bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrated proteomics analysis of bone tissues in response to mechanical stimulation
Authors: Li Jiliang , Zhang Fan , Chen Jake Y 
Published: December 2011

Abstract
Bone cells can sense physical forces and convert mechanical stimulation conditions into biochemical signals that lead to expression of mechanically sensitive genes and proteins. However, it is still poorly understood how genes and proteins in bone cells are orchestrated to respond to mechanical stimulations. In this research, we applied integrated proteomics, statistical, and network biology techniques to study proteome-level changes to bone tissue cells in response to two different conditions, normal loading and fatigue loading. We harvested ulna midshafts and isolated proteins from the control, loaded, and fatigue loaded Rats. Using a label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) experimental proteomics technique, we derived a comprehensive list of 1,058 proteins that are differentially expressed among normal loading, fatigue loading, and controls. By carefully developing protein selection filters and statistical models, we were able to identify 42 proteins representing 21 Rat genes that were significantly associated with bone cells' response to quantitative changes between normal loading and fatigue loading conditions. We further applied network biology techniques by building a fatigue loading activated protein-protein interaction subnetwork involving 9 of the human-homolog counterpart of the 21 rat genes in a large connected network component. Our study shows that the combination of decreased anti-apoptotic factor, Raf1, and increased pro-apoptotic factor, PDCD8, results in significant increase in the number of apoptotic osteocytes following fatigue loading. We believe controlling osteoblast differentiation/proliferation and osteocyte apoptosis could be promising directions for developing future therapeutic solutions for related bone diseases.
Bayesian parameter estimation for nonlinear modelling of biological pathways
Authors: Ghasemi Omid , Lindsey Merry L , Yang Tianyi , Nguyen Nguyen , Huang Yufei , Jin Yu-Fang 
Published: December 2011

Abstract

Background
The availability of temporal measurements on biological experiments has significantly promoted research areas in systems biology. To gain insight into the interaction and regulation of biological systems, mathematical frameworks such as ordinary differential equations have been widely applied to model biological pathways and interpret the temporal data. Hill equations are the preferred formats to represent the reaction rate in differential equation frameworks, due to their simple structures and their capabilities for easy fitting to saturated experimental measurements. However, Hill equations are highly nonlinearly parameterized functions, and parameters in these functions cannot be measured easily. Additionally, because of its high nonlinearity, adaptive parameter estimation algorithms developed for linear parameterized differential equations cannot be applied. Therefore, parameter estimation in nonlinearly parameterized differential equation models for biological pathways is both challenging and rewarding. In this study, we propose a Bayesian parameter estimation algorithm to estimate parameters in nonlinear mathematical models for biological pathways using time series data.

Results
We used the Runge-Kutta method to transform differential equations to difference equations assuming a known structure of the differential equations. This transformation allowed us to generate predictions dependent on previous states and to apply a Bayesian approach, namely, the Markov chain Monte Carlo (MCMC) method. We applied this approach to the biological pathways involved in the left ventricle (LV) response to myocardial infarction (MI) and verified our algorithm by estimating two parameters in a Hill equation embedded in the nonlinear model. We further evaluated our estimation performance with different parameter settings and signal to noise ratios. Our results demonstrated the effectiveness of the algorithm for both linearly and nonlinearly parameterized dynamic systems.

Conclusions
Our proposed Bayesian algorithm successfully estimated parameters in nonlinear mathematical models for biological pathways. This method can be further extended to high order systems and thus provides a useful tool to analyze biological dynamics and extract information using temporal data.
A Distal Modular Enhancer Complex Acts to Control Pituitary- and Nervous System-Specific Expression of the LHX3 Regulatory Gene
Authors: Mullen Rachel D. , Park Soyoung , Rhodes Simon J. 
Published: December 2011

AbstractLin-11, Isl-1, and Mec-3 (LIM)-homeodomain (HD)-class transcription factors are critical for many aspects of mammalian organogenesis. Of these, LHX3 is essential for pituitary gland and nervous system development. Pediatric patients with mutations in coding regions of the LHX3 gene have complex syndromes, including combined pituitary hormone deficiency and nervous system defects resulting in symptoms such as dwarfism, thyroid insufficiency, infertility, and developmental delay. The pathways underlying early pituitary development are poorly understood, and the mechanisms by which the LHX3 gene is regulated in vivo are not known. Using bioinformatic and transgenic mouse approaches, we show that multiple conserved enhancers downstream of the human LHX3 gene direct expression to the developing pituitary and spinal cord in a pattern consistent with endogenous LHX3 expression. Several transferable cis elements can individually guide nervous system expression. However, a single 180-bp minimal enhancer is sufficient to confer specific expression in the developing pituitary. Within this sequence, tandem binding sites recognized by the islet-1 (ISL1) LIM-HD protein are essential for enhancer activity in the pituitary and spine, and a pituitary homeobox 1 (PITX1) bicoid class HD element is required for spatial patterning in the developing pituitary. This study establishes ISL1 as a novel transcriptional regulator of LHX3 and describes a potential mechanism for regulation by PITX1. Moreover, these studies suggest models for analyses of the transcriptional pathways coordinating the expression of other LIM-HD genes and provide tools for the molecular analysis and genetic counseling of pediatric patients with combined pituitary hormone deficiency.
Structure and CO Oxidation Activity of Pt/CeO2 Catalysts Prepared Using Arc-Plasma
Authors: Hinokuma Satoshi , Okamoto Madoka , Ando Eriko , Ikeue Keita , Machida Masato 
Published: December 2011

Abstract
By applying a pulsed arc-plasma process, Pt nanoparticles were deposited from a Pt cathode onto CeO2 powders to study their structure and catalytic activity for CO oxidation. Highly dispersed uniform metallic Pt crystallites with the size of 2.6 ± 0.7 nm were obtained. Because of the highly dispersed metallic Pt nanoparticles suitable for CO chemisorption, the catalyst prepared by arc-plasma exhibited higher CO oxidation activity than those prepared by conventional wet impregnation. However, the catalyst was deactivated to a larger extent compared to the impregnated catalyst after thermal aging at 900 °C in a stream of 10% H2O in air.
Quantification of Methylated Markers with a Multiplex Methylation-Specific Technology
Authors: Zou Hongzhi , Allawi Hatim , Cao Xiaoming , Domanico Mike , Harrington Jonathan , Taylor William R , Yab Tracy , Ahlquist David A , Lidgard Graham 
Published: December 2011

Abstract

BACKGROUND
Aberrantly methylated genes represent important markers for cancer diagnosis. We describe a multiplex detection approach to efficiently quantify these markers for clinical applications such as colorectal cancer screening.

METHODS
Quantitative allele-specific real-time target and signal amplification (QuARTS) combines a polymerase-based target amplification with an invasive cleavage-based signal amplification. The fluorescence signal is detected in a fashion similar to real-time PCR. We measured the dynamic range and analytical sensitivity of multiplex QuARTS reactions with titrated plasmid DNA. We used the QuARTS technology to quantify methylated BMP3, NDRG4, VIM, and TFPI2 genes on 91 DNA samples extracted from colorectal tissues, including 37 cancers, 25 adenomas, and 29 healthy epithelia. The assays were designed in triplex format that incorporated ACTB as a reference gene. Percent methylation was calculated by dividing methylated strands over ACTB strands and multiplying by 100.

RESULTS
The QuARTS method linearly detected methylated or unmethylated VIM gene down to 10 copies. No cross-reactivity was observed when methylated assays were used to amplify 105 copies of unmethylated gene and vice versa. The multiplex assay detected methylated genes spiked in unmethylated genes at a 0.01% ratio and vice versa. At a diagnostic specificity cutoff of 95%, methylated BMP3, NDRG4, VIM, and TFPI2 detected 84%, 92%, 86%, and 92% of colorectal cancers and 68%, 76%, 76%, and 88% of adenomas, respectively.

CONCLUSIONS
The QuARTS technology provides a promising approach for quantifying methylated markers. The markers assayed highly discriminated colorectal neoplasia from healthy epithelia.
Surface and Dermal Sampling
Authors: Brisson Michael J. , Ashley Kevin 
Published: December 2011

Description
Get the latest research available on surface and dermal sampling to assess contamination levels and detect harmful agents. Twenty peer-reviewed papers discuss sampling techniques, analytical measurement technologies, reference materials, standardization, occupational hygiene, decontamination methods, and quality assurance.
Topics cover:
Standardization Issues—includes papers which summarize current standards for surface and dermal sampling and the need for additional standards, particularly in the area of dermal sampling
Dermal—addresses contaminants on skin, including sampling, removal, and adherence of contaminated materials to the skin
Lead—deals with sampling, sample preparation, analytical proficiency testing, and lead dust loadings on surfaces other than skin
Beryllium—covers beryllium surface contamination in various industries and measurement of beryllium on surface wipe samples
Asbestos—deals with evaluation of samples collected from surfaces contaminated with asbestos
Pharmaceuticals—focuses on occupational exposure to pharmaceutical substances, as well as spills and leakage of antibiotics on surfaces
General Topics—covers investigations of outdoor environmental surface particulate; microbiological contamination on surfaces; assessments of properties contaminated with methamphetamine; and more.
Local and Systemic Cellular Immunity in Early Renal Artery Atherosclerosis
Authors: Kotliar Carol , Juncos Luis , Inserra Felipe , de Cavanagh Elena M.V. , Chuluyan Eduardo , Aquino Jorge B. , Hita Alejandro , Navari Carlos , Sánchez Ramiro 
Published: December 2011

Summary

Background and objectives
Modern imaging techniques have increased the incidental detection of renal atherosclerotic disease (RAD). Because immune activation may hasten RAD progression, identifying cellular immune markers might provide clues to clinical activity. In this study, cellular immune markers were assessed in early RAD.

Design, setting, participants, & measurements
Immune cell markers in peripheral blood of two groups of hypertensive patients with normal carotid and coronary arteries were evaluated: 28 patients had incidental RAD and 22 patients had normal renal arteries; 21 renal arteries obtained at necropsy from individuals with history of hypertension and tissue evidence of RAD were examined and matched with 21 individuals with normal renal arteries. Cell subpopulations were measured by flow cytometry in peripheral blood and direct cell count, respectively, using T and dendritic cells monoclonal antibodies.

Results
Peripheral blood of RAD patients showed increased numbers of cells expressing CD3, CD4, CD83, and CD86. CD4 to CD8 ratio was 8.3 ± 1.4 (RAD) to 3.4 ± 0.9 (normal; P<0.001). No differences were found in CD25, CD8, and S100 among groups. Postmortem samples from RAD showed increased CD3+, CD4+, CD86+, and S100+ cells, whereas CD25+ and CD8+ were unmodified between groups. CD4+ to CD8+ ratio was higher in the RADPM group.

Conclusions
These results are consistent with an increased expression of immune cell markers in early RAD. Additional studies will explore if they may potentially turn into treatment targets to prevent disease progression.
Prolactin Levels, Endothelial Dysfunction, and the Risk of Cardiovascular Events and Mortality in Patients with CKD
Authors: Carrero Juan Jesús , Kyriazis John , Sonmez Alper , Tzanakis Ioannis , Qureshi Abdul Rashid , Stenvinkel Peter , Saglam Mutlu , Stylianou Kostas , Yaman Halil , Taslipinar Abdullah , Vural Abdulgaffar , Gok Mahmut , Yenicesu Mujdat , Daphnis Eugene , Yilmaz Mahmut Ilker 
Published: December 2011

Summary

Background and objectives
Both prolactin clearance and production are altered in CKD. In nonrenal populations, emerging evidence suggests that prolactin participates in the atherosclerotic process. Given the elevated cardiovascular risk of CKD, this study examined links between prolactinemia, vascular derangements, and outcomes.

Design, setting, participants, & measurements
This observational study was conducted in two cohorts: one with 457 nondialyzed CKD patients (mean age 52±12 years; 229 men) with measurements of flow-mediated dilation (FMD) and carotid intima-media thickness and one with 173 hemodialysis patients (65±12 years; 111 men) with measurements of pulse wave velocity (PWV). Patients were followed for cardiovascular events (n=146, nondialyzed cohort) or death (n=79, hemodialysis cohort).

Results
Prolactin levels increased along with reduced kidney function. Prolactin significantly and independently contributed to explain the variance of both FMD (in nondialyzed patients) and PWV (in hemodialysis patients), but not intima-media thickness. In Cox analyses, the risk of cardiovascular events in nondialyzed patients increased by 27% (hazard ratio [HR], 1.27; 95% confidence interval [95% CI], 1.17–1.38) for each 10 ng/ml increment of prolactin. Similarly, the risk for all-cause and cardiovascular mortality in hemodialysis patients increased by 12% (HR, 1.12; 95% CI, 1.06–1.17) and 15% (HR, 1.15; 95% CI, 1.08–1.21), respectively. This was true after multivariate adjustment for confounders and after adjustment within the purported causal pathway (FMD or PWV).

Conclusions
Prolactin levels directly associated with endothelial dysfunction/stiffness and with increased risk of cardiovascular events and mortality in two independent cohorts of CKD patients.
An Institutional Framework for Creating Authentic Digital Objects
Authors: Jantz Ronald 
Published: December 2011

In the future, a scholar or researcher will want to know that a digital object is trusted - that it is authentic and reliable.Â Digital objects can be surrogates, resulting from a digitization process, or they can be objects whose only form is digital.Â Much has been accomplished in existing open source digital library platforms to provide capabilities for preserving digital objects including now ubiquitous features such as persistent identifiers, integrity checks, audit trails, and versioning.Â However, achieving a level of digital object authenticity will require a multi-dimensional approach involving policies, processes, and continued technological innovation.Â This paper proposes steps that the institution can take to insure the availability of authentic digital objects in the future.Â In this proposal, authenticity is based on definitions from archival diplomatics and relies on methods from public key cryptography for digitally signing an object with a secure time stamp. Trustworthy processes, re-definition of traditional roles, and the implementation of technologies to support authenticity are all required to meet the needs of digital scholarship.Â Implementation and policy issues are discussed with specific attention to transformations required of the archival institution and the professional archivist.
Strategies for the Curation of CAD Engineering Models
Authors: Patel Manjula , Ball Alexander , Ding Lian 
Published: December 2011

Product Lifecycle Management (PLM) has become increasingly important in the engineering community over the last decade or so, due to the globalisation of markets and the rising popularity of products provided as services. It demands the efficient capture, representation, organisation, retrieval and reuse of product data over its entire life. Simultaneously, there is now a much greater reliance on CAD models for communicating designs to manufacturers, builders, maintenance crews and regulators, and for definitively expressing designs. Creating the engineering record digitally, however, presents problems not only for its long-term maintenance and accessibility - due in part to the rapid obsolescence of the hardware, software and file formats involved - but also for recording the evolution of designs, artefacts and products. We examine the curation and preservation requirements in PLM and suggest ways of alleviating the problems of sustaining CAD engineering models through the use of lightweight formats, layered annotation and the collection of Representation Information as defined in the Open Archival Information System (OAIS) Reference Model.Â We describe two tools which have been specifically developed to aid in the curation of CAD engineering models in the context of PLM: Lightweight Models with Multilayered Annotation (LiMMA) and a Registry/Repository of Representation Information for Engineering (RRoRIfE).
UK Government Web Continuity: Persisting Access through Aligning Infrastructures
Authors: Spencer Amanda , Sheridan John , Thomas David , Pullinger David 
Published: December 2011

Government's use of the Web in the UK is prolific and a wide range of services are now available though this channel. The government set out to address the problem that links from Hansard (the transcripts of Parliamentary debates) were not maintained over time and that therefore there was need for some long-term storage and stewardship of information, including maintaining access. Further investigation revealed that linking was key, not only in maintaining access to information, but also to the discovery of information. This resulted in a project that affects the entireÂ government Web estate, with a solution leveraging the basic building blocks of the Internet (DNS) and the Web (HTTP and URIs) in a pragmatic way, to ensure that an infrastructure is in place to provide access to important information both now and in the future.
ContextMiner: Supporting the Mining of Contextual Information for Ephemeral Digital Video Preservation
Authors: Shah Chirag 
Published: December 2011

Emerging information media present new challenges to the curators. While archiving objects, and building meaningful collection for long-term preservation and access, have been well-understood practice for centuaries, digital objects present new issues. In the previous article (Shah, 2009) I identified a number of these issues related to digital objects, specifically digital videos of an ephemeral nature. I argued that while preserving such objects, adding contextual information is essential. One of the interesting challenges is to identify what to collect and preserve as contextual information. For ephemeral digital videos, I proposed to harvest four kinds of relevances and five kinds of contexts. In order to implement this proposal, I presented ContextMiner, a framework and a system to support digital video curation. In this article, I will take a closer look at ContextMiner, analyzing it for its functionalities and usability. This is done by usability inspection and content analysis. For the former, we simulated two curatorial tasks, asked our users (curators) to use ContextMiner, and provide us feedback on its usability and functionalities. For the latter, we mined a collection prepared by ContextMiner for its potential usage in preservation. Finally, I have summarized the lessons learned from developing and using our system, providing implications for digital library curators interested in collecting and preserving digital objects of an ephemeral nature.Â Â Â
Multi-scale Data Sharing in the Life Sciences: Some Lessons for Policy Makers
Authors: Pryor Graham 
Published: December 2011

Drawing on the final report on a recent series of case studies in the life sciences at the University of Edinburgh, this paper explores the attitudes and perceptions of researchers towards data sharing and contrasts these with the policies of the major research funders. Notwithstanding economic, technical and cultural inhibitors, the general ethos in the Life Sciences is one of support to the principle of data sharing. However, this position is subject to a complex range of qualifications, not least the crucial need for sharing through collaboration. The kind of generic vision for data sharing that is currently promoted by national agencies is judged to be neither productive nor effective.Â Only close engagement with research practitioners in the identification of bottom-up strategies that preserve the exercise of informed choice - a fundamental and persistent element of scientific research - will produce change on a national scale.
A Framework for Software Preservation
Authors: Matthews Brian , Shaon Arif , Bicarregui Juan , Jones Catherine 
Published: December 2011

Software preservation has not had detailed consideration as a research topic or in practical application. In this paper, we present a conceptual framework to capture and organise the main notions of software preservation, which are required for a coherent and comprehensive approach.Â This framework has three main aspects. Firstly a discussion of what it means to preserve software via a performance model which considers how a software artefact can be rebuilt from preserved components and can then be seen to be representative of the original software product. Secondly the development of a model of software artefacts, describing the basic components of all software, loosely based on the FRBR model for representing digital artefacts and their history within a library context. Finally, the definition and categorisation of the properties of software artefacts which are required to ensure that the software product has been adequately preserved. These are broken down into a number of categories and related to the concepts defined in the OAIS standard. We also discuss our experience of recording these preservation properties for a number of BADC software products, which arose from a series of case studies conducted to evaluate the software preservation framework, and also briefly describe the SPEQS toolkit, a tool to capture software preservation properties within a software development.