bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of Forest Structure and Leaf Area in Secondary Forests Regenerating on Abandoned Pastures in Central Amazônia
Authors: Feldpausch Ted R. , Riha Susan J. , Fernandes Erick C. M. , Wandelli Elisa V.
Published: June 2005

The area of secondary forest (SF) regenerating from pastures is increasing in the Amazon basin; however, the return of forest and canopy structure following abandonment is not well understood. This study examined the development of leaf area index (LAI), canopy cover, aboveground biomass, stem density, diameter at breast height (DBH), and basal area (BA) by growth form and diameter class for 10 SFs regenerating from abandoned pastures. Biomass accrual was tree dominated, constituting ≥94% of the total measured biomass in all forests abandoned ≥4 to 6 yr. Vine biomass increased with forest age, but its relative contribution to total biomass decreased with time. The forests were dominated by the tree Vismia spp. (>50%). Tree stem density peaked after 6 to 8 yr (10 320 stems per hectare) before declining by 42% in the 12- to 14-yr-old SFs. Small-diameter tree stems in the 1–5-cm size class composed >58% of the total stems for all forests. After 12 to 14 yr, there was no significant leaf area below 150-cm height. Leaf area return (LAI = 3.2 after 12 to 14 yr) relative to biomass was slower than literature-reported recovery following slash-and-burn, where LAI can reach primary forest levels (LAI = 4–6) in 5 yr. After 12 to 14 yr, the colonizing vegetation returned some components of forest structure to values reported for primary forest. Basal area and LAI were 50%–60%, canopy cover and stem density were nearly 100%, and the rapid tree-dominated biomass accrual was 25%–50% of values reported for primary forest. Biomass accumulation may reach an asymptote earlier than expected because of even-aged, monospecific, untiered stand structure. The very slow leaf area accumulation relative to biomass and to reported values for recovery following slash-and-burn indicates a different canopy development pathway that warrants further investigation of causes (e.g., nutrient limitations, competition) and effects on processes such as evapotranspiration and soil water uptake, which would influence long-term recovery rates and have regional implications.
Influence of Perceived Neighborhood Diversity and Racism Experience on the Racial Socialization of Black Youth
Authors: Stevenson Howard C. , McNeil J. Derek , Herrero-Taylor Teresa , Davis Gwendolyn Y.
Published: June 2005

Research on ecological factors that influence the experience of racial socialization by African American adolescents is limited but necessary in understanding how youth come to be exposed to these messages. This study examines how the cultural diversity of an adolescent’s neighborhood and his or her experience with racism moderates the frequency of experiencing protective and proactive racial socialization communications received from their families. Results reveal that boys are more likely than girls to receive coping with antagonism and cultural pride communications in high culturally diverse neighborhoods when they’ve had a personal experience with racism. Conversely, girls from low culturally diverse neighborhoods, predominantly Black, report receiving more cultural pride messages from family if they had a personal experience with racism. The moderating effects of neighborhood cultural diversity and racism on the racial socialization of Black youth are discussed.
The Role of Budget Stabilization Funds in Smoothing Government Expenditures over the Business Cycle
Authors: Wagner Gary A. , Elder Erick M.
Published: June 2005

The economic downturn that began in 2001 resulted in sizable budget shortfalls and arguably the worst fiscal conditions for state governments in decades. The use of savings to stabilize cyclical fluctuations in the budget has been institutionalized in most states in the form of budget stabilization funds. In this article, the authors explore how state expenditure volatility is affected by the existence, size, and structure of stabilization funds using multiple measures of expenditure cyclicality over the period from 1969 to 1999. The results indicate that while most states have not witnessed a reduction in expenditure volatility over the business cycle, states with rule-bound stabilization funds experience significantly less expenditure volatility from utilizing a budget stabilization fund. In fact, the authors find that state expenditures are approximately 20 percent less volatile following the adoption of a rule-bound budget stabilization fund.
Only a specific subset of human peripheral-blood monocytes has endothelial-like functional capacity
Authors: Elsheikh Elzafir , Uzunel Mehmet , He Zhong , Holgersson Jan , Nowak Grzegorz , Sumitran-Holgersson Suchitra
Published: June 2005

The monocyte population in blood is considered a possible source of endothelial precursors. Because endothelial-specific receptor tyrosine kinases act as regulators of endothelial cell function, we investigated whether expression of the vascular endothelial growth factor receptor-2 (VEGFR-2) on monocytes is important for their endothelial-like functional capacity. Peripheral-blood monocytes expressing vascular endothelial growth factor receptor-2 (VEGFR-2), or CD14+/VEGFR-2+, were isolated, and their phenotypic, morphologic, and functional capacities were compared with those of monocytes negative for this marker (CD14+/VEGFR-2-). CD14+/VEGFR-2+ cells constituted approximately 2% ± 0.5% of the total population of monocytes and 0.08% ± 0.04% of mononuclear cells in blood. CD14+/VEGFR-2+ cells exhibited the potential to differentiate in vitro into cells with endothelial characteristics. The cells were efficiently transduced by a lentiviral vector driving expression of the green fluorescence protein (GFP). Transplantation of GFP-transduced cells into balloon-injured femoral arteries of nude mice significantly contributed to efficient reendothelialization. CD14+/VEGFR-2- did not exhibit any of these characteristics. These data demonstrate that the expression of VEGFR-2 on peripheral blood monocytes is essential for their endothelial-like functional capacity and support the notion of a common precursor for monocytic and endothelial cell lineage. Our results help clarify which subpopulations may restore damaged endothelium and may participate in the maintenance of vascular homeostasis.
The Jak2V617F mutation, PRV-1 overexpression, and EEC formation define a similar cohort of MPD patients
Authors: Goerttler Philipp S. , Steimle Cordula , März Edith , Johansson Peter L. , Andreasson Björn , Griesshammer Martin , Gisslinger Heinz , Heimpel Hermann , Pahl Heike L.
Published: June 2005

Recently, a Jak2V617F mutation has been described in the vast majority of patients with polycythemia vera (PV) as well as in subsets of patients with essential thrombocythemia (ET) and idiopathic myelofibrosis (IMF). The question arises whether this mutation is observed in those patients with ET and IMF who have also displayed previously described molecular markers, notably the ability to form endogenous erythroid colonies (EECs), overexpression of polycythemia rubra vera 1 (PRV-1), and decreased c-Mpl expression. We therefore analyzed the Janus kinase 2 (Jak2) DNA sequence, EEC growth, PRV-1 expression, and c-Mpl (myeloproliferative) levels in a cohort of 78 myeloproliferative disorder (MPD) patients (42 ET, 22 PV, and 14 IMF). Presence of the Jak2V617F mutation was very highly correlated with PRV-1 overexpression and the ability to form EECs in all 3 subtypes of MPDs (P < .001). (Blood. 2005;106:2862-2864)
Risk for heparin-induced thrombocytopenia with unfractionated and low-molecular-weight heparin thromboprophylaxis: a meta-analysis
Authors: Martel Nadine , Lee James , Wells Philip S.
Published: June 2005

Heparin-induced thrombocytopenia (HIT) is an uncommon but potentially devastating complication of anticoagulation with unfractionated heparin (UFH) or low-molecular-weight heparin (LMWH). Our objective was to determine and compare the incidences of HIT in surgical and medical patients receiving thromboprophylaxis with either UFH or LMWH. All relevant studies identified in the MEDLINE database (1984-2004), not limited by language, and from reference lists of key articles were evaluated. Randomized and nonrandomized controlled trials comparing prophylaxis with UFH and LMWH and measuring HIT or thrombocytopenia as outcomes were included. Two reviewers independently extracted data on thromboprophylaxis (type, dose, frequency, and duration), definition of thrombocytopenia, HIT assay, and rates of the following outcomes: HIT, thrombocytopenia, and thromboembolic events. HIT was defined as a decrease in platelets to less than 50% or to less than 100 × 109/L and positive laboratory HIT assay. Fifteen studies (7287 patients) were eligible: 2 randomized controlled trials (RCTs) measuring HIT (1014 patients), 3 prospective studies (1464 patients) with nonrandomized comparison groups in which HIT was appropriately measured in both groups, and 10 RCTs (4809 patients) measuring thrombocytopenia but not HIT. Three analyses were performed using a random effects model and favored the use of LMWH: (1) RCTs measuring HIT showed an odds ratio (OR) of 0.10 (95% confidence interval [CI], 0.01-0.2; P = .03); (2) prospective studies measuring HIT showed an OR of 0.10 (95% CI, 0.03-0.33; P < .001); (3) all 15 studies measured thrombocytopenia. The OR was 0.47 (95% CI, 0.22-1.02; P = .06). The inverse variance–weighted average that determined the absolute risk for HIT with LMWH was 0.2%, and with UFH the risk was 2.6%. Most studies were of patients after orthopedic surgery.
Botrocetin/VWF-induced signaling through GPIb-IX-V produces TxA2 in an αIIbβ3- and aggregation-independent manner
Authors: Liu Junling , Pestina Tamara I. , Berndt Michael C. , Jackson Carl W. , Gartner T. Kent
Published: June 2005

Binding of von Willebrand factor (VWF) to the platelet membrane glycoprotein (GP) Ib-IX-V complex initiates a signaling cascade that causes αIIbβ3 activation and platelet aggregation. Previous work demonstrated that botrocetin (bt)/VWF–mediated agglutination activates αIIbβ3 and elicits adenosine triphosphate (ATP) secretion in a thromboxane A2 (TxA2)– and Ca2+-dependent manner. This agglutination-elicited TxA2 production occurs in the absence of ATP secretion. However, the signaling components and signaling network or pathway activated by GPIb-mediated agglutination to cause TxA2 production have not been identified. Therefore, the focus of this study was to elucidate at least part of the signal transduction network or pathway activated by GPIb-mediated agglutination to cause TxA2 production. The phosphatidylinositol 3-kinase (PI3K) selective inhibitor wortmannin, and mouse platelets deficient in Lyn, Src, Syk, Src homology 2 (SH2) domain–containing leukocyte protein 76 (SLP-76), phospholipase Cγ2 (PLCγ2), linker for activation of T cells (LAT), or Fc receptor γ-chain (FcRγ-chain) were used for these studies. LAT and FcRγ-chain were found not to be required for agglutination-driven TxA2 production or activation of αIIbβ3, but were required for granule secretion and aggregation. The results also clearly demonstrate that bt/VWF-mediated agglutination-induced TxA2 production is dependent on signaling apparently initiated by Lyn, enhanced by Src, and propagated through Syk, SLP-76, PI3K, PLCγ2, and protein kinase C (PKC).
Mathematical modelling to centre low tidal volumes following acute lung injury: A study with biologically variable ventilation
Authors: Graham M Ruth , Haberman Craig J , Brewster John F , Girling Linda G , McManus Bruce M , Mutch W Alan C
Published: June 2005

Background

With biologically variable ventilation [BVV – using a computer-controller to add breath-to-breath variability to respiratory frequency (f) and tidal volume (VT)] gas exchange and respiratory mechanics were compared using the ARDSNet low VT algorithm (Control) versus an approach using mathematical modelling to individually optimise VT at the point of maximal compliance change on the convex portion of the inspiratory pressure-volume (P-V) curve (Experimental).

Methods

Pigs (n = 22) received pentothal/midazolam anaesthesia, oleic acid lung injury, then inspiratory P-V curve fitting to the four-parameter logistic Venegas equation F(P) = a + b[1 + e
-(P-c)/d
]-1 where: a = volume at lower asymptote, b = the vital capacity or the total change in volume between the lower and upper asymptotes, c = pressure at the inflection point and d = index related to linear compliance. Both groups received BVV with gas exchange and respiratory mechanics measured hourly for 5 hrs. Postmortem bronchoalveolar fluid was analysed for interleukin-8 (IL-8).

Results

All P-V curves fit the Venegas equation (R2 > 0.995). Control VT averaged 7.4 ± 0.4 mL/kg as compared to Experimental 9.5 ± 1.6 mL/kg (range 6.6 – 10.8 mL/kg; p < 0.05). Variable VTs were within the convex portion of the P-V curve. In such circumstances, Jensen's inequality states "if F(P) is a convex function defined on an interval (r, s), and if P is a random variable taking values in (r, s), then the average or expected value (E) of F(P); E(F(P)) > F(E(P))." In both groups the inequality applied, since F(P) defines volume in the Venegas equation and (P) pressure and the range of VTs varied within the convex interval for individual P-V curves. Over 5 hrs, there were no significant differences between groups in minute ventilation, airway pressure, blood gases, haemodynamics, respiratory compliance or IL-8 concentrations.

Conclusion

No difference between groups is a consequence of BVV occurring on the convex interval for individualised Venegas P-V curves in all experiments irrespective of group. Jensen's inequality provides theoretical proof of why a variable ventilatory approach is advantageous under these circumstances. When using BVV, with VT centred by Venegas P-V curve analysis at the point of maximal compliance change, some leeway in low VT settings beyond ARDSNet protocols may be possible in acute lung injury. This study also shows that in this model, the standard ARDSNet algorithm assures ventilation occurs on the convex portion of the P-V curve.
Estimation of airway obstruction using oximeter plethysmograph waveform data
Authors: Arnold Donald H , Spiro David M , Desmond Renee' A , Hagood James S
Published: June 2005

Background

Validated measures to assess the severity of airway obstruction in patients with obstructive airway disease are limited. Changes in the pulse oximeter plethysmograph waveform represent fluctuations in arterial flow. Analysis of these fluctuations might be useful clinically if they represent physiologic perturbations resulting from airway obstruction. We tested the hypothesis that the severity of airway obstruction could be estimated using plethysmograph waveform data.

Methods

Using a closed airway circuit with adjustable inspiratory and expiratory pressure relief valves, airway obstruction was induced in a prospective convenience sample of 31 healthy adult subjects. Maximal change in airway pressure at the mouthpiece was used as a surrogate measure of the degree of obstruction applied. Plethysmograph waveform data and mouthpiece airway pressure were acquired for 60 seconds at increasing levels of inspiratory and expiratory obstruction. At each level of applied obstruction, mean values for maximal change in waveform area under the curve and height as well as maximal change in mouth pressure were calculated for sequential 7.5 second intervals. Correlations of these waveform variables with mouth pressure values were then performed to determine if the magnitude of changes in these variables indicates the severity of airway obstruction.

Results

There were significant relationships between maximal change in area under the curve (P < .0001) or height (P < 0.0001) and mouth pressure.

Conclusion

The findings suggest that mathematic interpretation of plethysmograph waveform data may estimate the severity of airway obstruction and be of clinical utility in objective assessment of patients with obstructive airway diseases.
Signal transduction pathway profiling of individual tumor samples
Authors: Breslin Thomas , Krogh Morten , Peterson Carsten , Troein Carl
Published: June 2005

Background

Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to analyze tumor gene expression data from microarrays in the context of such pathways.

Results

We use pathways compiled from the TRANSPATH/TRANSFAC databases and the literature, and three publicly available cancer microarray data sets. Variation in pathway activity, across the samples, is gauged by the degree of correlation between downstream targets of a pathway. Two correlation scores are applied; one considers all pairs of downstream targets, and the other considers only pairs without common transcription factors. Several pathways are found to be differentially active in the data sets using these scores. Moreover, we devise a score for pathway activity in individual samples, based on the average expression value of the downstream targets. Statistical significance is assigned to the scores using permutation of genes as null model. Hence, for individual samples, the status of a pathway is given as a sign, + or -, and a p-value. This approach defines a projection of high-dimensional gene expression data onto low-dimensional pathway activity scores. For each dataset and many pathways we find a much larger number of significant samples than expected by chance. Finally, we find that several sample-wise pathway activities are significantly associated with clinical classifications of the samples.

Conclusion

This study shows that it is feasible to infer signal transduction pathway activity, in individual samples, from gene expression data. Furthermore, these pathway activities are biologically relevant in the three cancer data sets.
Species-specific analysis of protein sequence motifs using mutual information
Authors: Hummel Jan , Keshvari Nima , Weckwerth Wolfram , Selbig Joachim
Published: June 2005

Background

Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions. Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and, in particular, evolutionary features of the underlying sequences.

Results

We describe the tool PROfile analysis based onMutualInformation (PROMI) that enables comparative analysis of user-classified protein sequences. PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side. On the client-side platform-independence is achieved by generally applied internet delivery standards. As one possible application analysis of the zinc finger C2H2-type protein domain is introduced to illustrate the functionality of the tool.

Conclusion

The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences. It is available at http://promi.mpimp-golm.mpg.de where additional documentation can be found.
Conservation of pregnancy-specific glycoprotein (PSG) N domains following independent expansions of the gene families in rodents and primates
Authors: McLellan Andrew S , Zimmermann Wolfgang , Moore Tom
Published: June 2005

Background

Rodent and primate pregnancy-specific glycoprotein (PSG) gene families have expanded independently from a common ancestor and are expressed virtually exclusively in placental trophoblasts. However, within each species, it is unknown whether multiple paralogs have been selected for diversification of function, or for increased dosage of monofunctional PSG. We analysed the evolution of the mouse PSG sequences, and compared them to rat, human and baboon PSGs to attempt to understand the evolution of this complex gene family.

Results

Phylogenetic tree analyses indicate that the primate N domains and the rodent N1 domains exhibit a higher degree of conservation than that observed in a comparison of the mouse N1 and N2 domains, or mouse N1 and N3 domains. Compared to human and baboon PSG N domain exons, mouse and rat PSG N domain exons have undergone less sequence homogenisation. The high non-synonymous substitution rates observed in the CFG face of the mouse N1 domain, within a context of overall conservation, suggests divergence of function of mouse PSGs. The rat PSG family appears to have undergone less expansion than the mouse, exhibits lower divergence rates and increased sequence homogenisation in the CFG face of the N1 domain. In contrast to most primate PSG N domains, rodent PSG N1 domains do not contain an RGD tri-peptide motif, but do contain RGD-like sequences, which are not conserved in rodent N2 and N3 domains.

Conclusion

Relative conservation of primate N domains and rodent N1 domains suggests that, despite independent gene family expansions and structural diversification, mouse and human PSGs retain conserved functions. Human PSG gene family expansion and homogenisation suggests that evolution occurred in a concerted manner that maintains similar functions of PSGs, whilst increasing gene dosage of the family as a whole. In the mouse, gene family expansion, coupled with local diversification of the CFG face, suggests selection both for increased gene dosage and diversification of function. Partial conservation of RGD and RGD-like tri-peptides in primate and rodent N and N1 domains, respectively, supports a role for these motifs in PSG function.
Qualitatively and quantitatively similar effects of active and passive maternal tobacco smoke exposure on in utero mutagenesis at the HPRT locus
Authors: Grant Stephen G
Published: June 2005

Background

Induced mutagenesisin uterois likely to have life-long repercussions for the exposed fetus, affecting survival, birth weight and susceptibility to both childhood and adult-onset diseases, such as cancer. In the general population, such exposures are likely to be a consequence of the lifestyle choices of the parents, with exposure to tobacco smoke one of the most pervasive and easily documented. Previous studies attempting to establish a direct link between active smoking and levels of somatic mutation have largely discounted the effects of passive or secondary exposure, and have produced contradictory results.

Methods

Data from three studies of possible smoking effects onin uteromutagenesis at theHPRTlocus were compiled and reanalyzed, alone and in combination. Where possible, passive exposure to environmental tobacco smoke was considered as a separate category of exposure, rather than being included in the non-smoking controls. Molecular spectra from these studies were reanalyzed after adjustment for reported mutation frequencies from the individual studies and the entire data set.

Results

A series of related studies on mutation at the X-linkedHPRTlocus in human newborn cord blood samples has led to the novel conclusion that only passive maternal exposure to tobacco mutagens has a significant effect on the developing baby. We performed a pooled analysis of the complete data from these studies, at the levels of both induced mutation frequency and the resulting mutational spectrum.

Conclusion

Our analysis reveals a more commonsensical, yet no less cautionary result: both active maternal smoking and secondary maternal exposure produce quantitatively and qualitatively indistinguishable increases in fetalHPRTmutation. Further, it appears that this effect is not perceptibly ameliorated if the mother adjusts her behavior (i.e. stops smoking) when pregnancy is confirmed, although this conclusion may also be affected by continued passive exposure.
Reliability of upright posture measurements in primary school children
Authors: McEvoy Maureen P , Grimmer Karen
Published: June 2005

Background

Correct upright posture is considered to be a measure of good musculoskeletal health. Little is known about the usual variability of children's upright standing posture. The aim of this study was to assess differences between repeated measures of upright posture in a group of primary school children.

Methods

Sagittal plane photographs of usual, relaxed upright standing posture of 38 boys and girls aged 5–12 years were taken twice within an hour. Reflective markers were placed over the canthus, tragus, C7 spinous process, greater trochanter and lateral malleolus. Digitising software was used to calculate the x,y plane coordinates, from which five postural angles were calculated (trunk, neck, gaze, head on neck, lower limb). Height, weight, motor control estimates (as measured by the Brace Tests) and presence of recent pain were recorded for each child, and the association between the first test measure of posture angles and these factors was assessed using linear regression and ANOVA models. Multiple ANOVA models were applied to analyse the effect of repeated testing, and significant predictors on the angles.

Results

Four of the five postural angles (trunk, neck, head on neck, lower limb) were significantly influenced by age. As age was strongly associated with height (r2 = 0.84) and moderately associated with weight and motor control (r2 = 0.67, 0.56 respectively), these developmental parameters may well explain the age effect on angles. There was no relationship between age and pain reported on either the testing day, or recently, and there was no gender influence on any angle. There was no significant effect of repeated testing on any angle (ICC>0.93). None of the hypothesized predictors were associated with differences in angles from repeated testing.

Conclusion

This study outlined the variability of relaxed upright standing posture of children aged 5–12 years, when measured twice in an hour. Age influenced the size of the angles but not the variability. While the subject numbers in this study are small, the findings provide useful information on which further studies in posture and its development in pre-adolescent children can be based.
Genetic diversity in populations of asexual and sexual bag worm moths (Lepidoptera: Psychidae)
Authors: Grapputo Alessandro , Kumpulainen Tomi , Mappes Johanna , Parri Silja
Published: June 2005

Background

Despite the two-fold cost of sex, most of the higher animals reproduce sexually. The advantage of sex has been suggested to be its ability, through recombination, to generate greater genetic diversity than asexuality, thus enhancing adaptation in a changing environment. We studied the genetic diversity and the population structure of three closely related species of bag worm moths: two strictly sexual (Dahlica charlottae and Siederia rupicolella) and one strictly asexual (D. fennicella). These species compete for the same resources and share the same parasitoids.

Results

Allelic richness was comparable between the sexual species but it was higher than in the asexual species. All species showed high heterozygote deficiency and a large variation was observed among FIS values across loci and populations. Large genetic differentiation was observed between populations confirming the poor dispersal ability of these species. The asexual species showed lower genotype diversity than the sexual species. Nevertheless, genotype diversity was high in all asexual populations.

Conclusion

The three different species show a similar population structure characterised by high genetic differentiation among populations and low dispersal. Most of the populations showed high heterozygote deficiency likely due to the presence of null alleles at most of the loci and/or to the Wahlund effect. Although the parthenogenetic D. fennicella shows reduced genetic diversity compared to the sexual species, it still shows surprisingly high genotype diversity. While we can not totally rule out the presence of cryptic sex, would explain this high genotype diversity, we never observed sex in the parthenogenetic D. fennicella, nor was there any other evidence of this. Alternatively, a non-clonal parthenogenetic reproduction, such as automictic thelytoky, could explain the high genotypic diversity observed in D. fennicella.
Safe storage of methadone in the home - an audit of the effectiveness of safety information giving
Authors: Bloor Roger N , McAuley Rosanna , Smalldridge Norman
Published: June 2005

Background

Accidental poisoning by methadone occurs, particularly as a result of children ingesting a parent's methadone. Health care professionals have a responsibility to provide information and guidance to methadone users on safe storage of methadone. The objective of the study was to audit the effectiveness of information giving on the safety of methadone consumption, dose measurement and storage, and the effectiveness of sources of advice available for patients.

Methods

The study was undertaken prior to the introduction of a scheme for the supervised consumption of methadone, in the setting of an NHS Methadone clinic serving a district population of 490,000 in the UK. 185 consecutive patients attending a methadone clinic to collect a methadone prescription were the subject of an anonymous survey. Issues of safety of methadone consumption, storage and safety information provisions were assessed. A telephone survey of the community pharmacists dispensing the methadone covered the availability of measuring devices and provision of advice on safety was undertaken.

Results

Methadone was stored in a variety of locations, a cupboard being most frequent. 95 patients (60.1%) had children either living in or visiting their home. All stored their methadone in a bottle with a child resistant lid; the majority measured doses using either the container supplied by the pharmacist or a plastic measure. 126 patients (78%) confirmed that a pharmacist provided a measuring container on their first visit, 24 (15%) were given a measure on every visit to the pharmacist. Advice on safe storage was recalled by 30% of the patients, and advice on measuring methadone by 28%. Methadone was seen as potentially dangerous by 82% of the patients.

Conclusion

The risks resulting from unsafe storage of methadone may be reduced by daily instalment prescribing and provision of measuring containers on request. Recall of provision of information on safety issues is poor and the adoption of a standard policy on provision information should be seen as a priority. A re-audit of safety of storage of methadone is recommended following the introduction of a standard policy on information provision.
Role of viral evolutionary rate in HIV-1 disease progression in a linked cohort
Authors: Mikhail Meriet , Wang Bin , Lemey Philippe , Beckthold Brenda , Vandamme Anne-Mieke , Gill M John , Saksena Nitin K
Published: June 2005

Background

The actual relationship between viral variability and HIV disease progression and/or non-progression can only be extrapolated through epidemiologically-linked HIV-infected cohorts. The rarity of such cohorts accents their existence as invaluable human models for a clear understanding of molecular factors that may contribute to the various rates of HIV disease. We present here a cohort of three patients with the source termed donor A – a non-progressor and two recipients called B and C. Both recipients gradually progressed to HIV disease and patient C has died of AIDS recently. By conducting 15 near full-length genome (8.7 kb) analysis from longitudinally derived patient PBMC samples enabled us to investigate the extent of molecular factors, which govern HIV disease progression.

Results

Four time points were successfully amplified for patient A, 4 for patient B and 7 from patient C. Using phylogenetic analysis our data confirms the epidemiological-linkage and transmission of HIV-1 from a non-progressor to two recipients. Following transmission the two recipients gradually progressed to AIDS and one died of AIDS. Viral divergence, selective pressures, recombination, and evolutionary rates of HIV-1 in each member of the cohort were investigated over time. Genetic recombination and selective pressure was evident in the entire cohort. However, there was a striking correlation between evolutionary rate and disease progression.

Conclusion

Non-progressing individuals have the potential to transmit pathogenic variants, which in other host can lead to faster HIV disease progression. This was evident from our study and the accelerated disease progression in the recipient members of he cohort correlated with faster evolutionary rate of HIV-1, which is a unique aspect of this study.
The mitochondrial protein MTP18 contributes to mitochondrial fission in mammalian cells
Authors: Tondera Daniel , Czauderna Frank , Paulick Katharina , Schwarzer Rolf , Kaufmann Jörg , Santel Ansgar
Published: June 2005

Mitochondria are dynamic organelles that change morphology by controlled fission and fusion events. Mitochondrial fission is regulated by a conserved protein complex assembled at the outer membrane. Human MTP18 is a novel nuclear-encoded mitochondrial membrane protein, implicated in controlling mitochondrial fission. Upon overexpression of MTP18, mitochondrial morphology was altered from filamentous to punctate structures suggesting excessive mitochondrial fission. Mitochondrial fragmentation was blocked in cells coexpressing either the mitochondrial fusion protein Mfn1 or Drp1K38A, a dominant negative version of the fission protein Drp1. Also, a loss-of function of endogenous MTP18 by RNA interference (RNAi) resulted in highly fused mitochondria. Moreover, MTP18 appears to be required for mitochondrial fission because it is blocked after overexpression of hFis1 in cells with RNAi-mediated MTP18 knockdown. In conclusion, we propose that MTP18 functions as an essential intramitochondrial component of the mitochondrial division apparatus, contributing to the maintenance of mitochondrial morphology.
Cell-cycle-dependent resistance toBacillus thuringiensisCry1C toxin in Sf9 cells
Authors: Avisar Dror , Segal Michal , Sneh Baruch , Zilberstein Aviah
Published: June 2005

The Sf9 cell line, derived from the moth Spodoptera frugiperda, is highly and specifically sensitive to the Bacillus thuringiensis Cry1C toxin. Upon exposure to Cry1C, ionic pores are formed in the plasma membrane leading to cell swelling and death. Here, we describe a unique transient tolerance to Cry1C of dividing cells, which allowed completion of the division process in the presence of Cry1C. Correlatively, arresting the cells at G2-M phase by nocodazole treatment rendered them insensitive to Cry1C. When the arresting agent was removed, the cells completed their division and gradually regained Cry1C sensitivity. In comparison to normal cells with 1-2% cell-division frequency, the M-phase arrested cells bound less toxin in binding assays. Moreover, no lipid rafts could be isolated from the membranes of M-phase arrested cells. Caveolin-1, identified here for the first time in insect cells, was immunodetected as a lipid raft component of normal cells, but was only present in the membrane-soluble fraction of G2-M-arrested cells. Thus M-phase-linked changes in lipid raft organization may account for diminished Cry1C binding and toxicity. Furthermore, considering the pivotal role of lipid rafts in different cell functions of many cell types, the lack of organized lipid rafts in dividing cells may transiently affect cell susceptibility to pathogens, toxins and other lipid raft-linked functions.
Mutational analysis of action of mitochondrial fusion factor mitofusin-2
Authors: Honda Shinji , Aihara Takeshi , Hontani Masayasu , Okubo Katsuhiko , Hirose Shigehisa
Published: June 2005

Mitofusin-2 (Mfn2) is an essential component of mitochondrial fusion machinery, but its molecular mechanism of action is not clear. We found that a Mfn2 deletion mutant lacking two transmembrane spans (MfnΔTM) acts as a dominant-negative mutant and blocks mitochondrial fusion. Furthermore, detailed analysis of various mutants of MfnΔTM revealed that GTPase activity and four regions highly conserved from nematodes to mammals are necessary for the dominant-negative effect. Immunoprecipitation studies of the N- and C-terminal cytosolic tails of Mfn2 showed that in addition to the coiled-coil domains previously identified, a highly conserved domain in the most N-terminal region and GTPase activity are necessary for the interaction between the N- and C-terminal tails, which is in turn required for the dominant-negative effect. In addition, we found unexpectedly that overexpression of the deletion mutant composed of one short region each in the N- and C-terminal tails of Mfn2 resulted in loss of mitochondrial membrane potential, suggesting that Mfn2 might also be connected to maintenance of mitochondrial membrane potential.
Non-canonical YXXGΦ endocytic motifs: recognition by AP2 and preferential utilization in P2X4 receptors
Authors: Royle Stephen J. , Qureshi Omar S. , Bobanović Laura K. , Evans Philip R. , Owen David J. , Murrell-Lagnado Ruth D.
Published: June 2005

During clathrin-mediated endocytosis, proteins on the cell surface are selected for inclusion in clathrin-coated vesicles by clathrin adaptors, mainly the adaptor complex AP2. The P2X4 subtype of ATP-gated ion channel has in its C-terminus two putative endocytic motifs: a canonical YXXΦ motif and a non-canonical YXXGΦ motif (YEQGL). We demonstrate that endocytosis of P2X4 receptors is mediated preferentially by the YXXGΦ motif because the YXXΦ motif is inaccessible to AP2 owing to the structure of the channel. The crystal structure of a complex between residues 160-435 of the μ2 subunit of AP2 and a P2X4 C-terminal peptide showed that the YEQGL motif binds to μ2 at the same site as YXXΦ motifs. Y and Φ residues are accommodated in the same hydrophobic pockets in μ2 with the extra residue between them being accommodated by changes in the peptide's backbone configuration, when compared to YXXΦ motifs. These data demonstrate that the family of potential tyrosine-based endocytic signals must be expanded to include motifs with an additional glycine at Y+3 (YXXGΦ).
The Cm56 tRNA modification in archaea is catalyzed either by a specific 2′-O-methylase, or a C/D sRNP
Authors: RENALIER MARIE-HÉLÈNE , JOSEPH NICOLE , GASPIN CHRISTINE , THEBAULT PATRICIA , MOUGIN ANNIE
Published: June 2005

We identified the first archaeal tRNA ribose 2′-O-methylase, aTrm56, belonging to the Cluster of Orthologous Groups (COG) 1303 that contains archaeal genes only. The corresponding protein exhibits a SPOUT S-adenosylmethionine (AdoMet)-dependent methyltransferase domain found in bacterial and yeast G18 tRNA 2′-O-methylases (SpoU, Trm3). We cloned the Pyrococcus abyssi PAB1040 gene belonging to this COG, expressed and purified the corresponding protein, and showed that in vitro, it specifically catalyzes the AdoMet-dependent 2′-O-ribose methylation of C at position 56 in tRNA transcripts. This tRNA methylation is present only in archaea, and the gene for this enzyme is present in all the archaeal genomes sequenced up to now, except in the crenarchaeon Pyrobaculum aerophilum. In this archaea, the C56 2′-O-methylation is provided by a C/D sRNP. Our work is the first demonstration that, within the same kingdom, two different mechanisms are used to modify the same nucleoside in tRNAs.
A potential link between transgene silencing and poly(A) tails
Authors: SIOMI MIKIKO C. , TSUKUMO HIROKO , ISHIZUKA AKIRA , NAGAMI TOMOKO , SIOMI HARUHIKO
Published: June 2005

Argonaute proteins function in gene silencing induced by double-stranded RNA (dsRNA) in various organisms. In Drosophila, the Argonaute proteins AGO1 and AGO2 have been implicated in post-transcriptional gene-silencing (PTGS)/RNA interference (RNAi). In this study, we found that AGO1 and AGO2 depletion caused the accumulation of multicopied enhanced green fluorescence protein (EGFP) transgene transcripts in Drosophila S2 cells. Depletion of AGO1, the essential factor for miRNA biogenesis, led to an increased transcriptional rate of the transgenes. In contrast, depletion of AGO2, the essential factor for siRNA-directed RNAi, resulted in EGFP mRNA stabilization with concomitant shortening of the EGFP mRNA poly(A) tail. Our findings suggest that AGO1 and AGO2 mediate multicopied transgene silencing by different mechanisms. Intriguingly, Dicer2 depletion phenocopies AGO2 depletion, with an increase in EGFP protein levels and shortening of the EGFP mRNA poly(A) tail. The possibility that AGO2 and Dicer2 involve, at least in part, poly(A) length maintenance of transgene mRNA suggests a potentially important link between transgene silencing and poly(A) tails.
Evolutionary conservation of minor U12-type spliceosome between plants and humans
Authors: LORKOVIĆ ZDRAVKO J. , LEHNER REINHARD , FORSTNER CHRISTINA , BARTA ANDREA
Published: June 2005

Splicing of rare, U12-type or AT-AC introns is mediated by a distinct spliceosome that assembles from U11, U12, U4atac, U6atac, and U5 snRNPs. Although in human cells the protein composition of minor and major snRNPs is similar, differences, particularly in U11 and U12 snRNPs, have been recently described. We have identified an Arabidopsis U11 snRNP-specific 35K protein as an interacting partner of an RS-domain-containing cyclophilin. By using a transient expression system in Arabidopsis protoplasts, we show that the 35K protein incorporates into snRNP. Oligo affinity selection and glycerol gradient centrifugation revealed that the Arabidopsis 35K protein is present in monomeric U11 snRNP and in U11/U12-di snRNP. The interaction of the 35K protein with Arabidopsis SR proteins together with its strong sequence similarity to U1–70K suggests that its function in splicing of minor introns is analogous to that of U1–70K. Analysis of Arabidopsis and Oryza sativa genome sequences revealed that all U11/U12-di-snRNP-specific proteins are conserved in dicot and monocot plants. In addition, we have identified an Arabidopsis gene encoding the homolog of U4atac snRNA and a second Arabidopsis gene encoding U6atac snRNA. Secondary structure predictions indicate that the Arabidopsis U4atac is able to form dimeric complexes with both Arabidopsis U6atac snRNAs. As revealed by RNaseA/T1 protection assay, the U4atac snRNA gene is expressed as an ~160-nt RNA, whereas the second U6atac snRNA gene seems to be a pseudogene. Taken together, our data indicate that recognition and splicing of minor, AT-AC introns in plants is highly similar to that in humans.
The positional, structural, and sequence requirements of theDrosophilaTLS RNA localization element
Authors: COHEN ROBERT S. , ZHANG SUI , DOLLAR GRETCHEN L.
Published: June 2005

The subcellular localization of mRNAs is a key step in the polarization of cells in organisms from yeast to man. Here, we use a transgenic fly/in situ hybridization assay system to define the positional, structural, and sequence requirements of the TLS, a stem loop RNA sequence element that mediates the subcellular localization ofK10andOrbtranscripts inDrosophilaoocytes. We find that the TLS is a highly robust and modular element. It mediates efficient RNA localization regardless of sequence context or position within the transcript. Site-specific mutagenesis experiments indicate that the size and shape of the stem and loop regions are critical determinants of TLS activity. Such experiments also identify specific base residues that are important for TLS activity. All such residues map to the stem portion of the structure. Significantly, mutations at these residues interfere with TLS activity only when they alter the stereochemistry of the stem’s minor groove. For example, mutation of the A:U base pair at position 3 of the TLS stem to G:C severely reduces TLS activity, while mutation of the same base pair to U:A has no effect. Extensive searches for TLS-like elements in otherDrosophilamRNAs using sequence and structural parameters defined by our experiments indicate that the TLS is unique toK10andOrbmRNAs. This unexpected finding raises important questions as to how the many hundreds of other mRNAs that are known or thought to exhibitK10andOrb-like localization are localized.
The stem–loop binding protein stimulates histone translation at an early step in the initiation pathway
Authors: GORGONI BARBARA , ANDREWS STUART , SCHALLER ANDRÉ , SCHÜMPERLI DANIEL , GRAY NICOLA K. , MÜLLER BERNDT
Published: June 2005

Metazoan replication-dependent histone mRNAs do not have a poly(A) tail but end instead in a conserved stem–loop structure. Efficient translation of these mRNAs is dependent on the stem–loop binding protein (SLBP). Here we explore the mechanism by which SLBP stimulates translation in vertebrate cells, using the tethered function assay and analyzing protein–protein interactions. We show for the first time that translational stimulation by SLBP increases during oocyte maturation and that SLBP stimulates translation at the level of initiation. We demonstrate that SLBP can interact directly with subunit h of eIF3 and with Paip1; however, neither of these interactions is sufficient to mediate its effects on translation. We find that Xenopus SLBP1 functions primarily at an early stage in the cap-dependent initiation pathway, targeting small ribosomal subunit recruitment. Analysis of IRES-driven translation in Xenopus oocytes suggests that SLBP activity requires eIF4E. We propose a model in which a novel factor contacts eIF4E bound to the 5′ cap and SLBP bound to the 3′ end simultaneously, mediating formation of an alternative end-to-end complex.
Effect of Prophylactic Amiodarone on Clinical and Economic Outcomes After Cardiothoracic Surgery: A Meta-Analysis
Authors: Gillespie Effie L , Coleman Craig I , Sander Stephen , Kluger Jeffrey , Gryskiewicz Kristen A , White C Michael
Published: June 2005

BACKGROUND:

Two previous meta-analyses of amiodarone for prevention of postoperative atrial fibrillation (POAF) after cardiothoracic surgery did not evaluate total hospital cost, concluded that data on stroke are incomplete, and did not evaluate the effect of clinical heterogeneity between trials.

OBJECTIVE:

To conduct a meta-analysis examining amiodarone's prophylactic impact on cardiothoracic surgery POAF, length of stay (LOS), stroke, and total costs.

METHODS:

Three reviewers conducted a systematic literature search of MEDLINE, EMBASE, CINAHL, and the Cochrane Library (1966–September 2004%). Studies were included if they met the following criteria: (1%) randomized controlled trial versus placebo/routine treatment, (2%) coronary artery bypass graft and/or valvular surgery, (3%) Jadad score ≥3, (4%) reported data on incidence of POAF or stroke, LOS, or total costs, (5%) used electrocardiographic/Holter monitoring, and (6%) monitored subjects for ≥2 days. A random-effects model was utilized. Subgroup and sensitivity analyses were conducted.

RESULTS:

Fifteen trials were identified, including 1512 and 1429 patients in the amiodarone and control groups, respectively. Amiodarone reduced POAF (OR 0.50; 95% CI 0.42 to 0.60%) and decreased stroke (n = 8 studies), LOS (n = 10%), and total costs (n = 6%) (OR 0.47; 95% CI 0.23 to 0.96; −0.73 days, 95% CI −0.95 to −0.51; and –$1619, 95% CI −3395 to 156, respectively). Surgery type, β-blocker use, route of administration, use of a fixed-effects model, or exclusion of unblinded/unpublished studies did not affect the overall results. No statistical heterogeneity was observed for any endpoint evaluated (p > 0.22 for all comparisons).

CONCLUSIONS:

Prophylactic treatment with amiodarone decreases patients' risk of POAF and stroke while reducing LOS.