bluuebunny/crossref_metadata_2025_split huggingface dataset:
The eastern Baltic cod fishery: a fleet-based management strategy evaluation framework to assess the cod recovery plan of 2008
Authors: Bastardie Francois , Nielsen J. Rasmus , Kraus Gerd 
Published: September 2009

Abstract
Bastardie, F., Nielsen, J. R., and Kraus, G. 2010. The eastern Baltic cod fishery: a fleet-based management strategy evaluation framework to assess the cod recovery plan of 2008. – ICES Journal of Marine Science, 67: 71–86. A management strategy evaluation framework was developed for the international Baltic cod fishery to evaluate the performance and robustness of the 2008 multi-annual management plan for the eastern stock. The spatially explicit management evaluation covered two cod recruitment regimes and various fleet adaptation scenarios. The tested management options included total allowable catch control, direct effort control, and closed areas and seasons. The modelled fleet responded to management by misreporting, improving catching power, adapting capacity, and reallocating fishing effort. The model was calibrated with spatially and temporally disaggregated landings and effort data from five countries covering 83% of the total cod catches. The simulations revealed that the management plan is robust and likely to rebuild the stock in the medium term even under low recruitment. Direct effort reduction limited underreporting of catches, but the overall effect was impaired by the increased catching power or spatio-temporal effort reallocation. Closures had a positive effect, protecting part of the population from being caught, but the effect was impaired if there was seasonal effort reallocation. Over the entire 15-year simulation period, all fleets could realize variable but positive profits under all scenarios tested, owing to stock recovery.
Biochemical Characterization of AtRECQ3 Reveals Significant Differences Relative to Other RecQ Helicases
Authors: Kobbe Daniela , Blanck Sandra , Focke Manfred , Puchta Holger 
Published: September 2009

AbstractMembers of the conserved RecQ helicase family are important for the preservation of genomic stability. Multiple RecQ homologs within one organism raise the question of functional specialization. Whereas five different homologs are present in humans, the model plant Arabidopsis (Arabidopsis thaliana) carries seven RecQ homologs in its genome. We performed biochemical analysis of AtRECQ3, expanded upon a previous analysis of AtRECQ2, and compared their properties. Both proteins differ in their domain composition. Our analysis demonstrates that they are 3′ to 5′ helicases with similar activities on partial duplex DNA. However, they promote different outcomes with synthetic DNA structures that mimic Holliday junctions or a replication fork. AtRECQ2 catalyzes Holliday junction branch migration and replication fork regression, while AtRECQ3 cannot act on intact Holliday junctions. The observed reaction of AtRECQ3 on the replication fork is in line with unwinding the lagging strand. On nicked Holliday junctions, which have not been intensively studied with RecQ helicases before, AtRECQ3, but not AtRECQ2, shows a clear preference for one unwinding mechanism. In addition, AtRECQ3 is much more efficient at catalyzing DNA strand annealing. Thus, AtRECQ2 and AtRECQ3 are likely to perform different tasks in the cell, and AtRECQ3 differs in its biochemical properties from all other eukaryotic RECQ helicases characterized so far.
A Single Amino Acid Change in the Enhancer of Zeste Ortholog CURLY LEAF Results in Vernalization-Independent, Rapid Flowering in Arabidopsis
Authors: Doyle Mark R. , Amasino Richard M. 
Published: September 2009

AbstractMany strains of Arabidopsis (Arabidopsis thaliana) require exposure to prolonged cold for rapid flowering, a process known as vernalization. Vernalization in Arabidopsis results in the suppression of FLOWERING LOCUS C (FLC), a repressor of flowering. In a screen for mutants that no longer require vernalization for rapid flowering, we identified a dominant allele of the Enhancer of Zeste E(z) ortholog CURLY LEAF (CLF), clf-59. CLF is a Polycomb Group gene, and the clf-59 mutant protein contains a proline-to-serine transition in a cysteine-rich region that precedes the SET domain. Mutant plants are early flowering and have reduced FLC expression, but, unlike clf loss-of-function mutants, clf-59 mutants do not display additional pleiotropic phenotypes. clf-59 mutants have elevated levels of trimethylation on lysine 27 of histone H3 (H3K27me3) at FLC. Thus, clf-59 appears to be a gain-of-function allele, and this allele represses FLC without some of the components required for vernalization-mediated repression. In the course of this work, we also identified a marked difference in H3K27me3 levels at FLC between plants that contain and those that lack the FRIGIDA (FRI) gene. Furthermore, FRI appears to affect CLF occupancy at FLC; thus, our work provides insight into the molecular role that FRI plays in delaying the onset of flowering.
High‐resolution wide‐field microscopy with adaptive optics for spherical aberration correction and motionless focusing
Authors: KNER P. , SEDAT J.W. , AGARD D.A. , KAM Z. 
Published: September 2009

SummaryLive imaging in cell biology requires three‐dimensional data acquisition with the best resolution and signal‐to‐noise ratio possible. Depth aberrations are a major source of image degradation in three‐dimensional microscopy, causing a significant loss of resolution and intensity deep into the sample. These aberrations occur because of the mismatch between the sample refractive index and the immersion medium index. We have built a wide‐field fluorescence microscope that incorporates a large‐throw deformable mirror to simultaneously focus and correct for depth aberration in three‐dimensional imaging. Imaging fluorescent beads in water and glycerol with an oil immersion lens we demonstrate a corrected point spread function and a 2‐fold improvement in signal intensity. We apply this new microscope to imaging biological samples, and show sharper images and improved deconvolution.
Phytoplankton and ecological assessment of brackish and freshwater coastal lagoons in the Algarve, Portugal
Authors: Cartaxana Paulo , Mendes Carlos R. , Brotas Vanda 
Published: September 2009

AbstractPhytoplankton biomass and composition were monitored for four coastal lagoons of the Algarve, Portugal, from February to November 2006. The phytoplankton community in the freshwater lagoons – Dunas Douradas (FW1) and Garrão (FW2) – as determined by biomarker pigment concentration using high‐performance liquid chromatography and the program chemtax, was dominated by diatoms and chlorophytes. For the brackish lagoons – Salgados (BW1) and Almargem (BW2) – cyanophytes and diatoms were the most important groups respectively. The trophic state indices, based on algal biomass, classify FW1, FW2 and BW1 lagoons as hypertrophic, whereas BW2 is classified as mesotrophic. Signs of eutrophication in the former lagoons include large phytoplankton biomass (chlorophyll‐a) fluctuations, the presence of phytoplankton taxa that usually thrive under nutrient‐enriched conditions and high concentrations of chlorophyll‐a‐degradation products. Chemotaxonomic analyses derived from high‐performance liquid chromatography data might constitute a valuable tool for achieving Water Framework Directive requirements for an evaluation system based on phytoplankton taxonomic composition.
Assessment of the impacts of a new artificial lake mouth on the hydrobiology and fisheries of Chilika Lake, India
Authors: Mohanty Rajeeb K. , Mohapatra Anil , Mohanty S. K. 
Published: September 2009

AbstractThe degraded state of the fragile ecosystem of Chilika Lake, located on the east coast of India, was undergoing restoration through an effective hydrological intervention during the year 2000. Studies on the lake’s hydrobiology and fisheries for the period of 7 years before and 7 years after the hydrological intervention indicated a rapid recovery of the lake fishery immediately after opening of the new lake mouth, with a sixfold increase in the average annual fish landings. During 2000–2001 to 2006–2007, the average fisheries output (11 051.3 t), catch per unit effort (6.2 kg boat−1 day−1), the economic valuation of the average annual catch (637 million rupees) and productivity (11.97 t km−2) exhibited dramatic increases of 498%, 464%, 1177% and 498.5%, respectively, compared with the 7‐year pre‐intervention data. Multivariate statistical analysis inferred that most of the lake’s environmental variables are strongly associated with salinity factor, which seems to have governed the lake ecology. The salinity dynamics of the lake are governed by both freshwater inflows and seawater ingress through the new artificial lake mouth. Correlation analysis indicated that salinity was positively correlated with prawn catch (R2 = 0.542; d.f. = 25; P < 0.01), crab catch (R2 = 0.628; d.f. = 25; P < 0.001) and fish catch (R2 = 0.476; d.f. = 25, P < 0.05). The average increase in the salinity regime (43.8%) for the lake during the post‐hydrological intervention period, compared with the pre‐hydrological intervention period, appears to have positively impacted the fish, prawn and mud crab catches. A gradual decrease in total fisheries output since 2005–2006, however, was attributed mainly to a continuing increase in destructive fishing practices in the absence of any conservation and regulatory measures for fishing, and large‐scale collection of shrimp juveniles from the outer channel for shrimp aquaculture. Thus, carefully planned conservation and regulation measures must be ensured, with active participation of local communities during this early phase of lake restoration. In the absence of such measures, the present scenario of fisheries enhancement might not be sustained over the long term.
Serum trace element levels in COPD patient: The relation between trace element supplementation and period of mechanical ventilation in a randomized controlled trial
Authors: EL‐ATTAR May , SAID Mohamed , EL‐ASSAL Gehan , SABRY Nirmeen A. , OMAR Emad , ASHOUR Laila 
Published: September 2009

ABSTRACTBackground and objective:  Many trace elements play important roles in activating or inhibiting enzymatic reactions, by competing with other elements and metalloproteins for binding sites, by affecting the permeability of cell membranes and by other mechanisms. They play important roles in the oxidant/antioxidant balance. As such, trace elements are thought to be involved directly or indirectly in the pathogenesis of several diseases. The aim of the present study is to investigate the effect trace elements (Se, Mn and Zn) intravenously administered on the period the COPD patients spend on mechanical ventilation.Methods:  In a randomized double‐blinded controlled trial a set of 120 subjects (40 normal volunteers and 80 COPD) were recruited. Serum concentration levels of Se, Mn and Zn were determined for all enrolled subjects with Inductively Coupled Plasma spectroscopy. COPD patients received intravenous supplementation of the above trace elements and the period the patients spent on mechanical ventilation was determined.Results:  There was a significant reduction (P = 0.013) in the period the patients with COPD spent on the mechanical ventilation when received intravenous supplementation (9.4 ± 7.3 days) compared with the COPD patients who received placebo (17.8 ± 7.6 days).Conclusions:  Trace element (Se, Mn and Zn) status is altered in critically ill patients with COPD. The supplementation achieved a reduction in the period those patients spent on the mechanical ventilation. A larger multi‐centre trial is required to confirm this preventive effect and to explore its applicability to other critical care conditions.
Impact of massage therapy on motor outcomes in very low‐birthweight infants: Randomized controlled pilot study
Authors: Ho Yuen‐Bing , Lee Robert S.Y. , Chow Chun‐Bong , Pang Marco Y.C. 
Published: September 2009

AbstractBackground:  The purpose of the present study was to determine the effects of massage therapy on motor development, weight gain, and hospital discharge in preterm very low‐birthweight (VLBW) newborns.Methods:  Twenty‐four preterm VLBW newborns (<34 weeks and <1500 g) were enrolled in this randomized controlled pilot study. The intervention group (n = 12) received massage therapy starting at 34 weeks post‐conceptional age (15 min daily, 5 days/week for 4 weeks). The infants in the sham treatment group (n = 12) received similar duration of light still touch. Test of Infant Motor Performance (TIMP) score gain, weight gain, and post‐conceptional age at discharge were compared between the two groups after intervention using Mann–Whitney U‐test.Results:  No significant between‐group difference in TIMP score gain and weight gain was identified when all subjects were analyzed. In subgroup analysis, among those with below‐average pre‐treatment TIMP score (<35), the intervention group (n = 6) achieved significantly higher TIMP score gain (P = 0.043) and earlier hospital discharge (P = 0.045) than the sham treatment group (n = 5). These same infants, however, also had significantly shorter duration of total parenteral nutrition than their counterparts in the sham treatment group (P = 0.044).Conclusions:  Massage therapy might be a viable intervention to promote motor outcomes in a subgroup of VLBW newborns with poor motor performance. A larger randomized controlled trial is required to further explore the effects of massage therapy in this high‐risk group.
Biorthogonal Wavelets Based on Interpolatory  Subdivision
Authors: Wang H. , Ma W. 
Published: September 2009

AbstractThis article presents an efficient construction of biorthogonal wavelets built upon an interpolatory  subdivision for quadrilateral meshes. The interpolatory subdivision scheme is first turned into a scheme for reversible primitive wavelet synthesis. Some desired properties are then incorporated in the primitive wavelet using the lifting scheme. The analysis and synthesis algorithms of the resulting new wavelet are finally obtained as local and in‐place lifting operations. The wavelet inherits the advantage of  refinement with added levels of resolution. Numerical experiments show that the lifted wavelet built upon interpolatory  subdivision has sufficient stability and better performance in dealing with closed or open semi‐regular quadrilateral meshes compared with other existing wavelets for quadrilateral manifold meshes.
Are the cognitive functions of children with Down syndrome related to their participation?
Authors: RIHTMAN TANYA , TEKUZENER ESTI , PARUSH SHULA , TENENBAUM ALEX , BACHRACH STEVEN J , ORNOY ASHER 
Published: September 2009

Aim  There is a lack of investigation into the functional developmental profile of children with Down syndrome. On the basis of current international health paradigms, the purpose of this study was to assess the developmental profile of these children.Method  Sixty children (33 males, 27 females) with Down syndrome (age range 6–16y; mean age 9y 3mo, SD 28.8mo), who had received standard, holistic, early intervention, were assessed. Of these, 42 (70%) had congenital anomalies, 12 had severe congenital heart defects. Participants were assessed on measures of cognitive function (Beery–Buktenica Developmental Test of Visual–Motor Integration; Stanford–Binet Intelligence Scale) and participation (Vineland Adaptive Behaviour Scales).Results  No difference was found on any measure on the basis of severity of congenital anomaly. Results showed improvements in age‐related body function and correlations between specific body functions and participation. No decline in IQ was found with age, and significant correlations between IQ and all other measures were noted. Although sex differences were found in the body functions of short‐term memory and motor function, no difference in measures of activity performance and participation was found.Interpretation  Our findings emphasize the need for paediatric Down syndrome intervention to encourage improved body functions while emphasizing the acquisition of functional skills that enable enhanced participation in age‐appropriate activities.
Intensive speech and language therapy for older children with cerebral palsy: a systems approach
Authors: PENNINGTON LINDSAY , MILLER NICK , ROBSON SHEILA , STEEN NICK 
Published: September 2009

Aim To investigate whether speech therapy using a speech systems approach to controlling breath support, phonation, and speech rate can increase the speech intelligibility of children with dysarthria and cerebral palsy (CP).Method Sixteen children with dysarthria and CP participated in a modified time series design. Group characteristics were as follows: seven males, nine females; age range 12 to 18 years (mean 14y, SD 2); CP type: nine spastic, two dyskinetic, four mixed, one Worster–Drought; Gross Motor Function Classification System levels range I to V (median IV). Children received three 30‐ to 45‐minute sessions of individual therapy per week for 6 weeks. Intelligibility in single words and connected speech was compared across four points: 1 week and 6 weeks before therapy, and 1 week and 6 weeks after its completion. Three familiar listeners and three unfamiliar listeners scored each recording. Mean percentage intelligibility was compared using general linear modelling techniques.Results After treatment, familiar listeners understood 14.7% more single words and 12.1% more words in connected speech. Unfamiliar listeners understood 15% more single words and 15.9% more words in connected speech after therapy.Interpretation Therapy was associated with increases in speech intelligibility. Effects of the therapy should be investigated further, in an exploratory trial with younger children and in a randomized controlled trial.
Clinical, functional, and neurophysiologic assessment of dysplastic cortical networks: Implications for cortical functioning and surgical management
Authors: Duchowny Michael 
Published: September 2009

SummaryCortical malformations are highly epileptogenic lesions associated with complex, unanticipated, and often aberrant electrophysiologic and functional relationships. These relationships are inextricably linked to widespread cortical networks subserving eloquent functions, particularly language and motor ability. Cytomegalic neurons but not balloon cells in Palmini type 2 dysplastic cortex are intrinsically hyperexcitable and contribute to local epileptogenesis and functional responsiveness. However, there is much evidence that focal cortical dysplasia is rarely a localized or even regional process, and is a functionally, electrophysiologically, and ultimately clinically integrated neural network disorder. Not surprisingly, malformed cortex is implicated in cognitive dysfunction, particularly disturbances of linguistic processing. An understanding of these relationships is critical for successful epilepsy surgery. Gains in surgical prognosis rely on multiple diagnostic modalities to delineate complex anatomic, electrophysiologic, and functional relationships in magnetic resonance imaging (MRI)–negative patients with rates of seizure‐freedom roughly comparable to lesional patients
Expensive blood safety initiatives may offer less benefit than we think
Authors: Kamper‐Jørgensen Mads , Hjalgrim Henrik , Edgren Gustaf , Titlestad Kjell , Ullum Henrik , Shanwell Agneta , Reilly Marie , Melbye Mads , Nyrén Olof , Rostgaard Klaus 
Published: September 2009

BACKGROUND: Various blood safety initiatives have ensured a historically low risk of infection transmission through blood transfusion. Although further prevention of infection transmission is possible through, for example, nucleic acid testing and future introduction of pathogen inactivation, such initiatives are very costly in relation to the benefit they offer. Although estimation of the cost‐effectiveness requires detailed information about the survival of transfusion recipients, previous cost‐effectiveness analyses have relied on incorrect survival assumptions.STUDY DESIGN AND METHODS: Based on empirical data of more than 1 million Scandinavian transfusion recipients followed for up to 20 years, we present two new survival functions. In a fictitious example we assessed the impact of survival assumptions on the estimated costs per quality‐adjusted life‐year (QALY) gained, by using the survival functions of three previous cost‐effectiveness analyses along with the two new survival functions.CONCLUSIONS: We conclude that despite considerable costs, previous cost‐effectiveness studies may have underestimated the costs per QALY gained by as much as 44%.
Bioreactance: A new tool for cardiac output and thoracic fluid content monitoring during hemodialysis
Authors: KOSSARI Niloufar , HUFNAGEL Gilles , SQUARA Pierre 
Published: September 2009

AbstractOutpatient hemodialysis therapy (HD) can be associated with hemodynamic compromise. Bioreactance® has recently been shown to provide accurate, noninvasive, continuous, measurements of cardiac output (CO) and thoracic impedance (Zo) from which thoracic fluid content (TFC) can be derived assuming TFC=1000/Zo. This study was designed to evaluate the changes in TFC in comparison with the traditional indices of fluid removal (FR) and to understand the trends in CO changes in HD patients. Minute‐by‐minute changes in TFC and CO were prospectively collected using the bioreactance system (NICOM®) in HD patients of a single unit. Changes in body weight (ΔW), hematocrit (ΔHct), and amount of FR were also measured. Twenty‐five patients (age 77 ± 11 years) were included. The TFC decreased in all patients by an average of 5.4 ± 7.9 kΩ−1, weight decreased by 1.48 ± 0.98 kg, and FR averaged 2.07 ± 1.93 L over a 3‐ to 4‐hour HD session. There were good correlations between ΔTFC and ΔW (R=0.80, P<0.0001) and FR (R=0.85, P<0.0001). ΔHct (4.13 ± 3.42%) was poorly correlated with ΔTFC (R=0.35, P=0.12) and FR (R=0.40, P=0.07). The regression line between FR and TFC yielded FR=1.0024−0.1985TFC; thus, a 1 kΩ−1 change of Zo correlates with an ∼200 mL change in total body water. The change in CO (−0.52 ± 0.49 L/min m2) during HD did not correlate with FR (R=0.15, P=NS). Changes in TFC represented the monitored variable most closely related to FR. CO remained fairly constant in this stable patient cohort. Further studies in high‐risk patients are warranted to understand whether TFC and CO monitoring can improve HD session management.
Towards a proposal for assessment of blinding success in clinical trials: up‐to‐date review
Authors: Kolahi Jafar , Bang Heejung , Park Jongbae 
Published: September 2009

Abstract – The CONSORT statement recommended that investigators should clearly report which key trial persons were blinded to treatment allocation and test for the success of blinding. Clinical researchers, however, more often than not overlook the assessment of the success of blinding. The severe under‐reporting on the success of blinding may improve with awareness of existing quantitative methods. The two statistical methods, James’ blinding index (BI) and Bang’s BI, are currently available. Subjects could be asked to guess their treatment assignment, possibly with an option to express the degree of certainty. Assessments of blinding at various points may serve different purposes, i.e. to evaluate comparability between experimental versus control treatments before the trial by the third party; to examine further comparability and credibility of the control treatment and patients’ expectation about treatment received in early stage of the trial, and to summarize the overall maintenance of the blinding success at the end of the trial. In this article, we review BIs and how to use these methods along with discussion of other issues in blinding assessment and reporting. We contend the two BIs that were independently developed but carry complementary properties would characterize blinding behaviours in clinical trials qualitatively as well as quantitatively, and may also shed some lights on the interpretation of the study findings. Finally we urge the Item 11b of the CONSORT statement to be revised to require the assessment/reporting of blinding success for all trials that adopt blinding schemes.