bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel platform for virus-like particle-display of flaviviral envelope domain III: induction of Dengue and West Nile virus neutralizing antibodies
Authors: Chua Anthony JS , Vituret Cyrielle , Tan Melvin LC , Gonzalez Gaëlle , Boulanger Pierre , Ng Mah-Lee , Hong Saw-See 
Published: April 2013

AbstractCD16-RIgE is a chimeric human membrane glycoprotein consisting of the CD16 ectodomain fused to the transmembrane domain and cytoplasmic tail of the gamma chain of the high affinity receptor of IgE (RIgE). Coexpression of CD16-RIgE and HIV-1 Pr55Gag polyprotein precursor (Pr55GagHIV) in insect cells resulted in the incorporation of CD16-RIgE glycoprotein into the envelope of extracellular virus-like particles (VLPs), a phenomenon known as pseudotyping. Taking advantage of this property, we replaced the CD16 ectodomain of CD16-RIgE by the envelope glycoprotein domain III (DIII) of dengue virus serotype 1 (DENV1) or West Nile virus Kunjin (WNVKun). The two resulting chimeric proteins, DIII-DENV1-RIgE and DIII-WNVKun-RIgE, were addressed to the plasma membrane, exposed at the surface of human and insect cells, and incorporated into extracellular VLPs when coexpressed with Pr55GagHIVin insect cells. The DIII domains were accessible at the surface of retroviral VLPs, as shown by their reactivity with specific antibodies, and notably antibodies from patient sera. The DIII-RIgE proteins were found to be incorporated in VLPs made of SIV, MLV, or chimeric MLV-HIV Gag precursors, indicating that DIII-RIgE could pseudotype a wide variety of retroviral VLPs. VLP-displayed DIII were capable of inducing specific neutralizing antibodies against DENV and WNV in mice. Although the neutralization response was modest, our data confirmed the capability of DIII to induce a flavivirus neutralization response, and suggested that our VLP-displayed CD16-RIgE-based platform could be developed as a vaccine vector against different flaviviruses and other viral pathogens.
Expression and clinical significance of the proliferation marker minichromosome maintenance protein 2 (Mcm2) in diffuse astrocytomas WHO grade II
Authors: Lind-Landström Tove , Varughese Rosilin K , Sundstrøm Stein , Torp Sverre H 
Published: April 2013

AbstractBackgroundThe WHO classification system for astrocytomas is not considered optimal, mainly because of the subjective assessment of the histopathological features. Few prognostic variables have been found that stratify the risk of clinical progression in patients with grade II astrocytoma. For that reason there is a continuous search for biomarkers that can improve the histopathological diagnosis and prognostication of these tumours.AimThis study was designed to investigate the prognostic significance of the proliferative marker Mcm2 (minichromosome maintenance protein 2) in diffuse astrocytomas WHO grade II and correlate the findings with histopathology, mitoses, and Ki67/MIB-1 immunostaining.Method61 patients with histologically verified grade II astrocytoma (WHO 2007) were investigated. Paraffin sections were immunostained with anti-Mcm2, and the Mcm2 proliferative index (PI) was determined as the percentage of immunoreactive tumour cell nuclei.ResultsMcm2 PI was not associated with any histopathological features but correlated significantly with mitotic count and Ki67/MIB-1 PI (p<0.05). In the survival analyses Mcm2 showed trends to poorer survival, however, statistical significance was not achieved in the univariate analyses (p>0.05).ConclusionsIn our hands Mcm2 immunostaining has no advantage over Ki67/MIB-1 in the evaluation of grade II astrocytomas. Larger studies are needed to fully clarify the prognostic role of this biomarker.Virtual slidesThe virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/1715002791944037
Evaluation of normal appearing spinal cord by diffusion tensor imaging, fiber tracking, fractional anisotropy, and apparent diffusion coefficient measurement in 13 dogs
Authors: Hobert Marc K , Stein Veronika M , Dziallas Peter , Ludwig Davina C , Tipold Andrea 
Published: April 2013

Abstract

Background
Functional magnetic resonance (fMR) imaging offers plenty of new opportunities in the diagnosis of central nervous system diseases. Diffusion tensor imaging (DTI) is a technique sensitive to the random motion of water providing information about tissue architecture. We applied DTI to normal appearing spinal cords of 13 dogs of different breeds and body weights in a 3.0 T magnetic resonance (MR) scanner. The aim was to study fiber tracking (FT) patterns by tractography and the variations of the fractional anisotropy (FA) and the apparent diffusion coefficient (ADC) observed in the spinal cords of dogs with different sizes and at different locations (cervical and thoracolumbar). For that reason we added a DTI sequence to the standard clinical MR protocol. The values of FA and ADC were calculated by means of three regions of interest defined on the cervical or the thoracolumbar spinal cord (ROI 1, 2, and 3).

Results
The shape of the spinal cord fiber tracts was well illustrated following tractography and the exiting nerve roots could be differentiated from the spinal cord fiber tracts. Routine MR scanning times were extended for 8 to 12 min, depending on the size of the field of view (FOV), the slice thickness, and the size of the interslice gaps. In small breed dogs (< 15 kg body weight) the fibers could be tracked over a length of approximately 10 vertebral bodies with scanning times of about 8 min, whereas in large breed dogs (> 25 kg body weight) the traceable fiber length was about 5 vertebral bodies which took 10 to 12 min scanning time. FA and ADC values showed mean values of 0.447 (FA), and 0.560 × 10-3 mm2/s (ADC), respectively without any differences detected with regard to different dog sizes and spinal cord 45 segments examined.

Conclusion
FT is suitable for the graphical depiction of the canine spinal cord and the exiting nerve roots. The FA and ADC values offer an objective measure for evaluation of the spinal cord fiber integrity in dogs.
What are the impacts of urban agriculture programs on food security in low and middle-income countries?
Authors: Stewart Ruth , Korth Marcel , Langer Laurenz , Rafferty Shannon , Da Silva Natalie Rebelo , van Rooyen Carina 
Published: April 2013

Abstract
Background
Issues of food security and nutrition have wide reaching implications for people and their environments, particularly in low and middle-income countries. One proposed solution is urban agriculture, which has been widely upheld as a solution to the food-crisis facing increasingly metropolitan populations. It is believed to provide the urban poor with food and a source of potential income, whilst improving the urban environment and reducing pressure on finite farmland. Although it faded from many development agendas in the 1990’s, urban agriculture has seen a resurgence since a peak in global food prices in the late 2000’s. There are, however, potential disadvantages to this increasing drive for urban agriculture including associated urban health risks and implications for the environment. The usage of waste-water, for example, may contaminate produced food and intensive irrigation might lead to the spread of malaria and water borne diseases, as well as threatening already limited water supplies. Soil erosion and the intensive use of fertilizers and pesticides might also present health risks to urban populations and damage the environment. Despite the potential benefits and harms of urban agriculture, the evidence-base is not well understood. Given the current policy drive to promote urban agriculture, there is an urgent need to understand its effects on urban populations and their environments.

Methods/design
This review will seek out, select, appraise and synthesise evidence on the impacts of urban agriculture on food security and nutrition. We will employ systematic review methodology to ensure that our review of the evidence is comprehensive, transparent and replicable. In addition to searching electronic databases, we will examine websites and contact academics, practitioners and policy-makers for relevant research. All potentially relevant literature will be screened against pre-specified criteria and assessed for risk of bias using established critical appraisal tools. This is to ensure that we only include the evidence in which we have confidence. Depending on the nature of the available data, we will then synthesise the available evidence using statistical meta-analysis and/or narrative synthesis. Our findings will be disseminated in a variety of ways to ensure that the evidence is available for policy-makers and practitioners.
Sub-acute administration of (S)-dimethyl 2-(3-(phenyltellanyl) propanamido) succinate induces toxicity and oxidative stress in mice: unexpected effects of N-acetylcysteine
Authors: Meinerz Daiane F , Comparsi Bruna , Allebrandt Josiane , Mariano Douglas Oscar Ceolin , dos Santos Danúbia B , Zemolin Ana Paula Pegoraro , Farina Marcelo , Dafre Luiz Alcir , Rocha João B T , Posser Thaís , Franco Jeferson L 
Published: April 2013

Abstract
The organic tellurium compound (S)-dimethyl 2-(3-(phenyltellanyl) propanamide) succinate (TeAsp) exhibits thiol-peroxidase activity that could potentially offer protection against oxidative stress. However, data from the literature show that tellurium is a toxic agent to rodents. In order to mitigate such toxicity, N-acetylcysteine (NAC) was administered in parallel with TeAsp during 10 days. Mice were separated into four groups receiving daily injections of (A) vehicle (PBS 2.5 ml/kg, i.p. and DMSO 1 ml/kg, s.c.), (B) NAC (100 mg/kg, i.p. and DMSO s.c.), (C) PBS i.p. and TeAsp (92.5 μmol/kg, s.c), or (D) NAC plus TeAsp. TeAsp treatment started on the fourth day. Vehicle or NAC-treated animals showed an increase in body weight whereas TeAsp caused a significant reduction. Contrary to expected, NAC co-administration potentiated the toxic effect of TeAsp, causing a decrease in body weight. Vehicle, NAC or TeAsp did not affect the exploratory and motor activity in the open-field test at the end of the treatment, while the combination of NAC and TeAsp produced a significant decrease in these parameters. No DNA damage or alterations in cell viability were observed in leukocytes of treated animals. Treatments produced no or minor effects on the activities of antioxidant enzymes catalase, glutathione peroxidase and glutathione reductase, whereas the activity of the thioredoxin reductase was decreased in the brain and increased the liver of the animals in the groups receiving TeAsp or TeAsp plus NAC. In conclusion, the toxicity of TeAsp was potentiated by NAC and oxidative stress appears to play a central role in this process.
GENESIS-CBA: an agent-based model of peer evaluation and selection in the internet interdomain network
Authors: Lodhi Aemen , Dhamdhere Amogh , Dovrolis Constantine 
Published: April 2013

Abstract

Purpose
We propose an agent-based model for peer selection in the Internet at the Autonomous System (AS) level. The proposed model, GENESIS-CBA, is based on realistic constraints and provider selection mechanism, with ASes acting in a myopic and decentralized manner to optimize a cost-related fitness function. We introduce a new peering scheme, Cost-Benefit-Analysis, which, unlike existing peering strategies, gives ASes the ability to analyze the impact of each peering link on their economic fitness. Using this analysis, ASes engage in only those peering relations that can have a positive impact on their fitness.

Methods
Our proposed model captures the key factors that affect network formation dynamics: highly skewed traffic matrix, policy-based routing, geographic co-location constraints, and the costs of transit/peering agreements. As opposed to analytical game-theoretic models, which focus on proving the existence of equilibria, GENESIS-CBA is a computational model that simulates the network formation process and allows us to actually compute distinct equilibria (i.e., networks) and to also examine the behavior of sample paths that do not converge.

Results
We find that such oscillatory sample paths occur in about 7% of the runs, and they always involve tier-1 ASes. GENESIS-CBA results in many distinct equilibria that are highly sensitive to initial conditions and the order in which ASes (agents) act.

Conclusions
Our results imply that we cannot predict the properties of an individual AS in the Internet. However, certain properties of the global network or of certain classes of ASes are predictable.
Profiling of transcriptional and epigenetic changes during directed endothelial differentiation of human embryonic stem cells identifies FOXA2 as a marker of early mesoderm commitment
Authors: Howard Lynsey , Mackenzie Ruth M , Pchelintsev Nikolay A , McBryan Tony , McClure John D , McBride Martin W , Kane Nicole M , Adams Peter D , Milligan Graeme , Baker Andrew H 
Published: April 2013

Abstract
Introduction
Differentiation of vascular endothelial cells (ECs) in clinically relevant numbers for injection into ischaemic areas could offer therapeutic potential in the treatment of cardiovascular conditions, including myocardial infarction, peripheral vascular disease and stroke. While we and others have demonstrated successful generation of functional endothelial-like cells from human embryonic stem cells (hESCs), little is understood regarding the complex transcriptional and epigenetic changes that occur during differentiation, in particular during early commitment to a mesodermal lineage.

Methods
We performed the first gene expression microarray study of hESCs undergoing directed differentiation to ECs using a monolayer-based, feeder-free and serum-free protocol. Microarray results were confirmed by quantitative RT-PCR and immunocytochemistry, and chromatin immunoprecipitation (ChIP)-PCR analysis was utilised to determine the bivalent status of differentially expressed genes.

Results
We identified 22 transcription factors specific to early mesoderm commitment. Among these factors, FOXA2 was observed to be the most significantly differentially expressed at the hESC–EC day 2 timepoint. ChIP-PCR analysis revealed that the FOXA2 transcription start site is bivalently marked with histone modifications for both gene activation (H3K4me3) and repression (H3K27me3) in hESCs, suggesting the transcription factor may be a key regulator of hESC differentiation.

Conclusion
This enhanced knowledge of the lineage commitment process will help improve the design of directed differentiation protocols, increasing the yield of endothelial-like cells for regenerative medicine therapies in cardiovascular disease.
Bridging the gap between basic and applied biology: towards preclinical translation
Authors: Cagan Ross L. , Justice Monica J. , Tidmarsh George F. 
Published: April 2013

Summary
To better translate basic research findings into the clinic, we are moving away from the traditional one-gene–one-phenotype model towards the discovery of complex mechanisms. In this Editorial, the new Editor-in-Chief and Senior Editors of Disease Models & Mechanisms (DMM) discuss the role that the journal will play in this transition. DMM will continue to provide a platform for studies that bridge basic and applied science, and, by demanding the rigorous assessment of animal models of disease, will help drive the establishment of robust standards of preclinical testing for drug development.
Karyoskeletal proteins and the organization of the amphibian oocyte nucleus
Authors: Benavente Ricardo , Krohne Georg , Schmidt-Zachmann Marion S. , Hügle Barbara , Franke Werner W. 
Published: April 2013

ABSTRACT
We have investigated the existence of structural components in the nucleus of the oocyte of Xenopus laevis and other amphibia that are insoluble in non-denaturing detergents and buffers of low and high ionic strength. These cells are particularly suitable for such studies as they have a high frequency of extrachromosomal amplified nucleoli and pore complexes of the nuclear envelope. Using biochemical and immunological techniques, we have shown these structures to contain only two major proteins. These are a polypeptide of M, 145 000, which is located in a meshwork of filaments specific to the nucleolar cortex, and certain nucleoplasmic bodies probably derived therefrom, and a polypeptide of Mr 68 000, which is the predominant constituent of the lamina-pore complex structure. We show that the latter protein is related to, but not identical to, lamina proteins (‘lamins’) of somatic cells, indicating cell type-specificity of the expression of polypeptides of the lamin family. In addition, we describe a protein of Mr 180 000, which is the major constituent of the dense fibrillar component of the nucleolus. This can be partially solubilized in buffers of moderately high ionic strength. We interpret proteins of this category as karyoskeletal components involved in the architectural organization of specific functional topology within the nucleus. In contrast to previous reports for other cell types we have found no other prominent high-salt-insoluble structures in the nuclear interior, indicating the absence of an extended internal nuclear matrix in this kind of nucleus.
Spatial organization of the drosophila nucleus: a three-dimensional cytogenetic study
Authors: Gruenbaum Y. , Hochstrasser M. , Mathog D. , Saumweber H. , Agard D. A. , Sedat J. W. 
Published: April 2013

ABSTRACT
The combination of optical fluorescence microscopy with digital image processing and analysis has been used to examine the three-dimensional organization of chromosomes within intact polytene nuclei. Although the arrangement indicates a high degree of flexibility, there are many conserved features between nuclei at the same developmental state. For example, chromosome arms are loosely coiled with centromeres clustered at the opposite end of the nucleus from the telomeres. Individual chromosome arms are not interwoven but occupy different spatial domains. Chromosomal sites that contact the envelope correlate with intercalary heterochromatin. Connections are observed between actively transcribing regions.
Replication and transcription depend on attachment of DNA to the nuclear cage
Authors: Jackson D. A. , McCREADY S. J. , Cook P. R. 
Published: April 2013

ABSTRACT
When living cells are lysed in a non-ionic detergent and 2M-NaCl, structures are released that resemble nuclei. They contain naked nuclear DNA packaged within a flexible cage of RNA and protein. Since the DNA is supercoiled, it must be intact and looped by attachment to the cage. It is argued that this cage is the active site of the key nuclear functions, transcription and replication: outlying sequences are activated by attachment to polymerases at the cage. This thesis is supported by the close and specific association of nascent RNA with cages, the attachment of active viral sequences (in transformed and productively infected cells) and the attachment of nascent DNA during both normal and repair synthesis.
Some ultrastructural aspects of genetic activity in eukaryotes
Authors: Miller Oscar L. 
Published: April 2013

ABSTRACT
A brief overview is given of the types of information that have been obtained by chromatin spreading methods regarding the ultrastructure and regulation of genetic units. The examples used are : ribosomal RNA genes of the spotted newt ; the silk fibroin gene of Bombyx mori ; chorion gene amplification in Drosophila melanogaster-, RNA synthesis patterns during early embryogenesis of D. melanogaster-, regulation of transcription on homologous non-ribosomal transcription units of D. melanogaster-, specific nascent transcript cleavage in insects; and nascent polypeptides on insect polyribosomes. The conclusion is drawn that further innovations will be required before significant advances in the use of chromatin spreading techniques to study ultrastructural aspects of genetic activity can occur.
A structural analysis of the role of the nuclear matrix and DNA loops in the organization of the nucleus and chromosome
Authors: Pienta Kenneth J. , Coffey Donald S. 
Published: April 2013

ABSTRACT
The interphase nucleus is characterized by a nuclear matrix structure that forms a residual scaffolding composed of approximately 10% of the total nuclear proteins. The nuclear matrix contains residual elements of the pore-complex and lamina, the nucleolus, and an intranuclear fibrous network that provides the basic shape and structure of the nucleus. In the interphase nucleus this nuclear matrix has been reported to be a central element in the organization of DNA loop domains and to contain fixed sites for DNA replication and transcription. In this study, we have analysed the role of the nuclear matrix and the DNA loop domains in the organization and structure of the number 4 human chromosome. A model is proposed that closely approximates the observed structural dimensions of this chromosome. The model is composed of 30 nm diameter filaments formed from a solenoid of six nucleosomes per turn. This 30 nm solenoid filament is organized as loops of DNA each containing approximately 60 000 base-pairs; each loop is anchored at its base to the nuclear matrix. A radial loop model containing 18 of these loops per turn forms a new unit of chromosome structure termed the miniband. Approximately 106 of these minibands are arranged along a central axis to form the final chromatid. The role of the nuclear matrix in this organization is presented. The accuracy of the proposed model is tested by comparing its features with the known properties of the number 4 human chromosome.
Stimuli-responsive Synthetic Metallopeptides
Authors: Tashiro Shohei , Shionoya Mitsuhiko 
Published: April 2013

Abstract
Inspired by vital roles of metal ions as structure-stabilizing and regulating factors in biological systems, a great number of synthetic metallopeptides have been developed. This review focuses on metal-mediated stabilization and stimuli-responsive regulation of their secondary and higher-order structures by taking advantage of the characteristics of metal ions such as Lewis acidity, ligand-exchange ability, and redox properties.
Medical and Biological Effects of Pulse Noises and Distinctions of Their Hygienic Rationing (Review)
Authors: Кукушкин  , Kukushkin Yu. , Ворона  , Vorona A. , Симухин  , Simukhin V. , Богомолов  , Bogomolov A. , Рыженков  , Ryzhenkov S. 
Published: April 2013

Distinctions of pulse noises as dangerous technogenetics factors are described, modern ideas of medical and
biological effects of pulse noises action are generalized and modern approaches to their hygienic rationing are
stated.