bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Epigenetic Model for Pigment Patterning Based on Mechanical and Cellular Interactions
Authors: Caballero Lorena , BenÍtez Mariana , Alvarez‐buylla Elena R. , HernÁndez Sergio , Arzola Alejandro V. , Cocho Germinal 
Published: April 2012

ABSTRACTPigment patterning in animals generally occurs during early developmental stages and has ecological, physiological, ethological, and evolutionary significance. Despite the relative simplicity of color patterns, their emergence depends upon multilevel complex processes. Thus, theoretical models have become necessary tools to further understand how such patterns emerge. Recent studies have reevaluated the importance of epigenetic, as well as genetic factors in developmental pattern formation. Yet epigenetic phenomena, specially those related to physical constraints that might be involved in the emergence of color patterns, have not been fully studied. In this article, we propose a model of color patterning in which epigenetic aspects such as cell migration, cell–tissue interactions, and physical and mechanical phenomena are central. This model considers that motile cells embedded in a fibrous, viscoelastic matrix—mesenchyme—can deform it in such a way that tension tracks are formed. We postulate that these tracks act, in turn, as guides for subsequent cell migration and establishment, generating long‐range phenomenological interactions. We aim to describe some general aspects of this developmental phenomenon with a rather simple mathematical model. Then we discuss our model in the context of available experimental and morphological evidence for reptiles, amphibians, and fishes, and compare it with other patterning models. We also put forward novel testable predictions derived from our model, regarding, for instance, the localization of the postulated tension tracks, and we propose new experiments. Finally, we discuss how the proposed mechanism could constitute a dynamic patterning module accounting for pattern formation in many animal lineages. J. Exp. Zool. (Mol. Dev. Evol.) 318:209–223, 2012. © 2012 Wiley Periodicals, Inc.
A procedure for the detection of undocumented multiple abrupt changes in the mean value of daily temperature time series of a regional network
Authors: Rienzner M. , Gandolfi C. 
Published: April 2012

AbstractThis paper presents the new procedure MAC‐D for the automated detection of undocumented Multiple Abrupt Changes in the mean value of Daily temperature series, recorded in a network of meteorological stations. MAC‐D can be applied to series containing seasonality, multiple change points, outliers, and with a noise component that can be autocorrelated and non‐normally distributed. The main novelties of the procedure are (1) the pretreatment of the observed series, to derive a series of daily values that complies with the theoretical requirements of the change point detection tests and in (2) the combined use of the reference series and pairwise comparison approaches. MAC‐D consists of three phases in sequence. In phase 1, the seasonal and climatic fluctuations are estimated and removed, using the reference series approach. Phase 2 combines a linear filtering with a change point detection test in an iterative algorithm, which runs until full compliance between the characteristics of the filtered series and the test requirements is achieved. Phase 3 is aimed at removing the false change points, due to error propagation in the reference series analysis, by double checking the detected change points with the pairwise comparison approach. Monte Carlo estimations of the actual significance and overall performance of the procedure for different series features and test resolutions are provided. Results demonstrate that MAC‐D performs very well with daily series having a wide range of different characteristics. Copyright © 2012 Royal Meteorological Society
Systematic differences in future 20 year temperature extremes in AR4 model projections over Australia as a function of model skill
Authors: Perkins S. E. , Pitman A. J. , Sisson S. A. 
Published: April 2012

AbstractThe projection of temperature extremes by climate models participating in the Intergovernmental Panel on Climate Change Fourth Assessment Report (AR4) are examined regionally over Australia. Minimum and maximum temperature extremes are defined as the 20 year return value calculated using extreme value theory. Three measures of model evaluation, a means‐based, a distribution‐based [via probability density functions (PDFs)] and an extreme‐based (via the tails of PDFs) method, are used to compare daily model data to observed daily data over various climatic regions for a 20 year period. Model ensembles consisting of the ‘better’ and ‘poorer’ models determined by each measure of skill are created for each region. These are compared with an all‐model ensemble to examine the difference in more skilled ensemble projections of temperature extremes in the A2 (high emissions) scenario for 2046‐2065 and 2081‐2100. If either of the distribution‐based evaluation methods were used to distinguish models, the higher skilled models projected smaller increases in the 20 year return values than the all‐model ensemble for both maximum temperature and minimum temperature. For some regions, the 90% confidence intervals of the better and poorer ensemble ranges did not overlap, indicating that projections are statistically significantly different. We show that the means‐based evaluation produces less consistent results to the two distribution‐based evaluation methods. We conclude that specific AR4 models, shown to be relatively poor over most regions of Australia by different skill metrics, bias the projected increase in the 20 year temperature extremes towards higher values. We also suggest that performance in simulating the mean climate is an unreliable measure of climate model capacity used to select models for projecting changes in extremes over Australia. Copyright © 2012 Royal Meteorological Society
Sampling large landscapes with small‐scale stratification
Authors: Bart Jonathan , Dunn Leah , Leist Amy , Sabin Laura 
Published: April 2012

AbstractThis study, carried out for the United States Bureau of Reclamation (BOR), demonstrated methods for surveying large landscapes using small‐scale, habitat‐based stratification, a common problem that has heretofore received little attention. The goal was to design a sampling plan for detecting change in the density of breeding birds of 6 species occurring along the Colorado River around and south of Lake Mead in the southwestern United States. The main problem in designing the study was that the focal species were concentrated in small, irregularly shaped patches of habitat. We partitioned the study area into >15,000 plots configured to enclose the high‐quality habitat in the fewest possible plots with the constraint that plots could be surveyed in 1 morning by 1 person. Because of the irregular plot shapes and extremely dense vegetation, we used area searches to carry out the surveys. We used double‐sampling, including a large sample of plots surveyed with a rapid method and a subsample of plots surveyed intensively, to estimate detection ratios. A simulation study helped allocate effort between rapid and intensive surveys and indicated that conducting 80 surveys per year would achieve high power to detect a 50% decline occurring during 20 years. This is one of the first studies to show how large landscapes can be sampled using small‐scale stratification so that effort can be concentrated in the habitats of greatest interest. © 2012 The Wildlife Society.
Habitat and landscape correlates of southern flying squirrel use of red‐cockaded woodpecker clusters
Authors: Loeb Susan C. , Reid Shawna L. , Lipscomb Donald J. 
Published: April 2012

AbstractSouthern flying squirrels (Glaucomys volans) can have significant negative impacts on red‐cockaded woodpecker (Picoides borealis) reproductive success and group size. Although direct control of southern flying squirrels may be necessary in small red‐cockaded woodpecker populations (<30 groups), creation of high quality habitat through landscape management is the preferred method for managing larger woodpecker populations. Thus, we determined the habitat and landscape factors within 100 m, 400 m, and 800 m of cluster centers that were related to southern flying squirrel use of red‐cockaded woodpecker cavities at the Carolina Sandhills National Wildlife Refuge, South Carolina. At all spatial scales, the number of cavities in the cluster was the most influential variable determining use by southern flying squirrels. At the 400‐m and 800‐m scales, the amount of stream length was also positively associated with the presence of flying squirrels. The proximity and amount of hardwoods surrounding clusters were not related to southern flying squirrel use at any spatial scale; thus, removal or conversion of hardwood stands surrounding red‐cockaded woodpeckers may not be necessary for reducing cavity kleptoparasitism by flying squirrels. However, when establishing recruitment clusters, areas with streams should be avoided and addition of artificial cavities to existing clusters should be done judiciously to minimize the number of excess cavities. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.
Multi‐scale assessment of greater sage‐grouse fence collision as a function of site and broad scale factors
Authors: Stevens Bryan S. , Connelly John W. , Reese Kerry P. 
Published: April 2012

AbstractPrevious research in Europe and North America suggested grouse are susceptible to collision with infrastructure, and anecdotal observation suggested greater sage‐grouse (Centrocercus urophasianus) fence collision in breeding habitats may be prevalent. However, no previous research systematically studied greater sage‐grouse fence collision in any portion of their range. We used data from probability‐based sampling of fences in greater sage‐grouse breeding habitats of southern Idaho, USA, to model factors associated with collision at microsite and broad spatial scales. Site‐scale modeling suggested collision may be influenced by technical attributes of fences, with collisions common at fence segments absent wooden fence posts and with segment widths >4 m. Broad‐scale modeling suggested relative probability of collision was influenced by region, a terrain ruggedness index (TRI), and fence density per square km. Conditional on those factors, collision counts were also influenced by distance to nearest active sage‐grouse lek. Our models provide a conceptual framework for prioritizing sage‐grouse breeding habitats for collision mitigation such as fence marking or moving, and suggest mitigation in breeding habitats should start in areas with moderate‐high fence densities (>1 km/km2) within 2 km of active leks. However, TRI attenuated other covariate effects, and mean TRI/km2 >10 m nearly eliminated sage‐grouse collision. Thus, our data suggested mitigation should focus on sites with flat to gently rolling terrain. Moreover, site‐scale modeling suggested constructing fences with larger and more conspicuous wooden fence posts and segment widths <4 m may reduce collision. © 2012 The Wildlife Society.
“Assessing the RAFT Equilibrium Constant via Model Systems: An EPR Study”—Response to a Comment
Authors: Meiser Wibke , Buback Michael 
Published: April 2012

AbstractWe have presented an EPR‐based approach for deducing the RAFT equilibrium constant, Keq, of a dithiobenzoate‐mediated system [Meiser, W. and Buback M. Macromol. Rapid Commun. 2011, 32, 1490]. Our value is by four orders of magnitude below Keq from ab initio calculations for the identical monomer‐free system. Junkers et al. [Macromol. Rapid Commun. 2011, 32, 1891] claim that our EPR approach would be model dependent and our data could be equally well fitted by assuming slow addition of radicals to the RAFT agent and slow fragmentation of the so‐obtained intermediate radical as well as high cross‐termination rate. By identification of all side products, our EPR‐based method is shown to be model independent and to provide reliable Keq values, which demonstrate the validity of the intermediate radical termination model.
Further results on H ∞  control for discrete‐time uncertain singular systems with interval time‐varying delays in state and input
Authors: Zhu Huanyu , Zhang Xian , Cui Shaochun 
Published: April 2012

SUMMARYThis paper investigates the state feedback robust H ∞  control problem of a class of discrete‐time singular systems with norm‐bounded uncertainties and interval time‐varying delays in state and input. A new bounded real lemma for discrete‐time singular systems with a pair of time‐varying interval state delays is first investigated. Mathematical comparisons of the new bounded real lemma and two existing ones are presented. Then, on the basis of the bounded real lemma proposed here, a sufficient condition in the form of nonlinear matrix inequality, such that the considered state feedback robust H ∞  control problem is solvable, is given. In order to solve the nonlinear matrix inequality, a cone complementarity linearization algorithm is offered. Several numerical examples are presented to show the applicability of the proposed approach. Copyright © 2012 John Wiley & Sons, Ltd.
Expression and stability of hypoxia inducible factor 1α in osteosarcoma
Authors: El Naggar Amal , Clarkson Paul , Zhang Fan , Mathers Joan , Tognon Cristina , Sorensen Poul H. 
Published: April 2012

AbstractBackgroundHypoxia contributes to both physiological and pathological processes and its effects are mainly mediated through the transcription factors hypoxia‐inducible factor 1α and 2α (HIF1α and HIF2α). The purpose of this study was to examine the role of these proteins in osteosarcoma progression.ProceduresWe developed a method to isolate primary human osteoblast cell lines. HIF1α and HIF2α expression were then compared in osteoblast and osteosarcoma cell lines under 21% oxygen (normoxia) and 1% oxygen (hypoxia). We also used hypoxia‐responsive element (HRE)‐driven reporter constructs in conjunction with siRNAs specific to HIF1α or HIF2α to determine the contribution of each protein to HRE‐mediated transcription. Finally, we measured HIF1α expression in primary osteosarcoma tumors by immunohistochemistry.ResultsWe found that mainly HIF1α transcript was significantly higher in osteosarcoma cell lines compared to normal osteoblasts under both normoxia and hypoxia. At the protein level, HIF1α was preferentially stabilized in osteosarcoma cell lines under both conditions. HIF1α expression was required for the observed increases in HRE activity. Finally, nuclear or nucleocytoplasmic HIF1α staining in osteosarcoma cases was associated with high‐grade tumors.ConclusionsThese findings point to a role for HIF1α in osteosarcoma progression and suggest that the observed differences in HIF1α oxygen dependent degradation may play an important pathophysiological role in this disease. Pediatr Blood Cancer 2012; 59: 1215–1222. © 2012 Wiley Periodicals, Inc.
Validation of a claims‐based diagnostic code for Stevens–Johnson syndrome in a commercially insured population
Authors: Eisenberg Debra F , Daniel Gregory W , Jones Judith K , Goehring Earl L , Wahl Peter M , Winters Peter , Levin Jay , Bohn Rhonda L 
Published: April 2012

ABSTRACTPurposeTo validate the administrative claims identification of a diagnosis of Stevens–Johnson syndrome (SJS) using medical records as the “gold standard” in a large, commercially insured US population.MethodsPatients with >1 medical claim with the International Classification of Diseases, Ninth Revision, Clinical Modification code 695.1x between 1 July 2000 and 31 May 2007 were queried in the HealthCore Integrated Research DatabaseSM, which contains administrative claims data for 14 commercial health insurance plans. Trained nurses and pharmacists abstracted pertinent information from the identified patients' medical records, which were then reviewed by two independent dermatologists to identify criteria to determine SJS diagnosis. Positive predictive values (PPVs) based on the claims and chart data were computed for all the cases.ResultsMedical charts for 200 claims‐identified cases, with the International Classification of Diseases, Ninth Revision, Clinical Modification code 695.1x, were abstracted and reviewed by the dermatologists. A total of five cases (PPV = 2.50%, 95%CI = 0.8%–5.7%) were determined to be SJS with clinical certainty. PPVs varied with data stratification: PPV for inpatient claims only (PPV = 2.00%, 95%CI = 0.24%–7.04%), inpatient claims with 695.1x in first diagnosis field (PPV = 4.11%, 95%CI = 0.86%–11.54%), and final decisions of either clinical certainty or probable cases of SJS (PPV = 6.00%, 95%CI = 3.14%–10.25%).ConclusionThese findings demonstrate the difficulties associated with identifying rare disorders, which lack specific diagnostic criteria, within administrative claims databases. They underscore the challenges of using claims data to monitor ill‐defined clinical conditions as well as the need to validate claims‐identified cases with information from other sources, such as medical charts. Copyright © 2012 John Wiley & Sons, Ltd.
Packaging materials with tailor made light transmission properties for food protection
Authors: Intawiwat Natthorn , Myhre Elina , Øysæd Harry , Jamtvedt Svein H. , Pettersen Marit Kvalvåg 
Published: April 2012

AbstractPackaging material with optimal light barrier properties can prevent food quality deterioration. For dairy products, wavelength in the visible region between 400–450 nm and 600–650 nm should be blocked out due to the content of chlorophyll in dairy products. Six low density polyethylene blown films were formulated with the combination of four different pigments and additives: green, yellow, silver additive, and optical brightener, in addition to four reference samples. All films were transparent. Optical properties and light transmission were measured for each film, and microscopy analyses were used to investigate the surface topography. The sample containing high concentration of both green and yellow pigments had the lowest value in gloss and transmittance. This film blocked the light below 450 nm and transmitted 10% at 600–650 nm. Optical brightener had an effect only on visual appearance but not on light transmission properties. Samples containing silver additive were more intense green and gave a higher light transmission in blue region (380–500 nm) and lower in red region (600–700 nm) compared with samples without silver additive. These developed films can be applied in dairy products and other food products in the future. POLYM. ENG. SCI., 52:2015–2024, 2012. © 2012 Society of Plastics Engineers
PRL‐dock: Protein‐ligand docking based on hydrogen bond matching and probabilistic relaxation labeling
Authors: Wu Meng‐Yun , Dai Dao‐Qing , Yan Hong 
Published: April 2012

AbstractProtein‐ligand docking is widely applied to structure‐based virtual screening for drug discovery. This article presents a novel docking technique, PRL‐Dock, based on hydrogen bond matching and probabilistic relaxation labeling. It deals with multiple hydrogen bonds and can match many acceptors and donors simultaneously. In the matching process, the initial probability of matching an acceptor with a donor is estimated by an efficient scoring function and the compatibility coefficients are assigned according to the coexisting condition of two hydrogen bonds. After hydrogen bond matching, the geometric complementarity of the interacting donor and acceptor sites is taken into account for displacement of the ligand. It is reduced to an optimization problem to calculate the optimal translation and rotation matrixes that minimize the root mean square deviation between two sets of points, which can be solved using the Kabsch algorithm. In addition to the van der Waals interaction, the contribution of intermolecular hydrogen bonds in a complex is included in the scoring function to evaluate the docking quality. A modified Lennard‐Jones 12‐6 dispersion‐repulsion term is used to estimate the van der Waals interaction to make the scoring function fairly “soft” so that ligands are not heavily penalized for small errors in the binding geometry. The calculation of this scoring function is very convenient. The evaluation is carried out on 278 rigid complexes and 93 flexible ones where there is at least one intermolecular hydrogen bond. The experiment results of docking accuracy and prediction of binding affinity demonstrate that the proposed method is highly effective. Proteins 2012; © 2012 Wiley Periodicals, Inc.
CT‐guided stereotactic targeting accuracy of osteoid osteoma
Authors: Widmann Gerlig , Schullian Peter , Fasser Martin , Niederwanger Christian , Bale Reto 
Published: April 2012

AbstractBackgroundThe aim of this study was to evaluate the CT‐guided stereotactic targeting accuracy for radiofrequency ablation of osteoid osteoma (OO), a small, benign but painful osseous lesion.MethodsPatient and extremity were fixed in a vacuum cushion. The OO was targeted using an optical navigation system with a stereotactic targeting device. For evaluation of targeting errors, the control CT with the needle in place was fused with the planning CT.ResultsIn 16 consecutive patients, nine OOs in the femur, four in the tibia, one in the spine, one in the ulna and one in the pubic bone were successfully targeted without complications. The mean ± SD lateral targeting error was 2.6 ± 1.7 mm at the needle entry and 1.9 ± 1.2 mm at the needle tip, and the mean angular error was 2.0 ± 1.3°.ConclusionStereotaxy allows for accurate and safe targeting of OOs in various bone regions. Copyright © 2012 John Wiley & Sons, Ltd.
Topology discovery of sparse random graphs with few participants
Authors: Anandkumar Animashree , Hassidim Avinatan , Kelner Jonathan 
Published: April 2012

AbstractWe consider the task of topology discovery of sparse random graphs using end‐to‐end random measurements (e.g., delay) between a subset of nodes, referred to as the participants. The rest of the nodes are hidden, and do not provide any information for topology discovery. We consider topology discovery under two routing models: (a) the participants exchange messages along the shortest paths and obtain end‐to‐end measurements, and (b) additionally, the participants exchange messages along the second shortest path. For scenario (a), our proposed algorithm results in a sub‐linear edit‐distance guarantee using a sub‐linear number of uniformly selected participants. For scenario (b), we obtain a much stronger result, and show that we can achieve consistent reconstruction when a sub‐linear number of uniformly selected nodes participate. This implies that accurate discovery of sparse random graphs is tractable using an extremely small number of participants. We finally obtain a lower bound on the number of participants required by any algorithm to reconstruct the original random graph up to a given edit distance. We also demonstrate that while consistent discovery is tractable for sparse random graphs using a small number of participants, in general, there are graphs which cannot be discovered by any algorithm even with a significant number of participants, and with the availability of end‐to‐end information along all the paths between the participants. © 2012 Wiley Periodicals, Inc. Random Struct. Alg., 2013