bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of a variant surface antigen-supplemented microarray chip for whole transcriptome analysis of multiple Plasmodium falciparum cytoadherent strains, and identification of strain-transcendent rif and stevor genes
Authors: Claessens Antoine , Ghumra Ashfaq , Gupta Archna P , Mok Sachel , Bozdech Zbynek , Rowe J Alexandra 
Published: July 2011

Abstract

Background
The cytoadherence of Plasmodium falciparum is thought to be mediated by variant surface antigens (VSA), encoded by var, rif, stevor and pfmc-2tm genes. The last three families have rarely been studied in the context of cytoadherence. As most VSA genes are unique, the variability among sequences has impeded the functional study of VSA across different P. falciparum strains. However, many P. falciparum genomes have recently been sequenced, allowing the development of specific microarray probes for each VSA gene.

Methods
All VSA sequences from the HB3, Dd2 and IT/FCR3 genomes were extracted using HMMer software. Oligonucleotide probes were designed with OligoRankPick and added to the 3D7-based microarray chip. As a proof of concept, IT/R29 parasites were selected for and against rosette formation and the transcriptomes of isogenic rosetting and non-rosetting parasites were compared by microarray.

Results
From each parasite strain 50-56 var genes, 125-132 rif genes, 26-33 stevor genes and 3-8 pfmc-2tm genes were identified. Bioinformatic analysis of the new VSA sequences showed that 13 rif genes and five stevor genes were well-conserved across at least three strains (83-100% amino acid identity). The ability of the VSA-supplemented microarray chip to detect cytoadherence-related genes was assessed using P. falciparum clone IT/R29, in which rosetting is known to be mediated by PfEMP1 encoded by ITvar9. Whole transcriptome analysis showed that the most highly up-regulated gene in rosetting parasites was ITvar9 (19 to 429-fold up-regulated over six time points). Only one rif gene (IT4rifA_042) was up-regulated by more than four fold (five fold at 12 hours post-invasion), and no stevor or pfmc-2tm genes were up-regulated by more than two fold. 377 non-VSA genes were differentially expressed by three fold or more in rosetting parasites, although none was as markedly or consistently up-regulated as ITvar9.

Conclusions
Probes for the VSA of newly sequenced P. falciparum strains can be added to the 3D7-based microarray chip, allowing the analysis of the entire transcriptome of multiple strains. For the rosetting clone IT/R29, the striking transcriptional upregulation of ITvar9 was confirmed, and the data did not support the involvement of other VSA families in rosette formation.
CCL2/MCP-1 modulation of microglial activation and proliferation
Authors: Hinojosa Ara E , Garcia-Bueno Borja , Leza Juan C , Madrigal Jose LM 
Published: July 2011

AbstractBackgroundMonocyte chemoattractant protein (CCL2/MCP-1) is a chemokine that attracts cells involved in the immune/inflammatory response. As microglia are one of the main cell types sustaining inflammation in brain, we proposed here to analyze the direct effects of MCP-1 on cultured primary microglia.MethodsPrimary microglia and neuronal cultures were obtained from neonatal and embryonic Wistar rats, respectively. Microglia were incubated with different concentrations of recombinant MCP-1 and LPS. Cell proliferation was quantified by measuring incorporation of bromodeoxyuridine (BrdU). Nitrite accumulation was measured using the Griess assay. The expression and synthesis of different proteins was measured by RT-PCR and ELISA. Cell death was quantified by measuring release of LDH into the culture medium.ResultsMCP-1 treatment (50 ng/ml, 24 h) did not induce morphological changes in microglial cultures. Protein and mRNA levels of different cytokines were measured, showing that MCP-1 was not able to induce proinflammatory cytokines (IL-1β, IL6, MIP-1α), either by itself or in combination with LPS. A similar lack of effect was observed when measuring inducible nitric oxide synthase (NOS2) expression or accumulation of nitrites in the culture media as a different indicator of microglial activation. MCP-1 was also unable to alter the expression of different trophic factors that were reduced by LPS treatment. In order to explore the possible release of other products by microglia and their potential neurotoxicity, neurons were co-cultured with microglia: no death of neurons could be detected when treated with MCP-1. However, the presence of MCP-1 induced proliferation of microglia, an effect opposite to that observed with LPS.ConclusionThese data indicate that, while causing migration and proliferation of microglia, MCP-1 does not appear to directly activate an inflammatory response in this cell type, and therefore, other factors may be necessary to cause the changes that result in the neuronal damage commonly observed in situations where MCP-1 levels are elevated.
Microglial phagocytosis induced by fibrillar β-amyloid is attenuated by oligomeric β-amyloid: implications for Alzheimer's disease
Authors: Pan Xiao-dong , Zhu Yuan-gui , Lin Nan , Zhang Jing , Ye Qin-yong , Huang Hua-pin , Chen Xiao-chun 
Published: July 2011

Abstract

Background
Reactive microglia are associated with β-amyloid (Aβ) deposit and clearance in Alzhiemer's Disease (AD). Paradoxically, entocranial resident microglia fail to trigger an effective phagocytic response to clear Aβ deposits although they mainly exist in an "activated" state. Oligomeric Aβ (oAβ), a recent target in the pathogenesis of AD, can induce more potent neurotoxicity when compared with fibrillar Aβ (fAβ). However, the role of the different Aβ forms in microglial phagocytosis, induction of inflammation and oxidation, and subsequent regulation of phagocytic receptor system, remain unclear.

Results
We demonstrated that Aβ(1-42) fibrils, not Aβ(1-42) oligomers, increased the microglial phagocytosis. Intriguingly, the pretreatment of microglia with oAβ(1-42) not only attenuated fAβ(1-42)-triggered classical phagocytic response to fluorescent microspheres but also significantly inhibited phagocytosis of fluorescent labeled fAβ(1-42). Compared with the fAβ(1-42) treatment, the oAβ(1-42) treatment resulted in a rapid and transient increase in interleukin 1β (IL-1β) level and produced higher levels of tumor necrosis factor-α (TNF-α), nitric oxide (NO), prostaglandin E2 (PGE2) and intracellular superoxide anion (SOA). The further results demonstrated that microglial phagocytosis was negatively correlated with inflammatory mediators in this process and that the capacity of phagocytosis in fAβ(1-42)-induced microglia was decreased by IL-1β, lippolysaccharide (LPS) and tert-butyl hydroperoxide (t-BHP). The decreased phagocytosis could be relieved by pyrrolidone dithiocarbamate (PDTC), a nuclear factor-κB (NF-κB) inhibitor, and N-acetyl-L-cysteine (NAC), a free radical scavenger. These results suggest that the oAβ-impaired phagocytosis is mediated through inflammation and oxidative stress-mediated mechanism in microglial cells. Furthermore, oAβ(1-42) stimulation reduced the mRNA expression of CD36, integrin β1 (Itgb1), and Ig receptor FcγRIII, and significantly increased that of formyl peptide receptor 2 (FPR2) and scavenger receptor class B1 (SRB1), compared with the basal level. Interestingly, the pre-stimulation with oAβ(1-42) or the inflammatory and oxidative milieu (IL-1β, LPS or t-BHP) significantly downregulated the fAβ(1-42)-induced mRNA over-expression of CD36, CD47 and Itgb1 receptors in microglial cells.

Conclusion
These results imply that Aβ oligomers induce a potent inflammatory response and subsequently disturb microglial phagocytosis and clearance of Aβ fibrils, thereby contributing to an initial neurodegenerative characteristic of AD. Antiinflammatory and antioxidative therapies may indeed prove beneficial to delay the progression of AD.
Taxon ordering in phylogenetic trees by means of evolutionary algorithms
Authors: Cerutti Francesco , Bertolotti Luigi , Goldberg Tony L , Giacobini Mario 
Published: July 2011

Abstract

Background
In in a typical "left-to-right" phylogenetic tree, the vertical order of taxa is meaningless, as only the branch path between them reflects their degree of similarity. To make unresolved trees more informative, here we propose an innovative Evolutionary Algorithm (EA) method to search the best graphical representation of unresolved trees, in order to give a biological meaning to the vertical order of taxa.

Methods
Starting from a West Nile virus phylogenetic tree, in a (1 + 1)-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius) next taxa. After having set the radius to the best performance, we evolved the trees with (λ + μ)-EAs to study the influence of population on the algorithm.

Results
The (1 + 1)-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (λ + μ)-EAs performed as well as the (1 + 1), except the larger population (1000 + 1000).

Conclusions
The trees after the evolution showed an improvement both of the fitness (based on a genetic distance matrix, then close taxa are actually genetically close), and of the biological interpretation. Samples collected in the same state or year moved close each other, making the tree easier to interpret. Biological relationships between samples are also easier to observe.
CANGS DB: a stand-alone web-based database tool for processing, managing and analyzing 454 data in biodiversity studies
Authors: Pandey Ram Vinay , Nolte Viola , Boenigk Jens , Schlötterer Christian 
Published: July 2011

Abstract

Background
Next generation sequencing (NGS) is widely used in metagenomic and transcriptomic analyses in biodiversity. The ease of data generation provided by NGS platforms has allowed researchers to perform these analyses on their particular study systems. In particular the 454 platform has become the preferred choice for PCR amplicon based biodiversity surveys because it generates the longest sequence reads. Nevertheless, the handling and organization of massive amounts of sequencing data poses a major problem for the research community, particularly when multiple researchers are involved in data acquisition and analysis. An integrated and user-friendly tool, which performs quality control, read trimming, PCR primer removal, and data organization is desperately needed, therefore, to make data interpretation fast and manageable.

Findings
We developed CANGS DB (C leaning and A nalyzing N ext G eneration S equences D ataB ase) a flexible, stand alone and user-friendly integrated database tool. CANGS DB is specifically designed to organize and manage the massive amount of sequencing data arising from various NGS projects. CANGS DB also provides an intuitive user interface for sequence trimming and quality control, taxonomy analysis and rarefaction analysis. Our database tool can be easily adapted to handle multiple sequencing projects in parallel with different sample information, amplicon sizes, primer sequences, and quality thresholds, which makes this software especially useful for non-bioinformaticians. Furthermore, CANGS DB is especially suited for projects where multiple users need to access the data. CANGS DB is available at http://code.google.com/p/cangsdb/.

Conclusion
CANGS DB provides a simple and user-friendly solution to process, store and analyze 454 sequencing data. Being a local database that is accessible through a user-friendly interface, CANGS DB provides the perfect tool for collaborative amplicon based biodiversity surveys without requiring prior bioinformatics skills.
Static foot disorders: a major risk factor for chronic venous disease?
Authors: Uhl J-F , Chahim M , Allaert F-A 
Published: July 2011

Objective To study the relationship between the static foot disorders (SFDs) and chronic venous disease (CVD). Material and methods A retrospective study of 824 feet in unselected 412 patients seen by one phlebologist using a standardized record form. A complete clinical, aetiological, anatomical and pathological elements (CEAP) classification was determined. Alleged venous symptoms were recorded using a 10-point visual analogue scale and scored using a customized questionnaire. A standardized measurement of the Djian-Annonier angle was used to quantify and identify the presence of any static disorder of the foot. Results There were 156 men (37.8%) and 256 women (62.2%) who were included in this study. A majority of patients (59.3%) had a CEAP classification of C3 or greater. Static disorders of the feet were found to be very common in the study population: 137 feet were hollow feet (16.6%) and 120 flat feet (14.5%). Thus, 31% of all of the feet had some form of SFD. A significant correlation was found between the incidence of SFD and body mass index ( P < 0.01), the presence of symptoms ( P<0.001) and prolonged standing during the day (>5 hours, P < 0.05). The severity of the CVD, represented by the CEAP clinical classes, was also found to be very significantly related to the SFD ( P < 0.001). This correlation was found to be independent of age. Conclusion Static disorders of the foot can be considered as an important risk factor that negatively affects CVD. In daily practice, it is often underestimated. This emphasizes the crucial importance of the detection of SFD during the clinical exam of all CVD patients. Correction of static disorders of the feet will improve symptoms due to the SFD, as well as those related to venous stasis. These results can easily be explained by improvement of foot pump efficacy during walking.
National Call for Organizational Change From Sheltered to Integrated Employment
Authors: Rogan Patricia , Rinne Susan 
Published: July 2011

Abstract
Our purpose in this article is to contend that organizational change from sheltered to integrated employment is not only possible but necessary, and a federal Employment First agenda must be advanced. Findings are reported from interviews with senior managers from 10 organizations that have shifted their service delivery to community employment, and recommendations are provided based on these findings. Results reveal the commonalities among a diverse group of agencies, suggesting the viability of transformation of our current systems with the support and leadership of state and federal agencies and programs.
Late Talking and the Risk for Psychosocial Problems During Childhood and Adolescence
Authors: Whitehouse Andrew J. O. , Robinson Monique , Zubrick Stephen R. 
Published: July 2011

OBJECTIVE:
Although many toddlers with expressive vocabulary delay (“late talkers”) present with age-appropriate language skills by the time they are of school age, little is known about their broader behavioral and emotional profile. The aim of this study was to determine whether late talkers are at increased risk for behavioral and emotional problems during childhood and adolescence.

PATIENTS AND METHODS:
Participants were from the Western Australian Pregnancy Cohort Study. Early expressive vocabulary was measured by parent report at age 2 years using the Language Development Survey. Late talkers were defined as toddlers who scored at or below the 15th percentile on the Language Development Survey for their gender but were screened not to have any other developmental delays. The Child Behavior Checklist was used to measure problem child behavior with continuous z scores and clinical thresholds at ages 2, 5, 8, 10, 14, and 17 years. Potential confounders included maternal and family sociodemographic characteristics as well as prenatal smoking and alcohol exposure.

RESULTS:
At age 2 years, late talkers (n = 142) had higher Child Behavior Checklist scores (representing poorer behavior) than control toddlers (n = 1245) in total, internalizing, and externalizing scales and higher risk for clinically significant internalizing and externalizing problems. Regression models, incorporating the confounding variables, revealed no association between late-talking status at age 2 years and behavioral and emotional problems at the 5-, 8-, 10-, 14-, and 17-year follow-ups.

CONCLUSIONS:
Expressive vocabulary delay at the age of 2 years is not in itself a risk factor for later behavioral and emotional disturbances.
Sustaining and Spreading the Reduction of Adverse Drug Events in a Multicenter Collaborative
Authors: Tham Eric , Calmes Helen M. , Poppy Amy , Eliades Aris B. , Schlafly Stacey Morgan , Namtu Katie C. , Smith Dani M. , Vitaska Matthew C. , McConnell Cindy , Potts Amy L. , Jastrzembski Jenny , Logsdon Tina R. , Hall Matthew , Takata Glenn S. 
Published: July 2011

OBJECTIVES:
Adverse drug events (ADEs) occur more frequently in pediatric patients than adults. ADEs frequently cause serious harm to children and increase the cost of care. The purpose of this study was to decrease ADEs by targeting the entire medication-delivery system for all high-risk medications.

METHODS:
Thirteen freestanding children's hospitals participated in this ADE collaborative. An advisory panel developed a change package of interventions that consisted of standardization of medication-ordering (eg, consensus-based protocols and order sets and high-alert medication protocols), reliable medication-dispensing processes (eg, automated dispensing cabinets and redesign of floor stock procedures), reliable medication-administration processes (eg, safe pump use and reducing interruptions), improvement of patient safety culture (eg, safety-culture changes and reduction of staff intimidation), and clinical decision support (eg, increase ADE detection and redesign care systems). ADE rates were compared from the 3-month baseline period to quarters of the 12-month intervention phase. ADE rates were categorized further as opioid related and other medication related.

RESULTS:
From baseline to the final quarter, the collaborative resulted in a 42% decrease in total ADEs, a 51% decrease in opioid-related ADEs, and a 41% decrease in other medication ADEs.

CONCLUSION:
A pediatric collaborative that targeted the medication-delivery system decreased the rate of ADEs at participating institutions.
Investigation of the sintering pressure and thermal conductivity anisotropy of melt-spun spark-plasma-sintered (Bi,Sb)2Te3 thermoelectric materials
Authors: Xie Wenjie , He Jian , Zhu Song , Holgate Tim , Wang Shanyu , Tang Xinfeng , Zhang Qingjie , Tritt Terry M. 
Published: July 2011

Abstract
The Bonifacio formation (Miocene of Corsica): transition from a wave- to tide-dominated coastal system in mixed carbonate-siliciclastic setting
Authors: André Jean-Pierre , Barthet Yves , Ferrandini Michelle , Ferrandini Jean , Reynaud Jean-Yves , Tessier Bernadette 
Published: July 2011

AbstractThe wide outcrops along the cliffs of Bonifacio at the southern tip of Corsica expose two stratigraphic series of shallow marine deposits, the reefal Cala di Labra Formation (Upper Burdigalian), and the Bonifacio Formation (Lower Langhian at the youngest). Both series are transgressive on the faulted Hercynian basement. The Bonifacio Formation is divided into two members, the Pertusato Member at the base, and the Bonifacio Member at the top.The Pertusato Member, with an average thickness of about thirty meters, is composed mainly of siliciclastic marine deposits, and is weakly fossiliferous. The Pertusato deposits exhibit locally hummocky cross stratification at their distal lower part, and are commonly associated with synsedimentary deformations and water escape structures. In their upper part, and laterally, the coarse-grained Pertusato Member deposits are organized into a prograding coastal prism which bear structures of a barrier beach jagged by some local erosional discontinuities. The whole siliciclastic sequence of the Pertusato Member is wave and storm controlled. Due to the absence of precise biostratigraphic markers, the age of the Pertusato Member is not well constrained. However, it exhibits a thin silty clay layer, that suggests a possible link with the volcanic events recognized on the southwest corsican margin [Rossi et al., 1998], which delivered an absolute age of 16.1 ± 0.4 Ma (Burdigalian-Langhian boundary).The Bonifacio Member (Lower Langhian) is composed of a succession of sandstones and calcarenites over 50 m in thickness, organized into aggrading strata of large 2D and 3D dunes, with several bioturbated levels. The series is interpreted as an offshore tidal system, deposited in a slightly deeper environment (from 25 to 40 m water depth) than the Pertusato Member. The transition from a wave-dominated to a tide-dominated setting might occur as the response of the connection between the basin of Bonifacio and the recently formed Tyrrhenian Sea. The carbonate content of the sediments steadily increases to up to 80% towards the top of the series. At the same time, the skeletal grain associations increase from a Bryomol facies to Rhodalgal, interpreted as the result of an increase in water temperature in favour of carbonate factory.The transition from wave to tidal control in such a system illustrates the extreme sensitivity of morphologically complex coastal basins to hydrodynamic forcing caused by a transgression.
Evolution and palaeoecology of early turtles: a review based on recent discoveries in the Middle Jurassic
Authors: Anquetin Jérémy 
Published: July 2011

AbstractIn recent years, no less than five new species of early turtles have been described worldwide. Among them are three new turtles from Middle Jurassic deposits that partially fill a previous temporal and morphological gap in our knowledge of the early evolution of these shelled amniotes: Heckerochelys romani, Condorchelys antiqua and Eileanchelys waldmani. For the first time, the phylogenetic position of these three new species is tested in the context of the two presently competing cladistic models of turtle evolution. The addition of these taxa to each matrix does not favour or alter any of the two opposed hypotheses. However, it is demonstrated here that, by documenting yet unknown stages in the evolution of several morphological structures, these three species give stronger support to the model of an extended phylogenetic stem for turtles. These new lines of evidence include the structure of the vomer, the position of the aditus canalis stapedio-temporalis and of the posterior opening of the canalis cavernosus, and the morphology of the processus interfenestralis of the opisthotic.Recent discoveries also reinvigorate the debate about the palaeoecology of early turtles. Whereas simple morphological characters (e.g., shell fontanelle, ligamentous bridge, flattened carapace) can be misleading, forelimb proportions and shell bone histology have led to the conclusion that most stem turtles (i.e., Proganochelys quenstedti, Palaeochersis talampayensis, Proterochersis robusta, Kayentachelys aprix and meiolaniids) were terrestrial forms. At least two out of the five recently described early turtles have been convincingly interpreted as having aquatic habits: Odontochelys semitestacea and Eileanchelys waldmani. More investigation is needed, but this will undoubtedly trigger further debate on the primitive ecology of turtles and on the origin of aquatic habits in testudines (i.e., the crown-group), respectively.