bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatially explicit capture–recapture estimator for single‐catch traps
Authors: Distiller Greg , Borchers David L. 
Published: October 2015

AbstractSingle‐catch traps are frequently used in live‐trapping studies of small mammals. Thus far, a likelihood for single‐catch traps has proven elusive and usually the likelihood for multicatch traps is used for spatially explicit capture–recapture (SECR) analyses of such data. Previous work found the multicatch likelihood to provide a robust estimator of average density. We build on a recently developed continuous‐time model for SECR to derive a likelihood for single‐catch traps. We use this to develop an estimator based on observed capture times and compare its performance by simulation to that of the multicatch estimator for various scenarios with nonconstant density surfaces. While the multicatch estimator is found to be a surprisingly robust estimator of average density, its performance deteriorates with high trap saturation and increasing density gradients. Moreover, it is found to be a poor estimator of the height of the detection function. By contrast, the single‐catch estimators of density, distribution, and detection function parameters are found to be unbiased or nearly unbiased in all scenarios considered. This gain comes at the cost of higher variance. If there is no interest in interpreting the detection function parameters themselves, and if density is expected to be fairly constant over the survey region, then the multicatch estimator performs well with single‐catch traps. However if accurate estimation of the detection function is of interest, or if density is expected to vary substantially in space, then there is merit in using the single‐catch estimator when trap saturation is above about 60%. The estimator's performance is improved if care is taken to place traps so as to span the range of variables that affect animal distribution. As a single‐catch likelihood with unknown capture times remains intractable for now, researchers using single‐catch traps should aim to incorporate timing devices with their traps.
Plasma markers of oxidative stress are uncorrelated in a wild mammal
Authors: Christensen Louise L. , Selman Colin , Blount Jonathan D. , Pilkington Jill G. , Watt Kathryn A. , Pemberton Josephine M. , Reid Jane M. , Nussey Daniel H. 
Published: October 2015

AbstractOxidative stress, which results from an imbalance between the production of potentially damaging reactive oxygen species versus antioxidant defenses and repair mechanisms, has been proposed as an important mediator of life‐history trade‐offs. A plethora of biomarkers associated with oxidative stress exist, but few ecological studies have examined the relationships among different markers in organisms experiencing natural conditions or tested whether those relationships are stable across different environments and demographic groups. It is therefore not clear to what extent studies of different markers can be compared, or whether studies that focus on a single marker can draw general conclusions regarding oxidative stress. We measured widely used markers of oxidative damage (protein carbonyls and malondialdehyde) and antioxidant defense (superoxide dismutase and total antioxidant capacity) from 706 plasma samples collected over a 4‐year period in a wild population of Soay sheep on St Kilda. We quantified the correlation structure among these four markers across the entire sample set and also within separate years, age groups (lambs and adults), and sexes. We found some moderately strong correlations between some pairs of markers when data from all 4 years were pooled. However, these correlations were caused by considerable among‐year variation in mean marker values; correlation coefficients were small and not significantly different from zero after accounting for among‐year variation. Furthermore, within each year, age, and sex subgroup, the pairwise correlation coefficients among the four markers were weak, nonsignificant, and distributed around zero. In addition, principal component analysis confirmed that the four markers represented four independent axes of variation. Our results suggest that plasma markers of oxidative stress may vary dramatically among years, presumably due to environmental conditions, and that this variation can induce population‐level correlations among markers even in the absence of any correlations within contemporaneous subgroups. The absence of any consistent correlations within years or demographic subgroups implies that care must be taken when generalizing from observed relationships with oxidative stress markers, as each marker may reflect different and potentially uncoupled biochemical processes.
Wave: a distributed scheduling algorithm for convergecast in IEEE 802.15.4e TSCH networks
Authors: Soua Ridha , Minet Pascale , Livolant Erwan 
Published: October 2015

AbstractThe IEEE 802.15.4e MAC amendment has been proposed to meet the requirements of industrial applications. Using slotted medium access with channel hopping, the MAC layer orchestrates the medium accesses of nodes according to a given schedule. Nevertheless, this amendment does not specify how this schedule is computed. The purpose of this paper is to propose a distributed joint time slot and channel assignment, called Wave, for data gathering in low‐power lossy networks. This schedule targets minimised data convergecast delays by reducing the total number of slots in the schedule. Moreover, Wave ensures the absence of conflicting transmissions in the schedule provided. In such a schedule, a node is awake only during its transmission slots and those of its children in the convergecast routing graph. Thus, energy efficiency is ensured. In this paper, we present Wave with its properties (e.g. support of heterogeneous traffic, support of a sink equipped with multiple interfaces, worst case delays and buffer size) and compare it with a centralised scheduling algorithm like TMCP and a distributed one like DeTAS. Simulation results show the good performance of Wave compared with TMCP. Because in an industrial environment, several routing graphs can coexist, we study how Wave supports this coexistence. Copyright © 2015 John Wiley & Sons, Ltd.
Retracted: Early hominin biogeography in Island Southeast Asia
Authors: Larick Roy , Ciochon Russell L. 
Published: October 2015

The above article from Evolutionary Anthropology, published on 19 October 2015 in Wiley OnlineLibrary (www.onlinelibrary.wiley.com), and in Volume 24, Number 5, pp. 185‐213, has been retracted by Wiley Periodicals, Inc. The retraction has been made due to the inclusion without explicit permission of unpublished third‐party research data disclosed to the authors in personal correspondence. The Editor notes that the journal has since clarified its policy on citing unpublished research findings, and in particular those disclosed in personal correspondence, to avoid future instances of this nature.REFERENCE
Larick, R. and
Ciochon, R. L. (2015), . Anthropol., 24: 185–213. doi:10.1002/evan.21460
Nanoscale surface modification by anodic oxidation increased bone ingrowth and reduced fibrous tissue in the porous coating of titanium–alloy femoral hip arthroplasty implants
Authors: Hall Deborah J. , Urban Robert M. , Pourzal Robin , Turner Thomas M. , Skipor Anastasia K. , Jacobs Joshua J. 
Published: October 2015

AbstractHip arthroplasty femoral stems coated with Ti6Al4V beads were treated by anodic oxidation in H3PO4 for enhanced bioactivity and were studied in a 6‐month canine model to determine the effects of the treated surface on the ingrowth of bone and soft tissues. The area fractions of bone, marrow, and fibrous tissue in the porous coating of seven treated and seven untreated control implants were determined using histomorphological techniques. The area fraction of bone within the porous coating was greater for anodic oxide treated (23.6 ± 8.3%) compared to control implants (l2.7 ± 4.7%) (p = 0.013), and there was less fibrous tissue in the treated implants (18.0 ± 9.5%) compared to the controls (33.1 ± 7.9%) (p = 0.006). XPS, XRD, TEM, and SEM analyses of the treated implants revealed a 400 nm‐thick titanium oxide layer of low crystallinity with an undulating surface, populated with more than 25 nm‐size pores per square micrometer. There was no detectable increase in serum titanium or in generation of particulates locally compared to the control implants. Micro and nanoscale surface modification by anodic oxidation increased bone ingrowth and reduced fibrous tissue, which may extend the longevity of fixation, limiting pathways for particle migration, and impeding the progression of osteolysis and aseptic loosening of arthroplasty components. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 283–290, 2017.
Analysis of Multiple Families With Single Individuals Affected by Pseudohypoparathyroidism Type Ib (PHP1B) Reveals Only One Novel Maternally Inherited GNAS Deletion
Authors: Takatani Rieko , Molinaro Angelo , Grigelioniene Giedre , Tafaj Olta , Watanabe Tomoyuki , Reyes Monica , Sharma Amita , Singhal Vibha , Raymond F Lucy , Linglart Agnès , Jüppner Harald 
Published: October 2015

ABSTRACT

Proximal tubular resistance to parathyroid hormone (PTH) resulting in hypocalcemia and hyperphosphatemia are preeminent abnormalities in pseudohypoparathyroidism type Ib (PHP1B), but resistance toward other hormones as well as variable features of Albright's Hereditary Osteodystrophy (AHO) can occur also. Genomic DNA from PHP1B patients shows epigenetic changes at one or multiple differentially methylated regions (DMRs) within GNAS, the gene encoding Gαs and splice variants thereof. In the autosomal dominant disease variant, these methylation abnormalities are caused by deletions in STX16 or GNAS on the maternal allele. The molecular defect(s) leading to sporadic PHP1B (sporPHP1B) remains in most cases unknown and we therefore analyzed 60 sporPHP1B patients and available family members by microsatellite markers, single nucleotide polymorphisms (SNPs), multiplex ligation-dependent probe amplification (MLPA), and methylation-specific MLPA (MS-MLPA). All investigated cases revealed broad GNAS methylation changes, but no evidence for inheritance of two paternal chromosome 20q alleles. Some patients with partial epigenetic modifications in DNA from peripheral blood cells showed more complete GNAS methylation changes when testing their immortalized lymphoblastoid cells. Analysis of siblings and children of sporPHP1B patients provided no evidence for an abnormal mineral ion regulation and no changes in GNAS methylation. Only one patient revealed, based on MLPA and microsatellite analyses, evidence for an allelic loss, which resulted in the discovery of two adjacent, maternally inherited deletions (37,597 and 1427 bp, respectively) that remove the area between GNAS antisense exons 3 and 5, including exon NESP. Our findings thus emphasize that the region comprising antisense exons 3 and 4 is required for establishing all maternal GNAS methylation imprints. The genetic defect(s) leading in sporPHP1B to epigenetic GNAS changes and thus PTH-resistance remains unknown, but it seems unlikely that this disease variant is caused by heterozygous inherited or de novo mutations involving GNAS. © 2015 American Society for Bone and Mineral Research.
Digestive enzymatic activity during ontogenetic development in zebrafish (Danio rerio)
Authors: Guerrera Maria Cristina , De Pasquale Francesca , Muglia Ugo , Caruso Gabriella 
Published: October 2015

ABSTRACTDespite the growing importance of zebrafish (Danio rerio) as an experimental model in biomedical research, some aspect of physiological and related morphological age dependent changes in digestive system during larval development are still unknown. In this paper, a biochemical and morphological study of the digestive tract of zebrafish was undertaken to record the functional changes occurring in this species during its ontogenetic development, particularly from 24 hr to 47 days post fertilization (dpf). Endo‐ and exo‐proteases, as well as α‐amylase enzymes, were quantified in zebrafish larvae before first feeding (7 dpf). The most morphologically significant events during the ontogenesis of the gut occurred between 3 dpf (mouth opening) and 7 dpf (end of exocrine pancreas differentiation). The presence of a wide range of digestive enzymes, already active at earlier zebrafish larval stages, closely related with the omnivorous diet of this species. Increasing enzyme activities were found with increasing age, probably in relation with intestinal mucosa folding and consequent absorption surface increase. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 699–706, 2015. © 2015 Wiley Periodicals, Inc.
Initial validation of equilibrium contrast imaging for extracellular volume quantification using a three‐dimensional engineered tissue model
Authors: Bandula Steve , Magdeldin Tarig , Stevens Nicola , Yeung Jason , Moon James C. , Taylor Stuart A. , Cheema Umber , Punwani Shonit 
Published: October 2015

BackgroundTo test the principles underpinning equilibrium contrast imaging estimation of tissue extracellular volume (ECV) fraction, using a three‐dimensional (3D) engineered tissue model with known cellular and extracellular volumes.MethodsSix 3D tissue models (tumoroids) consisting of cell cultures within a collagen containing hydrogel were constructed after culture centrifugation and direct measurement of the cell component volume. Measured tumoroid ECV ranged from 0.89 to 1. ECV was calculated after measuring the T1 relaxation time at 3 Tesla using inversion recovery relaxometry (TI 100–1500 ms) within the tumoroids and surrounding medium before and 375 min after spiking the medium with Gadolinium (to achieve a concentration of 1.4 mM/L). Linear regression model prediction of directly measured ECV (ECVm) by EQ‐MRI measured ECV (ECVeq); and Bland‐Altman agreement between measures was assessed.ResultsThe fractional cellular volume measured by EQ‐MRI (ECVeq) within the tumoroids ranged from 0.821 to 0.963. ECVeq was a good predictor of ECVm (R2 = 0.77, P = 0.02). The regression line Y‐axis intercept (when X = 0) was 0.045 ± 0.019 with a slope of 1.28 ± 0.35. Bland‐Altman comparison demonstrated 95% limits of agreement between ‐0.002 and 0.114 with a bias (SD) of 0.056 (0.03).ConclusionThis study supports the principles of ECV estimation using equilibrium contrast MRI, but future development of this model may allow validation over a wider, more physiological ECV range and a greater understanding of the effect of tissue extracellular protein burden on ECV. J. Magn. Reson. Imaging 2016;43:1224–1229.
Age‐related changes in aortic 3D blood flow velocities and wall shear stress: Implications for the identification of altered hemodynamics in patients with aortic valve disease
Authors: van Ooij Pim , Garcia Julio , Potters Wouter V. , Malaisrie S. Chris , Collins Jeremy D. , Carr James C. , Markl Michael , Barker Alex J. 
Published: October 2015

PurposeTo investigate age‐related changes in peak systolic aortic 3D velocity and wall shear stress (WSS) in healthy controls and to investigate the importance of age‐matching for 3D mapping of abnormal aortic hemodynamics in bicuspid aortic valve disease (BAV).Materials and Methods4D flow MRI (fields strengths = 1.5–3T; resolution = 2.2–3.9 × 1.7–2.6 × 2.2–4.0 mm3; Venc = 150–250 cm/s; TE/TR/FA = 2.3–2.8/4.7–5.4msec/7–15°) was performed in 56 controls (age range: 19–78 years) and in two BAV patient groups each consisting of 10 subjects (group 1: 20–29 years, group 2: 52–57 years). Heat maps showing abnormal 3D velocity and WSS were created for the BAV patients by comparison with an age‐matched and with an unmatched control group. The fraction of the aorta exposed to abnormal velocity/WSS was calculated relative to the total aortic volume/surface.ResultsSignificant inverse relationships between age and healthy velocity/WSS were found (R2 = 0.32/0.39, P < 0.001). For BAV group 1, abnormally elevated velocity/WSS was overestimated when compared with older controls (51–60 years) than when correctly age‐matched (∼25 ± 14% vs. ∼8 ± 5%). For BAV group 2, abnormally decreased velocity/WSS was overestimated when compared with younger controls (21–30 years) than when correctly age‐matched (∼9 ± 7% vs. 1 ± 1%).ConclusionSignificant correlations exist between age and peak systolic velocity and WSS. Therefore, robust age‐matching is important when creating abnormal 3D aortic velocity and WSS maps for patients with BAV. J. Magn. Reson. Imaging 2016;43:1239–1249.
An evaluation of persistent meteorological drought using a homogeneous Island of Ireland precipitation network
Authors: Wilby R. L. , Noone S. , Murphy C. , Matthews T. , Harrigan S. , Broderick C. 
Published: October 2015

ABSTRACTThis paper investigates the spatial and temporal properties of persistent meteorological droughts using the homogeneous Island of Ireland Precipitation (IIP) network. Relative to a 1961–1990 baseline period it is shown that the longest observed run of below average precipitation since the 1850s lasted up to 5 years (10 half‐year seasons) at sites in southeast and east Ireland, or 3 years across the network as a whole. Dry spell and wet spell length distributions were represented by a first‐order Markov model which yields realistic runs of below average rainfall for individual sites and IIP series. This model shows that there is relatively high likelihood (p = 0.125) of a 5‐year dry spell at Dublin, and that near unbroken dry runs of 10 years or more are conceivable. We suggest that the IIP network and attendant rainfall deficit modelling provide credible data for stress testing water supply and drought plans under extreme conditions.
Temporal dynamics and spatial patterns of drought and the relation to ENSO: a case study in Northwest China
Authors: Liu Zhiyong , Menzel Lucas , Dong Chunyu , Fang Ruihong 
Published: October 2015

ABSTRACTAn investigation of temporal dynamics and spatial patterns of dryness/wetness conditions over the eastern part of Northwest China (including Shaanxi, Ningxia, the eastern part of Gansu, and a part of southern Inner Mongolia) during the period 1960–2009 is presented. The analysis of this study is threefold. First, the dryness/wetness conditions over the study area were characterized using the self‐calibrating Palmer Drought Severity Index (PDSI). The spatiotemporal variability of dryness/wetness conditions in the study area was then investigated by the rotated empirical orthogonal function (REOF) and Mann–Kendall trend test. Third, we examined the periodical oscillations of dryness/wetness conditions and the multi‐scale relationships between dryness/wetness conditions and El Niño‐Southern Oscillation (ENSO). The results indicate that most parts of the study area were characterized by a dry trend in both the rainy season (May–September) and winter. Four sub‐regions of dryness/wetness conditions across the study area were identified. Based on the wavelet analysis, the periodical features in the PDSI time series for each sub‐region were explored. Negative relationships between the PDSI in the sub‐region I (representing the central and southern parts of Shaanxi and the southeastern Gansu) and the Niño 3.4 index can be consistently detected on 2–6 year scales during the entire period 1960–2009. This suggests that the strong El Niño events generally lead to very dry conditions in the sub‐region I on multi‐year scales. In addition, we further investigated how the ENSO cycle modulates the strength of the East Asian summer monsoon (EASM) in both developing and decaying phases of El Niño and La Niña events. The results of this study could be beneficial for efficient water resources management and drought assessment in the current study area and also provide a valuable reference for other areas with similar climatic characteristics.
Importance of Glu53 in the C‐terminal region of brazzein, a sweet‐tasting protein
Authors: Lim Jin‐Kyung , Jang Jin‐Chul , Kong Ji‐Na , Kim Myung‐Chul , Kong Kwang‐Hoon 
Published: October 2015

AbstractBACKGROUNDThe sweetness of brazzein, one of the known sweet proteins, is dependent on charges and/or structures of its specific amino acid side chains. As the residues in the C‐terminus of brazzein are known to play a critical role in sweetness, the currently unknown function of Glu53 requires further study.RESULTSTo identify important residues responsible for the sweetness of the protein brazzein, four mutants of the Glu53 residue in the C‐terminal region of des‐pE1M‐brazzein, which lacks the N‐terminal pyroglutamate, were constructed using site‐directed mutagenesis. Mutations of Glu53 substitution to Ala or Asp significantly decreased the sweetness. On the other hand, a Lys mutation resulted in a molecule with sweetness similar to that of des‐pE1M‐brazzein. Mutation of Glu53 to Arg resulted in a molecule significantly sweeter than des‐pE1M‐brazzein, which agrees with previous findings showing that mutation with positively charged residues results in a sweeter protein.CONCLUSIONOur results suggest that the residue at position 53 is crucial for the sweetness of brazzein, which may be interacting with the sweet‐taste receptor. © 2015 Society of Chemical Industry
Molecular characterisation of a bio‐based active packaging containing Origanum vulgare L. essential oil using pyrolysis gas chromatography–mass spectrometry
Authors: Llana‐Ruíz‐Cabello María , Pichardo Silvia , Jiménez‐Morillo Nicasio T , Bermúdez José M , Aucejo Susana , González‐Vila Francisco J , Cameán Ana M , González‐Pérez José A 
Published: October 2015

AbstractBACKGROUNDEnvironmental, economic and safety challenges motivate shift towards safer materials for food packaging. New bioactive packaging techniques, i.e. addition of essential plant oils (EOs), are gaining attention by creating barriers to protect products from spoilage. Analytical pyrolysis gas chromatography–mass spectrometry (Py‐GC‐MS) was used to fingerprint a bioactive polylactic acid (PLA) with polybutylene succinate (PBS) (950 g kg−1:50 g kg−1) film extruded with variable quantities (0, 20, 50 and 100 g kg−1) of Origanum vulgare EO.RESULTSMain PLA:PBS pyrolysis products were lactide enantiomers and monomer units from the major PLA fraction and succinic acid anhydride from the PBS fraction. Oregano EO pyrolysis released cymene, terpinene and thymol/carvacrol peaks as diagnostic peaks for EO. In fact, linear correlation coefficients better than 0.950R2 value (P < 0.001) were found between the chromatographic area of the diagnostic peaks and the amount of oregano EO in the bioplastic.CONCLUSIONThe pyrolytic behaviour of a bio‐based active package polymer including EO is studied in detail. Identified diagnostic compounds provide a tool to monitor the quantity of EO incorporated into the PLA:PBS polymeric matrix. Analytical pyrolysis is proposed as a rapid technique for the identification and quantification of additives within bio‐based plastic matrices. © 2015 Society of Chemical Industry