bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiologic Evaluation of the Insertion Sites of the 2 Functional Bundles of the Anterior Cruciate Ligament Using 3-dimensional Computed Tomography
Authors: Lorenz Stephan , Elser Florian , Mitterer Martin , Obst Tobias , Imhoff Andreas B. 
Published: August 2009

Background Anterior cruciate ligament reconstruction with a double-bundle technique requires exact tunnel positioning. Reference values for the anatomic insertions are necessary for radiographic intra- and postoperative control and fluoroscopy-based navigation. Hypothesis The femoral and tibial insertions of the anteromedial bundle (AMB) and posterolateral bundle (PLB) of the anterior cruciate ligament can be described using standardized computed tomography scans. Study Design Descriptive laboratory study. Methods The insertion sites of the AMB and PLB were macroscopically identified and tagged by copper wire in 12 specimens. Computed tomography scans with predefined reconstructions were performed. Femorally, the geometric center of the insertions were determined in the sagittal view and described in a deep-high 10 × 10 grid. Tibially, the insertions were described as the ratio between the geometric center of the insertion sites with respect to the mediolateral and sagittal diameter of the tibia in frontal and sagittal reconstruction, respectively. The tibial insertions were described using a 10 × 10 grid in axial orientation. Results The geometric midpoints of the insertion areas at the femur of the AMB and PLB were located on the reticule at x = 21% ± 3% and y = 22% ± 2% for the AMB and x = 27% ± 3% and y = 45% ± 3% for the PLB. In the sagittal plane, the center of the tibial insertion was located at 41% ± 3% and 52% ± 3% of the tibial diameter from the anterior border for the AMB and PLB, respectively. The geometric centers of the tibial insertions in axial view were x = 52% ± 2% and y = 37% ± 3% for the AMB and x = 50% ± 2% and y = 48% ± 3% for the PLB. Conclusion The insertion site characteristics of the AMB and PLB can be evaluated by predefined reconstructions of computed tomography scans. Clinical relevance These results can serve as orientation landmarks for intra- and postoperative radiographic control and fluoroscopic-based navigation.
MDGs in a Global World
Authors: Montenegro Marisela , Montenegro Karla , Yufra Laura , Calaz Caterine 
Published: August 2009

In this article we reflect upon the relationship between the Millennium Development Goals (MDGs) formulated by the United Nations (2000) and the migration phenomena that is characteristic of the present globalised society. First, we argue that the Millennium Goals have not sufficiently considered migration processes as a structural phenomenon. Development goals must take in account this emergent phenomenon in post-industrial societies in order to achieve human rights and social equity and to promote the well-being of all people in their origin and host societies. Second, by interpreting the results of an ethnographic study carried out in social services aimed at migrant women in the city of Barcelona, while focusing on the 3rd Millennium Goal: gender equity and the empowerment of women, we reflect on the limits and possibilities of these intervention practices in advancing towards the goal in host societies. We conclude that changes in public policy and social services are necessary in order to advance towards the achievement of the gender equity goal and empowerment of women, a transformation that aims at the achievement of citizenship for all people in this global society.
Policies to Eradicate Extreme Poverty in Chile
Authors: Urrutia Bruno Bivort , Labrín Soledad Martínez 
Published: August 2009

The present article analyses the association between the way in which public policy conceptualises poverty (in discourse and practice), the conception of poverty of people who live in extreme poverty conditions and the strategies they develop to affront it, in the light of their participation in the Puente Programme in Chile. The data emanate from research work carried out from a qualitative perspective using in-depth interviews with people considered to be living in extreme poverty and including a gendered analytic. The ‘Puente Programme’ is part of Chilean public policy aimed to reduce levels of poverty and extreme poverty, in consonance with the Millennium Development Goal (MDG) One as stated by the UNDP. Indeed, such policies seem to have had the effect of generating a self-perception of lack of opportunities, low level of agency in the solutions of their problems and consequently, fewer possibilities of achievement of the ends that they have in mind among the users. Also, we conclude that the strategies used by the Puente Programme have neither strengthened community association, nor helped to regenerate community networks. Additionally, the interviewed people do not feel empowered or improved in their citizenship capacities. Instead, what results is a sense of dependency on institutions. Finally, we postulate that the Puente Programme has not contributed to the development of a community or in subjective welfare.
Characterization of W1745C and S1783A: 2 novel mutations causing defective collagen binding in the A3 domain of von Willebrand factor
Authors: Riddell Anne F. , Gomez Keith , Millar Carolyn M. , Mellars Gillian , Gill Saher , Brown Simon A. , Sutherland Megan , Laffan Mike A. , McKinnon Thomas A. J. 
Published: August 2009

AbstractInvestigation of 3 families with bleeding symptoms demonstrated a defect in the collagen-binding activity of von Willebrand factor (VWF) in association with a normal VWF multimeric pattern. Genetic analysis showed affected persons to be heterozygous for mutations in the A3 domain of VWF: S1731T, W1745C, and S1783A. One person showed compound heterozygosity for W1745C and R760H. W1745C and S1783A have not been reported previously. The mutations were reproduced by site-directed mutagenesis and mutant VWF expressed in HEK293T cells. Collagen-binding activity measured by immunosorbent assay varied according to collagen type: W1745C and S1783A were associated with a pronounced binding defect to both type I and type III collagen, whereas the principal abnormality in S1731T patients was a reduction in binding to type I collagen only. The multimer pattern and distribution of mutant proteins were indistinguishable from wild-type recombinant VWF, confirming that the defect in collagen binding resulted from the loss of affinity at the binding site and not impairment of high-molecular-weight multimer formation. Our findings demonstrate that mutations causing an abnormality in the binding of VWF to collagen may contribute to clinically significant bleeding symptoms. We propose that isolated collagen-binding defects are classified as a distinct subtype of von Willebrand disease.
A linked donor-recipient study to evaluate parvovirus B19 transmission by blood component transfusion
Authors: Kleinman Steven H. , Glynn Simone A. , Lee Tzong-Hae , Tobler Leslie H. , Schlumpf Karen S. , Todd Deborah S. , Qiao Hannah , Yu Mei-ying W. , Busch Michael P. 
Published: August 2009

Abstract
Parvovirus B19V infection can be a serious infection for hematology patients with underlying hemolysis or compromised erythropoiesis syndromes. Although case reports of B19V transmission by blood component transfusion (as contrasted to manufactured plasma derivatives) are rare, no studies have systematically determined a rate of transmission to recipients transfused with B19V DNA–positive components. We used a linked donor and recipient repository and a sensitive, quantitative B19V DNA polymerase chain reaction (PCR) assay to assess such transmission in B19V-susceptible (ie, anti-B19V immunoglobulin G [IgG] negative) recipients. We assessed 112 B19V DNA–positive components from 105 donors (of 12 529 tested donations) transfused into a population of surgical patients with a pretransfusion B19V IgG seroprevalence of 78%. We found no transmission to 24 susceptible recipients from transfusion of components with B19V DNA at concentrations less than 106 IU/mL (upper 95% confidence interval, 11.7%). We found an anamnestic IgG response in one pretransfusion seropositive recipient transfused with a component containing greater than 1010 IU/mL B19V DNA. These findings show either that transmission from components with less than 106 IU/mL does not occur, or, if it does, it is an uncommon event. These data do not support the need to routinely screen blood donations with a sensitive B19V DNA nucleic acid assay.
A fast and efficient gene-network reconstruction method from multiple over-expression experiments
Authors: Stokić Dejan , Hanel Rudolf , Thurner Stefan 
Published: August 2009

Abstract

Background
Reverse engineering of gene regulatory networks presents one of the big challenges in systems biology. Gene regulatory networks are usually inferred from a set of single-gene over-expressions and/or knockout experiments. Functional relationships between genes are retrieved either from the steady state gene expressions or from respective time series.

Results
We present a novel algorithm for gene network reconstruction on the basis of steady-state gene-chip data from over-expression experiments. The algorithm is based on a straight forward solution of a linear gene-dynamics equation, where experimental data is fed in as a first predictor for the solution. We compare the algorithm's performance with the NIR algorithm, both on the well known E. coli experimental data and on in-silico experiments.

Conclusion
We show superiority of the proposed algorithm in the number of correctly reconstructed links and discuss computational time and robustness. The proposed algorithm is not limited by combinatorial explosion problems and can be used in principle for large networks.
Moorean tree snail survival revisited: a multi-island genealogical perspective
Authors: Lee Taehwan , Burch John B , Coote Trevor , Pearce-Kelly Paul , Hickman Carole , Meyer Jean-Yves , Ó Foighil Diarmaid 
Published: August 2009

Abstract

Background
The mass extirpation of the island of Moorea's endemic partulid tree snail fauna, following the deliberate introduction of the alien predator Euglandina rosea, represents one of the highest profile conservation crises of the past thirty years. All of the island's partulids were thought to be extirpated by 1987, with five species persisting in zoos, but intensive field surveys have recently detected a number of surviving wild populations. We report here a mitochondrial (mt) phylogenetic estimate of Moorean partulid wild and captive lineage survival calibrated with a reference museum collection that pre-dates the predator's introduction and that also includes a parallel dataset from the neighboring island of Tahiti.

Results
Although severe winnowing of Moorea's mt lineage diversity has occurred, seven of eight (six Partula; two Samoana) partulid tip clades remain extant. The extinct mt clade occurred predominantly in the P. suturalis species complex and it represented a major component of Moorea's endemic partulid treespace. Extant Moorean mt clades exhibited a complex spectrum of persistence on Moorea, in captivity, and (in the form of five phylogenetically distinct sister lineages) on Tahiti. Most notably, three Partula taxa, bearing two multi-island mt lineages, have survived decades of E. rosea predation on Moorea (P. taeniata) and in the valleys of Tahiti (P. hyalina and P. clara). Their differential persistence was correlated with intrinsic attributes, such as taxonomy and mt lineages, rather than with their respective within-island distribution patterns.

Conclusion
Conservation efforts directed toward Moorean and Tahitian partulids have typically operated within a single island frame of reference, but our discovery of robust genealogical ties among survivors on both islands implies that a multi-island perspective is required. Understanding what genetic and/or ecological factors have enabled Partula taeniata, P. hyalina and P. clara to differentially survive long-term direct exposure to the predator may provide important clues toward developing a viable long term conservation plan for Society Island partulid tree snails.
High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs
Authors: Walter Nicole AR , Bottomly Daniel , Laderas Ted , Mooney Michael A , Darakjian Priscila , Searles Robert P , Harrington Christina A , McWeeney Shannon K , Hitzemann Robert , Buck Kari J 
Published: August 2009

Abstract

Background
Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not annotated) variation, is problematic for follow up analyses. Polymorphisms result in a high incidence of false positive and false negative results in hybridization based analyses and hinder the identification of the true variation underlying genetically determined differences in physiology and behavior. Given the proliferation of mouse genetic models (e.g., knockout models, selectively bred lines, heterogeneous stocks derived from standard inbred strains and wild mice) and the wealth of gene expression microarray and phenotypic studies using genetic models, the impact of naturally-occurring polymorphisms on these data is critical. With the advent of next-generation, high-throughput sequencing, we are now in a position to determine to what extent polymorphisms are currently cryptic in such models and their impact on downstream analyses.

Results
We sequenced the two most commonly used inbred mouse strains, DBA/2J and C57BL/6J, across a region of chromosome 1 (171.6 – 174.6 megabases) using two next generation high-throughput sequencing platforms: Applied Biosystems (SOLiD) and Illumina (Genome Analyzer). Using the same templates on both platforms, we compared realignments and single nucleotide polymorphism (SNP) detection with an 80 fold average read depth across platforms and samples. While public datasets currently annotate 4,527 SNPs between the two strains in this interval, thorough high-throughput sequencing identified a total of 11,824 SNPs in the interval, including 7,663 new SNPs. Furthermore, we confirmed 40 missense SNPs and discovered 36 new missense SNPs.

Conclusion
Comparisons utilizing even two of the best characterized mouse genetic models, DBA/2J and C57BL/6J, indicate that more than half of naturally-occurring SNPs remain cryptic. The magnitude of this problem is compounded when using more divergent or poorly annotated genetic models. This warrants full genomic sequencing of the mouse strains used as genetic models.
The degree of microbiome complexity influences the epithelial response to infection
Authors: Mans Jeffrey J , von Lackum Kate , Dorsey Cassandra , Willis Shaun , Wallet Shannon M , Baker Henry V , Lamont Richard J , Handfield Martin 
Published: August 2009

Abstract

Background
The human microflora is known to be extremely complex, yet most pathogenesis research is conducted in mono-species models of infection. Consequently, it remains unclear whether the level of complexity of a host's indigenous flora can affect the virulence potential of pathogenic species. Furthermore, it remains unclear whether the colonization by commensal species affects a host cell's response to pathogenic species beyond the direct physical saturation of surface receptors, the sequestration of nutrients, the modulation of the physico-chemical environment in the oral cavity, or the production of bacteriocins. Using oral epithelial cells as a model, we hypothesized that the virulence of pathogenic species may vary depending on the complexity of the flora that interacts with host cells.

Results
This is the first report that determines the global epithelial transcriptional response to co-culture with defined complex microbiota. In our model, human immortalized gingival keratinocytes (HIGK) were infected with mono- and mixed cultures of commensal and pathogenic species. The global transcriptional response of infected cells was validated and confirmed phenotypically. In our model, commensal species were able to modulate the expression of host genes with a broad diversity of physiological functions and antagonize the effect of pathogenic species at the cellular level. Unexpectedly, the inhibitory effect of commensal species was not correlated with its ability to inhibit adhesion or invasion by pathogenic species.

Conclusion
Studying the global transcriptome of epithelial cells to single and complex microbial challenges offers clues towards a better understanding of how bacteria-bacteria interactions and bacteria-host interactions impact the overall host response. This work provides evidence that the degree of complexity of a mixed microbiota does influence the transcriptional response to infection of host epithelial cells, and challenges the current dogma regarding the potential versus the actual pathogenicity of bacterial species. These findings support the concept that members of the commensal oral flora have evolved cellular mechanisms that directly modulate the host cell's response to pathogenic species and dampen their relative pathogenicity.
msbB deletion confers acute sensitivity to CO2 in Salmonella enterica serovar Typhimurium that can be suppressed by a loss-of-function mutation in zwf
Authors: Karsten Verena , Murray Sean R , Pike Jeremy , Troy Kimberly , Ittensohn Martina , Kondradzhyan Manvel , Low K Brooks , Bermudes David 
Published: August 2009

Abstract

Background
Pathogens tolerate stress conditions that include low pH, oxidative stress, high salt and high temperature in order to survive inside and outside their hosts. Lipopolysaccharide (LPS), which forms the outer-leaflet of the outer membrane in Gram-negative bacteria, acts as a permeability barrier. The lipid A moiety of LPS anchors it to the outer membrane bilayer. The MsbB enzyme myristoylates the lipid A precursor and loss of this enzyme, in Salmonella, is correlated with reduced virulence and severe growth defects that can both be compensated with extragenic suppressor mutations.

Results
We report here that msbB (or msbB somA) Salmonella are highly sensitive to physiological CO2 (5%), resulting in a 3-log reduction in plating efficiency. Under these conditions, msbB Salmonella form long filaments, bulge and lyse. These bacteria are also sensitive to acidic pH and high osmolarity. Although CO2 acidifies LB broth media, buffering LB to pH 7.5 did not restore growth of msbB mutants in CO2, indicating that the CO2-induced growth defects are not due to the effect of CO2 on the pH of the media. A transposon insertion in the glucose metabolism gene zwf compensates for the CO2 sensitivity of msbB Salmonella. The msbB zwf mutants grow on agar, or in broth, in the presence of 5% CO2. In addition, msbB zwf strains show improved growth in low pH or high osmolarity media compared to the single msbB mutant.

Conclusion
These results demonstrate that msbB confers acute sensitivity to CO2, acidic pH, and high osmolarity. Disruption of zwf in msbB mutants restores growth in 5% CO2 and results in improved growth in acidic media or in media with high osmolarity. These results add to a growing list of phenotypes caused by msbB and mutations that suppress specific growth defects.
Functional mapping of the fission yeast DNA polymerase δ B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis
Authors: Sanchez Garcia Javier , Baranovskiy Andrey G , Knatko Elena V , Gray Fiona C , Tahirov Tahir H , MacNeill Stuart A 
Published: August 2009

Abstract

Background
DNA polymerase δ plays an essential role in chromosomal DNA replication in eukaryotic cells, being responsible for synthesising the bulk of the lagging strand. In fission yeast, Pol δ is a heterotetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1. Pol3 binds directly to the B-subunit, Cdc1, which in turn binds the C-subunit, Cdc27. Human Pol δ comprises the same four subunits, and the crystal structure was recently reported of a complex of human p50 and the N-terminal domain of p66, the human orthologues of Cdc1 and Cdc27, respectively.

Results
To gain insights into the structure and function of Cdc1, random and directed mutagenesis techniques were used to create a collection of thirty alleles encoding mutant Cdc1 proteins. Each allele was tested for function in fission yeast and for binding of the altered protein to Pol3 and Cdc27 using the two-hybrid system. Additionally, the locations of the amino acid changes in each protein were mapped onto the three-dimensional structure of human p50. The results obtained from these studies identify amino acid residues and regions within the Cdc1 protein that are essential for interaction with Pol3 and Cdc27 and for in vivo function. Mutations specifically defective in Pol3-Cdc1 interactions allow the identification of a possible Pol3 binding surface on Cdc1.

Conclusion
In the absence of a three-dimensional structure of the entire Pol δ complex, the results of this study highlight regions in Cdc1 that are vital for protein function in vivo and provide valuable clues to possible protein-protein interaction surfaces on the Cdc1 protein that will be important targets for further study.
Notch signaling is required for maintaining stem-cell features of neuroprogenitor cells derived from human embryonic stem cells
Authors: Woo Sun-Mi , Kim Janghwan , Han Hyo-Won , Chae Jung-Il , Son Mi-Young , Cho Sunwha , Chung Hyung-Min , Han Yong-Mahn , Kang Yong-Kook 
Published: August 2009

Abstract

Background
Studies have provided important findings about the roles of Notch signaling in neural development. Unfortunately, however, most of these studies have investigated the neural stem cells (NSCs) of mice or other laboratory animals rather than humans, mainly owing to the difficulties associated with obtaining human brain samples. It prompted us to focus on neuroectodermal spheres (NESs) which are derived from human embryonic stem cell (hESC) and densely inhabited by NSCs. We here investigated the role of Notch signaling with the hESC-derived NESs.

Results
From hESCs, we derived NESs, the in-vitro version of brain-derived neurospheres. NES formation was confirmed by increased levels of various NSC marker genes and the emergence of rosette structures in which neuroprogenitors are known to reside. We found that Notch signaling, which maintains stem cell characteristics of in-vivo-derived neuroprogenitors, is active in these hESC-derived NESs, similar to their in-vivo counterpart. Expression levels of Notch signaling molecules such as NICD, DLLs, JAG1, HES1 and HES5 were increased in the NESs. Inhibition of the Notch signaling by a γ-secretase inhibitor reduced rosette structures, expression levels of NSC marker genes and proliferation potential in the NESs, and, if combined with withdrawal of growth factors, triggered differentiation toward neurons.

Conclusion
Our results indicate that the hESC-derived NESs, which share biochemical features with brain-derived neurospheres, maintain stem cell characteristics mainly through Notch signaling, which suggests that the hESC-derived NESs could be an in-vitro model for in-vivo neurogenesis.