer and Leukemia Group B study 19801
Authors: DeAngelo Daniel J. , Yu Daohai , Johnson Jeffrey L. , Coutre Steven E. , Stone Richard M. , Stopeck Alison T. , Gockerman Jon P. , Mitchell Beverly S. , Appelbaum Frederick R. , Larson Richard A.
Published: March 2007

Nelarabine (506U78) is a soluble pro-drug of 9-β-d-arabinofuranosylguanine (ara-G), a deoxyguanosine derivative. We treated 26 patients with T-cell acute lymphoblastic leukemia (T-ALL) and 13 with T-cell lymphoblastic lymphoma (T-LBL) with nelarabine. All patients were refractory to at least one multiagent regimen or had relapsed after achieving a complete remission. Nelarabine was administered on an alternate day schedule (days 1, 3, and 5) at 1.5 g/m2/day. Cycles were repeated every 22 days. The median age was 34 years (range, 16-66 years); 32 (82%) patients were male. The rate of complete remission was 31% (95% confidence interval [CI], 17%, 48%) and the overall response rate was 41% (95% CI, 26%, 58%). The principal toxicity was grade 3 or 4 neutropenia and thrombocytopenia, occurring in 37% and 26% of patients, respectively. There was only one grade 4 adverse event of the nervous system, which was a reversible depressed level of consciousness. The median disease-free survival (DFS) was 20 weeks (95% CI, 11, 56), and the median overall survival was 20 weeks (95% CI, 13, 36). The 1-year overall survival was 28% (95% CI, 15%, 43%). Nelarabine is well tolerated and has significant antitumor activity in relapsed or refractory T-ALL and T-LBL.
Fatal agranulocytosis after deferiprone therapy in a child with Diamond-Blackfan anemia
Authors: Henter Jan-Inge , Karlén Jonas
Published: March 2007

A 10-year-old girl with steroid-resistent Diamond-Blackfan anemia (DBA) developed agranulocytosis 9 weeks after chelation with deferiprone was initiated (45 mg/kg daily, 60% of recommended dose) in addition to her ordinary deferoxamine therapy. The blood counts, checked weekly, dropped markedly between weeks 8 and 9. She rapidly developed a septicemia and was admitted with high fever (40.9°C), white blood cell count 0.4 × 109/L, absolute neutrophil count 0.1 × 109/L and platelets 114 × 109/L. She was administered broad spectrum antibiotics, G-CSF (10 microgram/kg daily) and corticosteroids but remained neutropenic and died 6 weeks after admission. Bone marrow examination day 23 revealed areas with low cellularity (around 30%), but also areas with infiltrates of T cells; granulopoiesis and erythropoiesis were scarce. We conclude that weekly neutrophil monitoring is not sufficient to avoid fatal agranulocytosis. We suggest that deferiprone not be prescribed to DBA patients unless the clinical indications are particularly strong, and that the risk of agranulocytosis in thalassemia patients be carefully considered.
Orthology prediction at scalable resolution by phylogenetic tree analysis
Authors: van der Heijden René TJM , Snel Berend , van Noort Vera , Huynen Martijn A
Published: March 2007

Background

Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups.

Results

We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees) that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large) trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable.

Conclusion

The "levels of orthology" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from the LOFT website http://www.cmbi.ru.nl/LOFT.
On the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the Common Pathway genes
Authors: Fondi Marco , Brilli Matteo , Fani Renato
Published: March 2007

Background

The lysine, threonine, and methionine biosynthetic pathways share the three initial enzymatic steps, which are referred to as the Common Pathway (CP). In Escherichia coli three different aspartokinases (AKI, AKII, AKIII, the products of thrA, metL and lysC, respectively) can perform the first step of the CP. Moreover, two of them (AKI and AKII) are bifunctional, carrying also homoserine dehydrogenasic activity (hom product). The second step of the CP is catalyzed by a single aspartate semialdehyde dehydrogenase (ASDH, the product of asd). Thus, in the CP of E. coli while a single copy of ASDH performs the same reaction for three different metabolic routes, three different AKs perfom a unique step. Why and how such a situation did emerge and maintain? How is it correlated to the different regulatory mechanisms acting on these genes? The aim of this work was to trace the evolutionary pathway leading to the extant scenario in proteobacteria.

Results

The analysis of the structure, organization, phylogeny, and distribution of ask and hom genes revealed that the presence of multiple copies of these genes and their fusion events are restricted to the γ-subdivision of proteobacteria. This allowed us to depict a model to explain the evolution of ask and hom according to which the fused genes are the outcome of a cascade of gene duplication and fusion events that can be traced in the ancestor of γ-proteobacteria. Moreover, the appearance of fused genes paralleled the assembly of operons of different sizes, suggesting a strong correlation between the structure and organization of these genes. A statistic analysis of microarray data retrieved from experiments carried out on E. coli and Pseudomonas aeruginosa was also performed.

Conclusion

The integration of data concerning gene structure, organization, phylogeny, distribution, and microarray experiments allowed us to depict a model for the evolution of ask and hom genes in proteobacteria and to suggest a biological significance for the extant scenario.
A global gene evolution analysis on Vibrionaceae family using phylogenetic profile
Authors: Vitulo Nicola , Vezzi Alessandro , Romualdi Chiara , Campanaro Stefano , Valle Giorgio
Published: March 2007

Background

Vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens.

In this work we propose an improved phylogenetic profile analysis on 14 Vibrionaceae genomes, to study the evolution of this family on the basis of gene content.

The phylogenetic profile is based on the observation that genes involved in the same process (e.g. metabolic pathway or structural complex) tend to be concurrently present or absent within different genomes. This allows the prediction of hypothetical functions on the basis of a shared phylogenetic profiles. Moreover this approach is useful to identify putative laterally transferred elements on the basis of their presence on distantly phylogenetically related bacteria.

Results

Vibrionaceae ORFs were aligned against all the available bacterial proteomes. Phylogenetic profile is defined as an array of distances, based on aminoacid substitution matrixes, from single genes to all their orthologues. Final phylogenetic profiles, derived from non-redundant list of all ORFs, was defined as the median of all the profiles belonging to the cluster. The resulting phylogenetic profiles matrix contains gene clusters on the rows and organisms on the columns.

Cluster analysis identified groups of "core genes" with a widespread high similarity across all the organisms and several clusters that contain genes homologous only to a limited set of organisms. On each of these clusters, COG class enrichment has been calculated. The analysis reveals that clusters of core genes have the highest number of enriched classes, while the others are enriched just for few of them like DNA replication, recombination and repair.

Conclusion

We found that mobile elements have heterogeneous profiles not only across the entire set of organisms, but also within Vibrionaceae; this confirms their great influence on bacteria evolution even inside the same family. Furthermore, several hypothetical proteins highly correlate with mobile elements profiles suggesting a possible horizontal transfer mechanism for the evolution of these genes. Finally, we suggested the putative role of some ORFs having an unknown function on the basis of their phylogenetic profile similarity to well characterized genes.
ProtNet: a tool for stochastic simulations of protein interaction networks dynamics
Authors: Bernaschi Massimo , Castiglione Filippo , Ferranti Alessandra , Gavrila Caius , Tinti Michele , Cesareni Gianni
Published: March 2007

Background

Protein interactions support cell organization and mediate its response to any specific stimulus. Recent technological advances have produced large data-sets that aim at describing the cell interactome. These data are usually presented as graphs where proteins (nodes) are linked by edges to their experimentally determined partners. This representation reveals that protein-protein interaction (PPI) networks, like other kinds of complex networks, are not randomly organized and display properties that are typical of "hierarchical" networks, combining modularity and local clustering to scale free topology. However informative, this representation is static and provides no clue about the dynamic nature of protein interactions inside the cell.

Results

To fill this methodological gap, we designed and implemented a computer model that captures the discrete and stochastic nature of protein interactions. In ProtNet, our simplified model, the intracellular space is mapped onto either a two-dimensional or a three-dimensional lattice with each lattice site having a linear size (5 nm) comparable to the diameter of an average globular protein. The protein filled lattice has an occupancy (e.g. 20%) compatible with the estimated crowding of proteins in the cell cytoplasm. Proteins or protein complexes are free to translate and rotate on the lattice that represents a sort of naïve unstructured cell (devoid of compartments). At each time step, molecular entities (proteins or complexes) that happen to be in neighboring cells may interact and form larger complexes or dissociate depending on the interaction rules defined in an experimental protein interaction network. This whole procedure can be seen as a sort of "discrete molecular dynamics" applied to interacting proteins in a cell.

We have tested our model by performing different simulations using as interaction rules those derived from an experimental interactome of Saccharomyces cerevisiae (1378 nodes, 2491 edges) and we have compared the dynamics of complex formation in a two and a three dimensional lattice model.

Conclusion

ProtNet is a cellular automaton model, where each protein molecule or complex is explicitly represented and where simple interaction rules are applied to populations of discrete particles. This tool can be used to simulate the dynamics of protein interactions in the cell.
The MEPS server for identifying protein conformational epitopes
Authors: Castrignanò Tiziana , De Meo Paolo D'Onorio , Carrabino Danilo , Orsini Massimilano , Floris Matteo , Tramontano Anna
Published: March 2007

Background

One of the most interesting problems in molecular immunology is epitope mapping, i.e. the identification of the regions of interaction between an antigen and an antibody. The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues involved in the interaction and could be instrumental both in designing peptides able to mimic the interacting surface of the antigen and in understanding where immunologically important regions are located in its three-dimensional structure. From an experimental point of view, both genetically encoded and chemically synthesised peptide libraries can be used to identify sequences recognized by a given antibody. The problem then arises of which region of a folded protein the selected peptides correspond to.

Results

We have developed a method able to find the surface region of a protein that can be effectively mimicked by a peptide, given the structure of the protein and the maximum number of side chains deemed to be required for recognition. The method is implemented as a publicly available server. It can also find and report all peptide sequences of a specified length that can mimic the surface of a given protein and store them in a database.

The immediate application of the server is the mapping of antibody epitopes, however the system is sufficiently flexible for allowing other questions to be asked, for example one can compare the peptides representing the surface of two proteins known to interact with the same macromolecule to find which is the most likely interacting region.

Conclusion

We believe that the MEPS server, available at http://www.caspur.it/meps, will be a useful tool for immunologists and structural and computational biologists. We plan to use it ourselves to implement a database of "surface mimicking peptides" for all proteins of known structure and proteins that can be reliably modelled by comparative modelling.