bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arabidopsis thaliana as a model organism in systems biology
Authors: Van Norman Jaimie M. , Benfey Philip N. 
Published: April 2009

AbstractSignificant progress has been made in the identification of genes and gene networks involved in key biological processes. Yet, how these genes and networks are coordinated over increasing levels of biological complexity, from cells to tissues to organs, remains unclear. To address complex biological questions, biologists are increasingly using high‐throughput tools and systems biology approaches to examine complex biological systems at a global scale. A system is a network of interacting and interdependent components that shape the system's unique properties. Systems biology studies the organization of system components and their interactions, with the idea that unique properties of that system can be observed only through study of the system as a whole. The application of systems biology approaches to questions in plant biology has been informative. In this review, we give examples of how systems biology is currently being used in Arabidopsis to investigate the transcriptional networks regulating root development, the metabolic response to stress, and the genetic regulation of metabolic variability. From these studies, we are beginning to obtain sufficient data to generate more accurate models for system function. Further investigation of plant systems will require data gathering from specific cells and tissues, continued improvement in metabolic technologies, and novel computational methods for data visualization and modeling. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Physiology > Physiology of Model Organisms
Synthesis and Description of a Novel Metal‐organic Framework Based on Trigonal Prismatic Building Blocks
Authors: Li Bing , Zheng Shou‐Tian , Yang Guo‐Yu 
Published: April 2009

AbstractA novel metal‐organic framework based on trigonal prismatic building blocks has been hydrothermally prepared and structurally characterized. It crystallizes in the cubic space group Pa$\bar{3}$ with Z = 8. The oxo‐centered trinuclear complex units are bridged by 1,3‐benzenedicarboxylate (1,3‐BDC) ligands, forming a new 3D open‐framework [Fe3O(H2O)3(1,3‐BDC)3][Cl]·9H2O (1). Its magnetic behavior has been quantitively analyzed by the Bleaney–Bowers equation, indicating the presence of antiferromagnetic interactions within the trinuclear FeIII atoms.
Intra‐Abdominal Pressure and Abdominal Compartment Syndrome in Acute General Surgery
Authors: Sugrue Michael , Buhkari Yasir 
Published: April 2009

AbstractBackgroundIntra‐abdominal pressure (IAP) is a harbinger of intra‐abdominal mischief, and its measurement is cheap, simple to perform, and reproducible. Intra‐abdominal hypertension (IAH), especially grades 3 and 4 (IAP > 18 mmHg), occurs in over a third of patients and is associated with an increase in intra‐abdominal sepsis, bleeding, renal failure, and death.Patients and methodsIncreased IAP reading may provide an objective bedside stimulus for surgeons to expedite diagnostic and therapeutic work‐up of critically ill patients. One of the greatest challenges surgeons and intensivists face worldwide is lack of recognition of the known association between IAH, ACS, and intra‐abdominal sepsis. This lack of awareness of IAH and its progression to ACS may delay timely intervention and contribute to excessive patient resuscitation.ConclusionsAll patients entering the intensive care unit (ICU) after emergency general surgery or massive fluid resuscitation should have an IAP measurement performed every 6 h. Each ICU should have guidelines relating to techniques of IAP measurement and an algorithm for management of IAH.
Dynamics of Parathyroid Hormone Secretion After Total Parathyroidectomy and Autotransplantation
Authors: Conti‐Freitas Luiz Carlos , Foss‐Freitas Maria Cristina , Lucca Leandro Junior , da Costa Jose Abrão Cardeal , Mamede Rui Celso Martins , Foss Milton Cesar 
Published: April 2009

AbstractBackgroundSecondary hyperparathyroidism is a common complication in uremic patients. Total parathyroidectomy combined with partial autotransplantation into brachioradialis muscle has been the preference among the options for surgical treatment. This study was designed to evaluate the reserve and ability of suppression of autotransplanted parathyroid tissue using dynamics tests.MethodsWe studied, prospectively, 12 patients in recent (RP) and late (LP) postoperative of total parathyroidectomy with autotransplantation. For analysis of the secretory reserve capacity, we induced hypocalcemia by ethylenediaminetetraacetic acid (EDTA) infusion. Furthermore, for analysis of the ability for parathyroid hormone (PTH) suppression, the hypercalcemia test was used, by intravenous administration of calcium in LP.ResultsIn RP, there was a decrease in the average serum levels of PTH, phosphorus, and alkaline phosphatase, which ranged from 13 to 231 (87 ± 65) pg/ml, 2.3 to 6.2 (3.3 ± 1.1) mg/dl, and 77 to 504 (250 ± 135) U/L, respectively, similar to that observed in LP. The analysis of the average curve of variations in PTH during testing of the stimulus with EDTA showed lack of secretion in RP and partial response in LP. Impaired suppression ability of the graft in LP was observed in the test with intravenous calcium.ConclusionsTotal parathyroidectomy followed by partial autotransplantation was effective in reducing PTH serum levels in patients with terminal kidney disease. The elevation of serum calcium during the suppression test was not able to inhibit the autograft gland secretion of PTH. The assessment of parathyroid graft function demonstrated an inability to respond to the stimulus of hypocalcemia induced by EDTA, although there was a partial recovery, in late postoperative period.
Cognitive functions and glycemic control in children and adolescents with type 1 diabetes
Authors: Ohmann S. , Popow C. , Rami B. , König M. , Blaas S. , Fliri C. , Schober E. 
Published: April 2009

BackgroundThe relationship between metabolic control and cognitive function in adolescents with type 1 diabetes (DM type 1) is not clear. We compared the quality of glycemic control (GC) and cognitive measures in adolescents with DM type 1 to find out if the quality of diabetes management is related to cognitive impairment.MethodWe assessed executive functions (EFs) and other neuropsychological and psychosocial variables in 70 adolescent patients with DM type 1 and 20 age-matched controls. Patients were divided into two groups according to their last hemoglobin A1c (HbA1c): acceptable (HbA1c 5.9–8.0%, mean 6.9%, 36 patients, mean age 14 years) and non-optimal (HbA1c 8.2–11.6%, mean 9.3%, 34 patients, mean age 15.6 years).ResultsWe found impaired EFs, mainly problems of concept formation (p=0.038), cognitive flexibility (p=0.011) and anticipation (p=0.000), in the patients with DM type 1. Both groups did not differ in intelligence, most assessed EFs and adjustment to chronic illness (Youth Self-Report; YSR). Younger patients (<15 years) were cognitively less flexible. GC was worse in older patients and in patients with longer duration of the disease. We also found significant differences between patients with diabetes and controls concerning somatic complaints, internalizing problems (Child Behavior Checklist; CBCL) and social activity (CBCL and YSR).ConclusionsDM type 1 is associated with cognitive deficits in adolescents independent of the quality of metabolic control and the duration of the disease. These deficits are probably related to the disease, especially in patients with early-onset diabetes.
Leibniz on ‘prophets’, prophecy, and revelation
Authors: COOK DANIEL J. 
Published: April 2009

AbstractDuring Leibniz's lifetime, interest in the interpretation of the Bible and biblical prophecy became central to the theological and political concerns of Protestant Europe. Leibniz's treatment of this phenomenon will be examined in the light of his views on the nature of revelation and its role in his defence of Christianity. It will be argued that Leibniz's defence of the miracle of revelation (and its vehicle, biblical prophecy) – unlike his arguments on behalf of the core Christian mysteries of the Trinity and Incarnation – is demonstrable by purely natural and scientific means, especially the verification of history.
Security and the problem of context: a hermeneutical critique of securitisation theory
Authors: CIUTǍ FELIX 
Published: April 2009

AbstractHow do we know when we are dealing with security issue? This is a cardinal question in Security Studies, and securitisation theory provides and authoritative yet incomplete answer, mainly because it rules out that the meaning of security can vary contextually. To overcome this limitation, we need a hermeneutical perspective centred on the liminality of security as a category in-between theory and policy, which produces a more precise algorithm for empirical research. A contextual hermeneutics of security signals that normative awareness is necessary even in the absence of a unifying normative manifesto, also confronts the spectre of the “death of security” invoked by those who object to the potentially endless broadening of its meaning.
Bi-directional pheromone communication between robots
Authors: Purnamadjaja Anies Hannawati , Russell R. Andrew 
Published: April 2009

SUMMARYThis paper describes a project that aims to demonstrate two-way communication between robots using chemical signals. The project is part of a wider investigation examining the potential advantages and drawbacks of implementing pheromone signalling between robots. It is well known that all kinds of biological creatures use chemicals as a means of attracting, repelling, controlling, guiding and informing their fellow creatures. This very wide range of effective biological forms of chemical communication is the inspiration to look at potential robotic applications. In previous work involving the use of physical chemical signals in robotics the case of one robot releasing or depositing a chemical for other robots (or the same robot) to detect and act upon has been addressed. This project moves a step forward to investigate a group of robots where each group member emits and detects pheromone chemicals. The example task addressed in the project is to use chemical signalling to help a collection of robots to assess group size. Bacteria provide a model for this kind of chemical communication. By monitoring chemical concentration bacteria can assess group size and hence modify their behaviour as appropriate. Although not intending to model bacterial quorum sensing in detail this behaviour provides inspiration for our demonstration of bi-directional communication. This paper provides details of the implementation of quorum sensing in a group of robots. The robots used in the project, their control algorithms and experimental results are presented. Both beneficial aspects and the pitfalls of pheromone communication in robotic systems are also discussed.
Truncated Fourier series formulation for bipedal walking balance control
Authors: Yang Lin , Chew Chee-Meng , Zheng Yu , Poo Aun-Neow 
Published: April 2009

SUMMARYThis paper studies the parameters contained in the truncated Fourier series (TFS) formulation for bipedal walking balance control. Using the TFS generated lateral motion reference, 3D bipedal walking can be directly achieved without any parameter adjustment. Furthermore, the potential of this TFS formulation for motion balance control has also been investigated. One more motion balance strategy is developed through the reinforcement learning, which adjusts the motion's reference trajectory according to the selected dynamic feedback in real time. Dynamic simulation results of the presented balance control method show that the resulting motion can be constrained periodical and long-distance 3D bipedal walking motions are achievable.
Modifications of chemically induced-enucleated nuclear transfer technique by reverse-order nuclear transfer in mouse
Authors: Wang Yongsheng , Liu Jun , Tang Shuang , An Zhixing , Guo Zhilin , Ding Xiangbin , Liu Fengjun , Cao Zelei , Zhang Tuo , Zhang Yong 
Published: April 2009

SummaryTo improve the developmental potential of somatic cell cloned embryos derived from demecolcine (DC) induced-enucleated nuclear transfer (INT), we modified the INT procedures by transferring donor nuclei into recipient cytoplasts prior to the induced enucleation of the recipient cytoplasts, and we called this modified INT technique as reverse-order and induced-enucleated nuclear transfer (RINT). Standard nuclear transfer (SNT) and INT were performed as controls. The dynamic changes of maternal and transferred donor nuclei in the RINT oocytes were monitored to evaluate the feasibility of this new nuclear transfer (NT) technique by timed immunofluorescence. Timed immunofluorescence showed that RINT is feasible because none of the transferred donor nuclei were expelled with the second polar body (Pb) in the RINT oocytes, while 42.2% of the oocytes showed extrusion of all maternal chromosome and spindles with the second Pb at 60 min after activation and DC treatment. Although there was no difference in cleavage rate (86.6% vs. 82.1%), the rates of successful enucleation and blastocyst formation were significantly increased in RINT compared with INT (44.1% vs. 27.5% and 43.3% vs. 12.8%, respectively;p< 0.01). Compared with SNT, there was no difference in cleavage rate (86.6% vs. 78.4%), but the blastocyst developmental rate was significantly increased in the RINT group (43.3% vs. 25.3%;p< 0.01). Blastocysts derived from RINT had a higher total cell number than those from SNT (45.1 ± 3 vs. 37.6 ± 4;p< 0.05). Our results provide evidence that RINT is feasible and may provide a more efficient and simple method for NT than INT.
Apoptotic processes and DNA cytosine methylation in mouse embryos arrested at the 2-cell stage
Authors: Fabian Dušan , Bukovská Alexandra , Juhás Štefan , Koppel Juraj 
Published: April 2009

SummaryThe present study evaluates the role of apoptotic cell death and DNA methylation reprogramming in early developmental failures occurring in embryos at the 2-cell stage. Mouse 2-cell embryos were culturedin vitroand treated with chemicals that cause developmental arrest and apoptosis (α-amanitin, actinomycin D, TNF-α). After 24 h, 48 h and 72 h culture, embryos were analysed using cell-death assays (annexin V staining, TUNEL labelling and immunodetection of active caspase-3) and genome methylation assay (immunodetection of 5-methylcytosine). The ability of embryos at the 2-cell stage to undergo apoptotic processes was very low. In arrested embryos, the presence of all evaluated features of apoptosis was recorded only after 72 h culture and their incidence was sporadical. Interestingly, the most frequently observed apoptotic sign was nuclear condensation and the timing of its appearance preceded even the phosphatidylserine flip. Both normally developing and arrested embryos displayed reduction in DNA cytosine methylation. In arrested embryos, this process was independent of cellular cleavage, was more pronounced and finished in almost complete demethylation of the embryonic genome. The timing of the demethylation overlapped with the onset of major apoptotic events. Although observed apoptotic cells showed either demethylated or methylated DNA cytosine in their nuclei, at blastocyst stage the demethylated status appeared more frequently in them.
Perceptual Control Theory as an integrative framework and Method of Levels as a cognitive therapy: what are the pros and cons?
Authors: Mansell Warren 
Published: April 2009

AbstractThis article considers the pros and cons of using Method of Levels (MOL), a therapy based on Perceptual Control Theory (PCT). Five concerns about PCT are that it is an early theory, is not well known, originates from outside psychology, implies that established theories are inaccurate and has a mechanistic approach. Five positive features are that it explains how ‘control’ works, takes a phenomenological perspective, is grounded in biology, integrates many disciplines and has an evidence base. Five features of MOL can raise caution: it is not well known, emphasizes intrinsic change, requires the therapist to let go of control, concentrate intensively and use alternative evaluations of outcome. There are major advantages: it is a simple process to learn; theory-practice links are clear, it is ‘ultra cognitive therapy’ – focused on the present moment, client-centred and enables shifting in perspective, promotes service empowerment, and has an evidence base. This article will help therapists make an informed choice about using MOL.
PCT and MOL: a brief history of Perceptual Control Theory and the Method of Levels
Authors: Powers William T. 
Published: April 2009

AbstractI have been asked to describe how Perceptual Control Theory (PCT) and Method of Levels (MOL) came into being, and as I approach the age of 82 that seems a prudent request. Some parts of the following should probably be taken more as a reconstruction than a verifiable record of the past, but I will strive for realism.
Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison
Authors: Mithani Aziz , Preston Gail M. , Hein Jotun 
Published: April 2009

Abstract
Summary:We present a tool called Rahnuma for prediction and analysis of metabolic pathways and comparison of metabolic networks. Rahnuma represents metabolic networks as hypergraphs and computes all possible pathways between two or more metabolites. It provides an intuitive way to answer biological ques- tions focusing on differences between organisms or the evolution of different species by allowing pathway-based metabolic network comparisons at an organism as well as at a phylogenetic level.
Availability: Rahnuma is available online at http://portal.stats.ox.ac.uk:8080/rahnuma/.
Contact: gail.preston@plants.ox.ac.uk
Supplementary information: Supplementary data are available at the Bioinformatics online.
List-decoding methods for inferring polynomials in finite dynamical gene network models
Authors: Dingel Janis , Milenkovic Olgica 
Published: April 2009

Abstract
Motivation: The problem of reverse engineering the dynamics of gene expression profiles is of focal importance in systems biology. Due to noise and the inherent lack of sufficiently large datasets generated via high-throughput measurements, known reconstruction frameworks based on dynamical systems models fail to provide adequate settings for network analysis. This motivates the study of new approaches that produce stochastic lists of explanations for the observed network dynamics that can be efficiently inferred from small sample sets and in the presence of errors.
Results: We introduce a novel algebraic modeling framework, termed stochastic polynomial dynamical systems (SPDSs) that can capture the dynamics of regulatory networks based on microarray expression data. Here, we refer to dynamics of the network as the trajectories of gene expression profiles over time. The model assumes that the expression data is quantized in a manner that allows for imposing a finite field structure on the observations, and the existence of polynomial update functions for each gene in the network. The underlying reverse engineering algorithm is based on ideas borrowed from coding theory, and in particular, list-decoding methods for so called Reed-Muller codes. The list-decoding method was tested on synthetic data and on microarray expression measurements from the M3D database, corresponding to a subnetwork of the Escherichia coli SOS repair system, as well as on the complete transcription factor network, available at RegulonDB. The results show that SPDSs constructed via list-decoders significantly outperform other algebraic reverse engineering methods, and that they also provide good guidelines for estimating the influence of genes on the dynamics of the network.
Availability: Software codes for list-decoding algorithms suitable for direct application to quantized expression data will be publicly available at the authors' web-pages.
Contact: janis.dingel@tum.de; milenkov@uiuc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets
Authors: Hazelett Dennis J. , Lakeland Daniel L. , Weiss Joseph B. 
Published: April 2009

Abstract
Methods: A new method was developed for identifying novel transcription factor regulatory targets based on calculating Local Affinity Density. Techniques from the signal-processing field were used, in particular the Hann digital filter, to calculate the relative binding affinity of different regions based on previously published in vitro binding data. To illustrate this approach, the complete genomes of Drosophila melanogaster and D.pseudoobscura were analyzed for binding sites of the homeodomain proteinc Tinman, an essential heart development gene in both Drosophila and Mouse. The significant binding regions were identified relative to genomic background and assigned to putative target genes. Valid candidates common to both species of Drosophila were selected as a test of conservation.
Results: The new method was more sensitive than cluster searches for conserved binding motifs with respect to positive identification of known Tinman targets. Our Local Affinity Density method also identified a significantly greater proportion of Tinman-coexpressed genes than equivalent, optimized cluster searching. In addition, this new method predicted a significantly greater than expected number of genes with previously published RNAi phenotypes in the heart.
Availability: Algorithms were implemented in Python, LISP, R and maxima, using MySQL to access locally mirrored sequence data from Ensembl (D.melanogaster release 4.3) and flybase (D.pseudoobscura). All code is licensed under GPL and freely available at http://www.ohsu.edu/cellbio/dev_biol_prog/affinitydensity/.
Contact: hazelett@ohsu.edu
Optimizing static thermodynamic models of transcriptional regulation
Authors: Bauer Denis C. , Bailey Timothy L. 
Published: April 2009

Abstract
Motivation: Modeling transcriptional regulation using thermo-dynamic modeling approaches has become increasingly relevant as a way to gain a detailed understanding of transcriptional regulation. Thermodynamic models are able to model the interactions between transcription factors (TFs) and DNA that lead to a specific transcriptional output of the target gene. Such models can be ‘trained’ by fitting their free parameters to data on the transcription rate of a gene and the concentrations of its regulating factors. However, the parameter fitting process is computationally very expensive and this limits the number of alternative types of model that can be explored.
Results: In this study, we evaluate the ‘optimization landscape’ of a class of static, quantitative models of regulation and explore the efficiency of a range of optimization methods. We evaluate eight optimization methods: two variants of simulated annealing (SA), four variants of gradient descent (GD), a hybrid SA/GD algorithm and a genetic algorithm. We show that the optimization landscape has numerous local optima, resulting in poor performance for the GD methods. SA with a simple geometric cooling schedule performs best among all tested methods. In particular, we see no advantage to using the more sophisticated ‘LAM’ cooling schedule. Overall, a good approximate solution is achievable in minutes using SA with a simple cooling schedule.
Contact: d.bauer@uq.edu.au; t.bailey@imb.uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.