bluuebunny/crossref_metadata_2025_split huggingface dataset:
A predictive thermal dynamic model for parameter generation in the laser assisted direct write process
Authors: Shang Shuo , Fearon Eamonn , Wellburn Dan , Sato Taku , Edwardson Stuart , Dearden G , Watkins K G 
Published: October 2011

The laser assisted direct write (LADW) method can be used to generate electrical circuitry on a substrate by depositing metallic ink and curing the ink thermally by a laser. Laser curing has emerged over recent years as a novel yet efficient alternative to oven curing. This method can be used in situ, over complicated 3D contours of large parts (e.g. aircraft wings) and selectively cure over heat sensitive substrates, with little or no thermal damage.
In previous studies, empirical methods have been used to generate processing windows for this technique, relating to the several interdependent processing parameters on which the curing quality and efficiency strongly depend. Incorrect parameters can result in a track that is cured in some areas and uncured in others, or in damaged substrates. This paper addresses the strong need for a quantitative model which can systematically output the processing conditions for a given combination of ink, substrate and laser source; transforming the LADW technique from a purely empirical approach, to a simple, repeatable, mathematically sound, efficient and predictable process.
The method comprises a novel and generic finite element model (FEM) that for the first time predicts the evolution of the thermal profile of the ink track during laser curing and thus generates a parametric map which indicates the most suitable combination of parameters for process optimization. Experimental data are compared with simulation results to verify the accuracy of the model.
The strength of intron donor splice sites in human genes displays a bell-shaped pattern
Authors: Wang Kai , Wernersson Rasmus , Brunak Søren 
Published: October 2011

Abstract
Motivation: The gene concept has recently changed from the classical one protein notion into a much more diverse picture, where overlapping or fused transcripts, alternative transcription initiation, and genes within genes, add to the complexity generated by alternative splicing. Increased understanding of the mechanisms controlling pre-mRNA splicing is thus important for a wide range of aspects relating to gene expression.
Results: We have discovered a convex gene delineating pattern in the strength of 5′ intron splice sites. When comparing the strengths of &gt;18 000 intron containing Human genes, we found that when analysing them separately according to the number of introns they contain, initial splice sites were always stronger on average than subsequent ones, and that a similar reversed trend exist towards the terminal gene part. The convex pattern is strongest for genes with up to 10 introns. Interestingly, when analysing the intron containing gene pool from mouse consisting of &gt;15 000 genes, we found the convex pattern to be conserved despite &gt;75 million years of evolutionary divergence between the two organisms. We also analysed an interesting, novel class of chimeric genes which during spliceosome assembly are fused and in tandem are transcribed and spliced into a single mature mRNA sequence. In their splice site patterns, these genes individually seem to deviate from the convex pattern, offering a possible rationale behind their fusion into a single transcript.
Contact: brunak@cbs.dtu.dk
Supplementary Information: Supplementary data are available at Bioinformatics online.
Neural fate decisions mediated by trans-activation and cis-inhibition in Notch signaling
Authors: Wang Ruiqi , Liu Kaihui , Chen Luonan , Aihara Kazuyuki 
Published: October 2011

Abstract
Motivation: In the developing nervous system, the expression of proneural genes, i.e. Hes1, Neurogenin-2 (Ngn2) and Deltalike-1 (Dll1), oscillates in neural progenitors with a period of 2–3 h, but is persistent in post-mitotic neurons. Unlike the synchronization of segmentation clocks, oscillations in neural progenitors are asynchronous between cells. It is known that Notch signaling, in which Notch in a cell can be activated by Dll1 in neighboring cells (trans-activation) and can also be inhibited by Dll1 within the same cell (cis-inhibition), is important for neural fate decisions. There have been extensive studies of trans-activation, but the operating mechanisms and potential implications of cis-inhibition are less clear and need to be further investigated.
Results: In this article, we present a computational model for neural fate decisions based on intertwined dynamics with trans-activation and cis-inhibition involving the Hes1, Notch and Dll1 proteins. In agreement with experimental observations, the model predicts that both trans-activation and cis-inhibition play critical roles in regulating the choice between remaining as a progenitor and embarking on neural differentiation. In particular, trans-activation is essential for generation of oscillations in neural progenitors, and cis-inhibition is important for the asynchrony between adjacent cells, indicating that the asynchronous oscillations in neural progenitors depend on cooperation between trans-activation and cis-inhibition. In contrast, cis-inhibition plays more critical roles in embarking on neural differentiation by inactivating intercellular Notch signaling. The model presented here might be a good candidate for providing the first qualitative mechanism of neural fate decisions mediated by both trans-activation and cis-inhibition.
Contact: rqwang@shu.edu.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
Visualization and quality assessment of de novo genome assemblies
Authors: Riba-Grognuz Oksana , Keller Laurent , Falquet Laurent , Xenarios Ioannis , Wurm Yannick 
Published: October 2011

Abstract
Summary: Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis. We present a method to evaluate genome scaffolding by aligning independently obtained transcriptome sequences to the genome and visually summarizing the alignments using the Cytoscape software. Applying this method to the genome of the red fire ant Solenopsis invicta allowed us to identify inconsistencies in 7%, confirm contig order in 20% and extend 16% of scaffolds.
Contact: oksana.ribagrognuz@unil.ch; yannick.wurm@unil.ch
Availability: Scripts that generate tables for visualization in Cytoscape from FASTA sequence and scaffolding information files are publicly available at https://github.com/ksanao/TGNet.
Supplementary Information: Supplementary data are available at Bioinformatics online.
An automatic method for CASP9 free modeling structure prediction assessment
Authors: Cong Qian , Kinch Lisa N. , Pei Jimin , Shi Shuoyong , Grishin Vyacheslav N. , Li Wenlin , Grishin Nick V. 
Published: October 2011

Abstract
Motivation: Manual inspection has been applied to and is well accepted for assessing critical assessment of protein structure prediction (CASP) free modeling (FM) category predictions over the years. Such manual assessment requires expertise and significant time investment, yet has the problems of being subjective and unable to differentiate models of similar quality. It is beneficial to incorporate the ideas behind manual inspection to an automatic score system, which could provide objective and reproducible assessment of structure models.
Results: Inspired by our experience in CASP9 FM category assessment, we developed an automatic superimposition independent method named Quality Control Score (QCS) for structure prediction assessment. QCS captures both global and local structural features, with emphasis on global topology. We applied this method to all FM targets from CASP9, and overall the results showed the best agreement with Manual Inspection Scores among automatic prediction assessment methods previously applied in CASPs, such as Global Distance Test Total Score (GDT_TS) and Contact Score (CS). As one of the important components to guide our assessment of CASP9 FM category predictions, this method correlates well with other scoring methods and yet is able to reveal good-quality models that are missed by GDT_TS.
Availability: The script for QCS calculation is available at http://prodata.swmed.edu/QCS/.
Contact: grishin@chop.swmed.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
The Binding Protein BiP Attenuates Stress-Induced Cell Death in Soybean via Modulation of the N-Rich Protein-Mediated Signaling Pathway
Authors: Reis Pedro A.A. , Rosado Gustavo L. , Silva Lucas A.C. , Oliveira Luciana C. , Oliveira Lucas B. , Costa Maximiller D.L. , Alvim Fátima C. , Fontes Elizabeth P.B. 
Published: October 2011

Abstract
The molecular chaperone binding protein (BiP) participates in the constitutive function of the endoplasmic reticulum (ER) and protects the cell against stresses. In this study, we investigated the underlying mechanism by which BiP protects plant cells from stress-induced cell death. We found that enhanced expression of BiP in soybean (Glycine max) attenuated ER stress- and osmotic stress-mediated cell death. Ectopic expression of BiP in transgenic lines attenuated the leaf necrotic lesions that are caused by the ER stress inducer tunicamycin and also maintained shoot turgidity upon polyethylene glycol-induced dehydration. BiP-mediated attenuation of stress-induced cell death was confirmed by the decreased percentage of dead cell, the reduced induction of the senescence-associated marker gene GmCystP, and reduced DNA fragmentation in BiP-overexpressing lines. These phenotypes were accompanied by a delay in the induction of the cell death marker genes N-RICH PROTEIN-A (NRP-A), NRP-B, and GmNAC6, which are involved in transducing a cell death signal generated by ER stress and osmotic stress through the NRP-mediated signaling pathway. The prosurvival effect of BiP was associated with modulation of the ER stress- and osmotic stress-induced NRP-mediated cell death signaling, as determined in transgenic tobacco (Nicotiana tabacum) lines with enhanced (sense) and suppressed (antisense) BiP levels. Enhanced expression of BiP prevented NRP- and NAC6-mediated chlorosis and the appearance of senescence-associated markers, whereas silencing of endogenous BiP accelerated the onset of leaf senescence mediated by NRPs and GmNAC6. Collectively, these results implicate BiP as a negative regulator of the stress-induced NRP-mediated cell death response.
Evolution of Diterpene Metabolism: Sitka Spruce CYP720B4 Catalyzes Multiple Oxidations in Resin Acid Biosynthesis of Conifer Defense against Insects
Authors: Hamberger Björn , Ohnishi Toshiyuki , Hamberger Britta , Séguin Armand , Bohlmann Jörg 
Published: October 2011

Abstract
Diterpene resin acids (DRAs) are specialized (secondary) metabolites of the oleoresin defense of conifers produced by diterpene synthases and cytochrome P450s of the CYP720B family. The evolution of DRA metabolism shares common origins with the biosynthesis of ent-kaurenoic acid, which is highly conserved in general (primary) metabolism of gibberellin biosynthesis. Transcriptome mining in species of spruce (Picea) and pine (Pinus) revealed CYP720Bs of four distinct clades. We cloned a comprehensive set of 12 different Sitka spruce (Picea sitchensis) CYP720Bs as full-length cDNAs. Spatial expression profiles, methyl jasmonate induction, and transcript enrichment in terpenoid-producing resin ducts suggested a role of CYP720B4 in DRA biosynthesis. CYP720B4 was characterized as a multisubstrate, multifunctional enzyme by the formation of oxygenated diterpenoids in metabolically engineered yeast, yeast in vivo transformation of diterpene substrates, in vitro assays with CYP720B4 protein produced in Escherichia coli, and alteration of DRA profiles in RNA interference-suppressed spruce seedlings. CYP720B4 was active with 24 different diterpenoid substrates, catalyzing consecutive C-18 oxidations in the biosynthesis of an array of diterpene alcohols, aldehydes, and acids. CYP720B4 was most active in the formation of dehydroabietic acid, a compound associated with insect resistance of Sitka spruce. We identified patterns of convergent evolution of CYP720B4 in DRA metabolism and ent-kaurene oxidase CYP701 in gibberellin metabolism and revealed differences in the evolution of specialized and general diterpene metabolism in a gymnosperm. The genomic and functional characterization of the gymnosperm CYP720B family highlights that the evolution of specialized metabolism involves substantial diversification relative to conserved, general metabolism.
Individual psychomotor impairment in relation to zopiclone and ethanol concentrations in blood – a randomized controlled double‐blinded trial
Authors: Gustavsen Ingebjørg , Hjelmeland Knut , Bernard Jean‐Paul , Mørland Jørg 
Published: October 2011

ABSTRACTAims  To investigate individual traffic‐relevant impairment related to measured blood zopiclone and ethanol concentrations. Also, we aimed to study possible development of acute tolerance.Design  A randomized controlled four‐way cross‐over double‐blind trial. Study drugs were zopiclone 5 or 10 mg, 50 g ethanol or placebo.Setting  Laboratory study with computerized tests: Connor's Continuous Performance test, Choice Reaction Time and Stockings of Cambridge. Altogether, the tests consisted of 15 test components, representing three levels of behaviour (automotive, control, executive planning), relevant to traffic safety.Participants  Sixteen healthy male volunteers.Measurements  Each study day, 10 blood samples were collected from each volunteer. Fifteen psychomotor test components were registered at baseline and a further three times after intake. Impairment was defined as any individual deterioration in performance compared to individual baseline performance.Findings  Blood drug concentrations up to 74 µg/l zopiclone and 0.100% ethanol were measured. We found a clear positive concentration–effect relationship for zopiclone and ethanol for both automotive and control behaviours, and a modest relationship for executive planning behaviour. Significant impairment started to be observed at concentrations above 16 µg/l zopiclone (automotive and control behaviour) and above 0.026% ethanol (automotive behaviour). Acute tolerance was found for both drugs.Conclusions  The hypnotic, zopiclone, can impair psychomotor performance at blood concentrations as low as 16 µg/l.
The effect of sterilisation on the light intensity of the reusable Trachlight™*
Authors: Milne A. D. , Cave A. L. , Brousseau P. A. , Hung O. R. 
Published: October 2011

SummaryWe examined the light intensity delivered by the Trachlight™ reusable lightwand and the effect of repeated sterilisation on this light intensity. Using a light meter and test chamber, the light intensity of 12 new Trachlights and 31 Trachlights available in operating theatres was measured. In addition, five new devices underwent 30 repeated sterilisations with light intensity measurement after each cleaning. There was no difference between the light intensity of new Trachlights (median (IQR [range]) 2282 (2202–2780 [1970–4400])) lux and the devices currently in service (2295 (2018–2796 [1649–3280]) lux (p = 0.27)). The median (range) number of uses for devices currently in service was only 3 (0–9). There was, however, significant light intensity loss after 10, 20 and 30 cleanings (p = 0.001). After 10 cleanings, the mean light intensity was 75% of initial output, and after 30 cycles, light intensity was 59% of initial output.
Genetic diversity and admixture of indigenous cattle from North Ethiopia: implications of historical introgressions in the gateway region to Africa
Authors: Zerabruk M. , Li M.‐H. , Kantanen J. , Olsaker I. , Ibeagha‐Awemu E. M. , Erhardt G. , Vangen O. 
Published: October 2011

SummaryMicrosatellite variation was surveyed to determine the genetic diversity, population structure and admixture of seven North Ethiopian cattle breeds by combining multiple microsatellite data sets of Indian and West African zebu, and European, African and Near‐Eastern taurine in genetic analyses. Based on allelic distribution, we identified four diagnostic alleles (HEL1‐123 bp, CSSM66‐201 bp, BM2113‐150 bp and ILSTS6‐285 bp) specific to the Near‐Eastern taurine. Results of genetic relationship and population structure analyses confirmed the previously established marked genetic distinction between taurine and zebu, and indicated further divergence among the bio‐geographical groupings of breeds such as North Ethiopian, Indian and West African zebu, and African, European and Near‐Eastern taurine. Using the diagnostic alleles for bio‐geographical groupings and a Bayesian method for population structure inference, we estimated the genetic influences of major historical introgressions in North Ethiopian cattle. The breeds have been heavily (>90%) influenced by zebu, followed by African, European and the Near‐Eastern taurine. Overall, North Ethiopian cattle show a high level of within‐population genetic variation (e.g. observed heterozygosity = 0.659–0.687), which is in the upper range of that reported for domestic cattle and indicates their potential for future breeding applications, even in a global context. Rather low but significant population differentiation (FST = 1.1%, P < 0.05) was recorded as a result of multiple introgression events and strong genetic exchanges among the North Ethiopian breeds.
Implementing a transition pathway in diabetes: a qualitative study of the experiences and suggestions of young people with diabetes
Authors: Price C. S. , Corbett S. , Lewis‐Barned N. , Morgan J. , Oliver L. E. , Dovey‐Pearce G. 
Published: October 2011

AbstractBackground  The prevalence of Type 1 diabetes is increasing with more children and adolescents being diagnosed with this chronic condition. There has been an increasing focus in recent years on the transition through adolescence and supporting young people who have chronic health conditions, with the recognition that young people are at risk of dropping out of healthcare services following transfer from paediatric to adult services. To date, there have been limited evaluations of transition models. The purpose of this study is to evaluate one such model in diabetes, the ‘Transition Pathway’ via interviews with young people who have experienced it first‐hand. The results are discussed in terms of understanding the unique needs of adolescents with regard to psychosocial developmental theory, and what this means for healthcare providers of transition/adolescent services.Methods  Semi‐structured interviews were carried out with 11 young people, two of whom returned a year later for a second interview. Qualitative analysis of these interviews using a ‘Framework’ approach enabled the data to be sorted according to initial themes. Following this, further analysis enabled the identification of ‘super‐ordinate’ or overall themes.Results  Six initial themes emerged from the data. These concerned the transition pathway process, the experience and organization of transfer, organization of services, information and education, the healthcare consultation and the need for services to be inclusive of all young people's needs. From these initial themes, two overall/super‐ordinate themes were identified: the need for transition services to be developmentally appropriate and to be based around individual needs. The consultation experience was central to keeping young people engaged with adolescent healthcare services.Conclusion  Several key elements of adolescent/transition healthcare services have been proposed, one of which is training for professionals delivering the service. This study suggests that communication skills form a vital component of such training.
‘Down the rabbit hole’: enhancing the transition process for youth with cystic fibrosis and congenital heart disease by re‐imagining the future and time
Authors: Moola F. J. , Norman M. E. 
Published: October 2011

AbstractBackground  Although the transition from paediatric to adult clinical care is an important one, the process is far from seamless. Little is known about the transition experiences of youth with cystic fibrosis (CF) and congenital heart disease (CHD).Method  Informed by the new social studies of childhood, this qualitative study adopted a thematic analytical approach in order to explore how 50 youth and 28 parents affected by CF and CHD at a large children's hospital in Canada negotiate constructions of ‘normal developmental time’– in both anticipating and dealing with the transition from adolescence to adulthood.Results  Illness appeared to render the future as an uncertain terrain for youth living with CF and CHD. Concerns related to deteriorating health and occupational restrictions in the future were paramount for these youth. For young women with CF and CHD, the loss of ‘normal’ gendered roles – such as motherhood – was also a distressing future concern. For youth living with CF and their parents in particular, time was thought to be stolen and the future was abbreviated. Despite these seemingly anxiety‐inducing experiences, youth and their parents demonstrated considerable creativity as they devised strategies to deal with the future and stolen time.Recommendations and conclusion  In addition to challenging ideological assumptions about developmental time which may alienate youth with chronic illnesses, the results from this study suggest that attending to youth's temporal anxieties and future concerns may ultimately enhance the transition process for youth with CF and CHD.
Interleukin‐4 and interleukin‐13 prime migrational responses of haemopoietic progenitor cells to stromal cell‐derived factor‐1α
Authors: Punia N. , Smith S. , Thomson J. V. , Irshad A. , Nair P. , Sehmi R. 
Published: October 2011

SummaryBackgroundLung‐homing of progenitor cells is associated with inflammatory and remodelling changes in asthma. Factors that modulate the increased traffic of progenitor cells to the site of inflammation in asthma remain to be defined. Interleukin (IL)‐4 and IL‐13 are Th2 cytokines that are key regulators of asthma pathology.ObjectiveWe investigated the role of IL‐4 and IL‐13 in modulating the trans‐migrational responses of haemopoietic progenitor cells (HPC).MethodsHPC were enriched from cord blood (CB) and peripheral blood (PB) samples. Migration of HPC was assessed using transwell migration assays, and responding cells were enumerated by flow cytometry.ResultsIL‐4 and IL‐13 primed migration of CB‐ and PB‐derived HPC (CD34+45+ cells) to stromal cell‐derived factor‐1α (SDF‐1α), in vitro. However, these cytokines had no effect on migrational responses of eosinophil‐lineage committed progenitors (CD34+45+IL‐5Rα+ cells) or mature eosinophils to SDF‐1α. For HPC, priming effects of IL‐4 (0.1 ng/mL) and IL‐13 (0.1 ng/mL) were detectable within 1 h and optimal at 18‐h post‐incubation, and IL‐4 was the more effective priming agent. Pre‐incubation with IL‐4 or IL‐13 had no effect on the intensity of cell surface expression of SDF‐1α receptor, CXCR4. Disruption of cell membrane cholesterol content by pre‐incubation with polyene antibiotics inhibited IL‐4 priming of SDF‐1α stimulated migration of HPC indicating that increased incorporation of CXCR4 into membrane lipid rafts mediated the cytokine primed migrational response of HPC. This was confirmed by confocal fluorescent microscopy.Conclusions and Clinical RelevanceIL‐4 and IL‐13 prime the migrational response of HPC to SDF‐1α by enhancing the incorporation of CXCR4 into lipid rafts. The priming effect of these cytokines is specific to primitive HPC. These data suggest that increased local production of IL‐4 and IL‐13 within the lungs may promote increased SDF‐1α mediated homing of HPC to the airways in asthma.