bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protonated Melonate Ca[HC6N7(NCN)3]·7H2O – Synthesis, Crystal Structure, and Thermal Properties
Authors: Makowski Sophia J. , Gunzelmann Daniel , Senker Jürgen , Schnick Wolfgang 
Published: July 2009

AbstractCalcium hydrogenmelonate heptahydrate Ca[HC6N7(NCN)3]·7H2O was obtained by metathesis reaction in aqueous solution. The structure of the molecular salt was elucidated by single‐crystal X‐ray diffraction. The crystal structure consists of alternating layers of planar monopronated melonate ions, Ca2+ and crystal water molecules. The anions of adjacent layers are staggered so that no π–π stacking occurs. The melonate entities are interconnected by hydrogen bonds within and between the layers. Ca[HC6N7(NCN)3]·7H2O was investigated by solid‐state NMR and FTIR spectroscopy, TG and DTA measurements.
Altered retinal cell differentiation in the AP‐3 delta mutant (Mocha) mouse
Authors: Baguma‐Nibasheka Mark , Kablar Boris 
Published: July 2009

AbstractAdaptor‐related protein complex 3 delta 1 (Ap3d1) encodes the delta 1 subunit of an adaptor protein regulating intracellular vesicle‐mediated transport, and the Ap3d‐deletion mutant (Mocha) mouse undergoes rapid photoreceptor degeneration leading to blindness soon after birth. Previous microarray analysis revealed Ap3d down‐regulation in the retina of mouse embryos specifically lacking cholinergic amacrine cells as a result of the absence of skeletal musculature. To investigate the role of Ap3d in the determination of retinal cell fate, the present study examined retinal morphology in newborn Ap3d−/− mice. The Ap3d−/− retina showed a complete absence of cholinergic amacrine cells and a decrease in parvalbumin‐expressing amacrine cells and syntaxin‐ and VC1.1‐expressing amacrine precursor cells, but had a normal number of cell layers and number of cells in each layer with no detectable difference in cell proliferation or apoptosis. These findings indicate that, despite having no apparent effect on the basic spatial organization of the retina at this stage of development, Ap3d could be involved in the regulation of progenitor cell competence and the eventual ratio of resulting differentiated cells. Finding the mouse mutant which phenocopies the eye defect seen in fetuses with no striated muscle was accomplished by the Systematic Subtractive Microarray Analysis Approach (SSMAA), explained in the discussion section.
Recent Technologies Usher in New Era of Coastal Geomorphology Research
Authors: Hanes Daniel M. 
Published: July 2009

Research in the field of coastal geomorphology has been energized by the development of two new complementary high‐spatial‐resolution technologies: swath bathymetry sonar systems (SBSSs), and process‐based numerical models (PBNMs) of hydrodynamics, sediment transport, and morphodynamics.The combination and integration of the two should lead to rapid expansion of scientific understanding of the genesis and evolution of morphology in coastal regions, the accretion and erosion of coastlines, and the effects of climate change on fluvial systems, estuaries, and coasts. For example, dredging shipping channels and harbors, protecting coastal property from erosion, evaluating risks due to coastal flooding, and other chronic and enduring societal problems can now be approached with new optimism due to the high spatial resolution of SBSSs and PBNMs.
The Unexpected Awakening of Chaitén Volcano, Chile
Authors: Carn Simon A. , Pallister John S. , Lara Luis , Ewert John W. , Watt Sebastian , Prata Alfred J. , Thomas Ronald J. , Villarosa Gustavo 
Published: July 2009

On 2 May 2008, a large eruption began unexpectedly at the inconspicuous Chaitén volcano in Chile's southern volcanic zone. Ash columns abruptly jetted from the volcano into the stratosphere, followed by lava dome effusion and continuous low‐altitude ash plumes [Lara, 2009]. Apocalyptic photographs of eruption plumes suffused with lightning were circulated globally.Effects of the eruption were extensive. Floods and lahars inundated the town of Chaitén, and its 4625 residents were evacuated. Widespread ashfall and drifting ash clouds closed regional airports and cancelled hundreds of domestic flights in Argentina and Chile and numerous international flights [Guffanti et al., 2008]. Ash heavily affected the aquaculture industry in the nearby Gulf of Corcovado, curtailed ecotourism, and closed regional nature preserves. To better prepare for future eruptions, the Chilean government has boosted support for monitoring and hazard mitigation at Chaitén and at 42 other highly hazardous, active volcanoes in Chile.
New Study Finds Increasing Gender Equity at U.S. Research Institutions
Authors: Showstack Randy 
Published: July 2009

Women and men faculty in science, engineering, and mathematics for the most part have comparable opportunities within major U.S. research universities, according to a report released 2 June by the U.S. National Research Council (NRC). The report found that gender does not appear to have been a factor in a number of important career transitions and outcomes, including hiring for tenure track and tenure positions and promotions.“That is probably going to be surprising to many people. It was surprising to our own panel. And it may not have been the case if we had done the study in 1985 instead of 2005,” said Claude Canizares, co‐chair of the NRC committee that prepared the report, entitled Gender Differences at Critical Transitions in the Careers of Science, Engineering and Mathematics Faculty.
The Eukaryote Genome Annotation Platform at Genoscope
Authors: Porcel Betina , Aniere Franck , Bonneval Sylvain , Noel Benjamin , Aury Jean-Marc , Da Silva Corinne , Jaillon Olivier , Denoeud France , Scarpelli Claude , Weissenbach Jean , Wincker Patrick , Artiguenave François 
Published: July 2009

AbstractThe Genoscope annotation workflow for eukaryote genomes relies on evidence from ab initio gene models predictions combined with homology searches, using collections of expressed sequences - full length cDNAs, ESTs or massive-scale mRNA sequences from the same or closely related organisms – proteins or other genomic sequences. Global analysis of these drafts or complete sequences are then combining both approaches in the form of gene prediction data integration using GAZE, capable to identify a majority of the existing gene features. Although of very good quality, gene-modelling remains still tentative at the end of the process. Even though computational predictors are useful on large scale annotation for global genomics analysis, there is no complete genome for which all gene structures, in terms of exons, introns and coding regions, have been experimentally confirmed.Finished genomes can provide exciting insights into the genome organization and evolution. Additional experimental data generated by genome sequencing projects give assistance to genome annotation aiming to a better understanding of the biology of the organism. Therefore, gene models and annotation can be improved by human curation to find errors or to resolve incongruous evidence on the automatic annotation of the genome. We now provide to collaborators carrying sequencing projects with a distributed annotation platform allowing expert evaluation of the annotation, in addition to our automated gene prediction pipeline.To ensure at most the participation of the scientific community, an annotation tool for revising annotations has been set up using components of the Generic Model Organism Database toolkit, which provides tools for managing organism databases. A CHADO database, linked to an Apollo graphical interface, permit users to correct gene structures and store them in a dedicated organism database, as we will show on a few examples. Such a tool would facilitate connecting and comparing predicted annotations with existing biological data, becoming the repository of complete annotated finished genome sequence.
Pyruvate dehydrogenase kinase isoenzyme 4 (PDHK4) deficiency attenuates the long-term negative effects of a high-saturated fat diet
Authors: Hwang Byounghoon , Jeoung Nam Ho , Harris Robert A. 
Published: July 2009

The hypothesis that PDHK4 (pyruvate dehydrogenase kinase isoenzyme 4) has potential as a target for the treatment of type 2 diabetes was tested by feeding wild-type and PDHK4 knockout mice a high saturated fat diet that induces hyperglycemia, hyperinsulinaemia, glucose intolerance, hepatic steatosis and obesity. Previous studies have shown that PDHK4 deficiency lowers blood glucose by limiting the supply of three carbon gluconeogenic substrates to the liver. There is concern, however, that the increase in glucose oxidation caused by less inhibition of the pyruvate dehydrogenase complex by phosphorylation will inhibit fatty acid oxidation, promote ectopic fat accumulation and worsen insulin sensitivity. This was examined by feeding wild-type and PDHK4 knockout mice a high saturated fat diet for 8 months. Fasting blood glucose levels increased gradually in both groups but remained significantly lower in the PDHK4 knockout mice. Hyperinsulinaemia developed in both groups, but glucose tolerance was better and body weight was lower in the PDHK4 knockout mice. At termination, less fat was present in the liver and skeletal muscle of the PDHK4 knockout mice. Higher amounts of PGC-1α [PPARγ (peroxisome proliferator-activated receptor γ) coactivator 1α] and PPARα and lower amounts of fatty acid synthase and acetyl-CoA carboxylase isoenzyme 1 were present in the liver of the PDHK4 knockout mice. These findings suggest PDHK4 deficiency creates conditions that alter upstream signalling components involved in the regulation of lipid metabolism. The findings support the hypothesis that PDHK4 is a viable target for the treatment of type 2 diabetes.
Community Outcomes of Mentally Disordered Homicide Offenders in Victoria
Authors: Ong Kevin , Carroll Andrew , Reid Shannon , Deacon Adam 
Published: July 2009

Objective: The aim of the present study was to describe characteristics and post-release outcomes of Victorian homicide offenders under the Crimes (Mental Impairment and Unfitness to be Tried) Act 1997 (and/or its forerunner legislation) released from forensic inpatient psychiatric care since the development of specialist forensic services. Method: A legal database identified subjects meeting inclusion criteria: hospitalized in forensic psychiatric care due to finding of mental impairment or unfitness to stand trial for homicide in Victoria; released into the community; and released between 1 January 1991 and 30 April 2002. Using clinical records, demographics, index offence, progress in hospital, diagnosis, psychosocial and criminological data were obtained. Outcomes (offending or readmission into secure care) were obtained from the clinical records. Results: Of the 25 subjects, 19 (76%) were male. Primary diagnoses on admission to forensic hospital care were schizophrenia, n = 16 (64%); other psychotic disorder, n = 5 (20%); depression, n = 3 (12%); and personality disorder, n = 1 (4%). Mean time in custodial supervision was 11 years and 2 months, less for those whose offence occurred after the development of forensic rehabilitation services. In the first 3 years after release, there was a single episode of criminal recidivism, representing a recidivism rate of 1 in 25 (4%) over 3 years. Twelve subjects (48%) were readmitted at some point in the 3 year follow up. Conclusion: There was a very low rate of recidivism after discharge, but readmissions to hospital were common. Lengths of custodial care were reduced after the introduction of forensic rehabilitation facilities. Recidivism is low when there are well-designed and implemented forensic community treatment programmes, consistent with other data suggesting a reciprocal relationship between safe community care and a low threshold for readmission to hospital, lessening re-offending at times of crisis. Further research should be directed at timing of release decisions, based on reducing identified risk factors to acceptable levels.
Abnormal Hippocampal Distribution of TDP-43 in Patients With-Late Onset Psychosis
Authors: Velakoulis Dennis , Walterfang Mark , Mocellin Ramon , Pantelis Christos , Dean Brian , McLean Catriona 
Published: July 2009

Objective: Young patients with frontotemporal dementia (FTD) may present with schizophrenia-like psychosis. Few studies have investigated whether FTD-like neuropathological changes are present in schizophrenia. The purpose of the present study was therefore to determine whether FTD-like abnormalities in TARDNA binding protein (TDP-43) and ubiquitin are detectable in hippocampal dentate gyrus of patients with schizophrenia and bipolar disorder. A secondary objective was to identify clinicopathological relationships of any such abnormalities. Methods: Hippocampal sections from 12 patients (nine with schizophrenia and three with bipolar disorder) and 11 control subjects Facility from the National Neural Tissue Resource Centre, Melbourne were blindly rated for the presence or absence of normal TDP-43 staining or ubiquitin-positive neuronal inclusions within the dentate gyrus. The clinical files of all subjects were reviewed for demographic and clinical information. Results: In three patients the normal expression of nuclear TDP-43 staining was not detected. Significantly, all three subjects presented after the age of 50 and had an adult child diagnosed with the same psychiatric disorder. Conclusion: Abnormalities in TDP-43 nuclear expression were identified in patients with late-onset psychosis and a positive family history.
Bolus compared with continuous infusion of microbubble contrast agent using real-time contrast harmonic imaging ultrasound in breast tumors
Authors: Saracco A. , Aspelin P. , Leifland K. , Themudo R. , Wilczek B. , Axelsson R. 
Published: July 2009

Background: Contrast-enhanced ultrasound (CEUS) has gained interest because of its ability to gather vascular information in various organs. There is still a matter of debate concerning its value in breast lesions. The method of choice on how to administer the contrast agent varies depending on the organ to be studied. Infusion of microbubbles is used in echocardiography, while bolus administration is the preferred technique for abdominal organs. Purpose: To compare—in equal doses—bolus versus continuous infusion of microbubbles, using real-time contrast harmonic imaging in breast tumors. Material and Methods: A total of 29 female patients (mean age 54 years) with either clear malignant or benign findings in the breast or axilla were included. Contrast harmonic imaging (CHI US) was performed with a Philips iU22 using an L9-3 MHz linear probe, especially designed for this purpose. A low mechanical index (0.06–0.07) was used to avoid massive destruction of the microbubbles. A dose of 2.4 ml of Sono Vue was first infused intravenously over 1 min with an infusion pump. After 10 min, the same dose was injected as a bolus over 2 s, followed by a flush of 10 ml of saline solution. Contrast uptakes by the tumors were recorded 2 min from the moment of injection, with both methods for each patient. Results: Bolus administration of contrast agent provided a sharply demarcated enhancement and wash-out pattern for all lesions. The continuous infusion of the same contrast agent failed to show any wash-in/wash-out or time-to-peak/peak intensity phenomena in all cases. Conclusion: CEUS using real-time harmonic imaging in order to evaluate breast tumors should be performed with bolus administration of contrast agent in order to achieve better intensity/time curve outcomes.
Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential
Authors: Levy-Moonshine Ami , Amir El-ad David , Keasar Chen 
Published: July 2009

AbstractMotivation: The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches to spend much time struggling to escape numerous traps. Specifically, beta-sheet formation is prone to stray, since many possible combinations of hydrogen bonds are dead ends in terms of beta-sheet assembly. It has been shown that cooperative terms for backbone hydrogen bonds ease this problem by augmenting hydrogen bond patterns that are consistent with beta sheets. Here, we present a novel cooperative hydrogen-bond term that is both effective in promoting beta sheets and computationally efficient. In addition, the new term is differentiable and operates on all-atom protein models.Results: Energy optimization of poly-alanine chains under the new term led to significantly more beta-sheet content than optimization under a non-cooperative term. Furthermore, the optimized structure included very few non-native patterns.Availability: The new term is implemented within the MESHI package and is freely available at http://cs.bgu.ac.il/∼meshi.Contact: chen.keasar@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
PathBuilder—open source software for annotating and developing pathway resources
Authors: Kandasamy Kumaran , Keerthikumar Shivakumar , Raju Rajesh , Keshava Prasad T. S. , Ramachandra Y. L. , Mohan Sujatha , Pandey Akhilesh 
Published: July 2009

Abstract
Summary: We have developed PathBuilder, an open-source web application to annotate biological information pertaining to signaling pathways and to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein–protein interactions, enzyme–substrate relationships and protein translocation events either manually or through automated importing of data from other databases. Salient features of PathBuilder include automatic validation of data formats, built-in modules for visualization of pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving existing pathway datasets.
Availability: PathBuilder is freely available for download at http://pathbuilder.sourceforge.net/ under the terms of GNU lesser general public license (LGPL: http://www.gnu.org/copyleft/lesser.html). The software is platform independent and has been tested on Windows and Linux platforms.
Contact: pandey@jhmi.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
High WT1 gene expression before haematopoietic stem cell transplant in children with acute myeloid leukaemia predicts poor event‐free survival
Authors: Jacobsohn David A. , Tse William T. , Chaleff Stanley , Rademaker Alfred , Duerst Reggie , Olszewski Marie , Huang Wei , Chou Pauline M. , Kletzel Morris 
Published: July 2009

Summary WT1 gene expression has been proposed as a useful marker of minimal residual disease in leukaemia. Its utility in paediatric haematopoietic stem cell transplantation (HSCT) has not been studied. We studied the prognostic value of WT1 expression in peripheral blood prior to HSCT in 36 children with acute myeloid leukaemia (AML). Samples were obtained 2 weeks pre‐transplant to determine the level of WT1 expression. WT1 expression was normalized using K562 cells as a control and a relative value of 0·5 was chosen as the cut‐off point between high and low WT1 expression. The median level of pre‐transplant WT1 expression in the 36 patients was 0·09 (range 0·0001–11·0), with 11patients having WT1 ≥ 0·5 and 25, WT1 < 0·5. After HSCT, 76% of patients with high pre‐transplant WT1 expression relapsed, in contrast to 0% of the patients with low WT1 expression. Those with high WT1 expression had significantly lower 5‐year event‐free survival (EFS) (18%, 95% CI 0–40%) as compared to those with low WT1 expression (68%, 95% CI 50–86%, P = 0·007). Multivariate analysis showed that pre‐transplant WT1 level is the only significant prognostic factor for the difference in EFS. Our finding suggests that elevated WT1 gene expression before HSCT in paediatric AML predicts relapse and poor long‐term EFS. A larger prospective study is warranted to compare the value of high WT1 expression and other markers of minimal residue disease in predicting clinical outcomes after HSCT.
Anti‐oxidized LDL antibody levels are reduced in women with hypertension
Authors: Garrido‐Sánchez L. , García‐Fuentes E. , Cardona F. , Rojo‐Martínez G. , Soriguer F. , Tinahones F. J. 
Published: July 2009

AbstractBackground  Previous studies have suggested that hypertension may be associated with increased oxidized low‐density lipoprotein (LDL). Increased in vitro oxidizability of LDL or elevated titers of anti‐oxidized LDL antibodies have been shown in subjects with essential hypertension. However, the relationship between oxidized LDL and hypertension is equivocal. We examined the association between hypertension and levels of IgG anti‐oxidized LDL antibodies in a group of women from the general population.Materials and methods  The study included 619 women classified according to their blood pressure values. IgG anti‐oxidized LDL antibodies were measured by enzyme‐linked immunosorbent assay and the women were classified as being above or below the 50th percentile.Results  Hypertension was present in 54·3% of the women. These women had significantly lower levels of IgG anti‐oxidized LDL antibodies than the normotensive women (0·280 ± 0·117 vs. 0·336 ± 0·125, P < 0·001). Both systolic and the diastolic blood pressures showed a significant negative correlation with the levels of IgG anti‐oxidized LDL antibodies (r = −0·204, P < 0·001; r = −0·225, P < 0·001, respectively). Women with IgG anti‐oxidized LDL antibody levels above the 50th percentile had a lower prevalence of hypertension than those with IgG anti‐oxidized LDL antibody levels below the 50th percentile (40·2% vs. 59·8%) (P < 0·001).Conclusions  Women with hypertension had lower levels of IgG anti‐oxidized LDL antibodies than normotensive women.
User involvement in developing mobile and temporarily interconnected systems
Authors: Henfridsson Ola , Lindgren Rikard 
Published: July 2009

AbstractInformation systems (IS) research on user involvement has primarily theorized relationships between developers, managers and users in systems development. However, so far, marginal attention has been paid to differences in user involvement practices between information systems. This paper explores user involvement in developing mobile and temporarily interconnected systems (MTIS). We refer to MTIS as heterogeneous systems that rely on network technologies for increasing the ubiquity of information services for users on the move. Such systems are becoming increasingly important in leveraging, e.g. car infotainment, supply chain management and wireless e‐commerce. With particular emphasis on the nature of MTIS and its implications for user involvement, the paper analyses the systems development process of an action research project. The findings suggest that user involvement practices need to be adapted to accommodate features of this class of systems. Being an early attempt to trace the implications of technology features such as use context switches and temporary system relationships, the paper contributes to the development of an updated theory of the user role in an era of increased system complexity and stakeholder ambiguity.