bluuebunny/crossref_metadata_2025 huggingface dataset:
High resolution and stability roll angle measurement method for precision linear displacement stages
Authors: Jin Tao , Xia Guizheng , Hou Wenmei , Le Yanfen , Han Sen
Published: February 2017

A method for high resolution roll angle measurement of linear displacement stages is developed theoretically and tested experimentally. The new optical configuration is based on a special differential plane mirror interferometer, a wedge prism assembly, and a wedge mirror assembly. The wedge prisms assembly is used as a roll angle sensor, which converts roll angle to the changes of optical path. The special interferometer, composed a polarization splitter plane, a half wave plate, a beam splitter, a retro-reflector and a quarter wave plate, is designed for high resolution measurement of the changes of the optical path. The interferometric beams are a completely common path for the adoption of the centrosymmetrical measurement structure, and the cross talk of the straightness, yaw, and pitch errors is avoided. The angle measurement resolution of the proposed method is 3.5 μrad in theoretical with a phase meter which has a resolution of 2π/512. The experimental result also shows the great stability and accuracy of the present roll angle measurement system.
A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions
Authors: Michalowsky Julian , Schäfer Lars V. , Holm Christian , Smiatek Jens
Published: February 2017

We present a refined version of the polarizable Martini water model – coined refPOL – designed specifically for the use with long-range electrostatics. The refPOL model improves the agreement with the experimentally measured dielectric constant and the mass density of water at room temperature compared to the original polarizable Martini water force field when particle mesh Ewald electrostatics are employed. Our study reveals that the model remains applicable with various commonly used settings for the non-bonded interactions, including reaction field electrostatics. The oil/water partitioning behavior of uncharged Martini bead types is thoroughly investigated: Lennard-Jones interactions between the refPOL model and the remaining Martini beads are adjusted to reproduce the hydration free energies obtained with the original polarizable water model, while free energies of solvation in apolar media remain unchanged. The cross-interactions with charged bead types are parameterized to agree with the experimentally observed area per lipid of a fully solvated dipalmitoylphosphatidylcholine bilayer. We additionally verify the model by analyzing the potentials of mean force between different sample pairs in refPOL water and comparing the results to reference data obtained using the original polarizable Martini water model as well as fully atomistic simulations. Based on the results, we suggest to replace the original polarizable Martini water model with the new refPOL model for future applications.
Quantum-state-resolved reactivity of overtone excited CH4 on Ni(111): Comparing experiment and theory
Authors: Hundt P. Morten , van Reijzen Maarten E. , Beck Rainer D. , Guo Han , Jackson Bret
Published: February 2017

Quantum state resolved reactivity measurements probe the role of vibrational symmetry on the vibrational activation of the dissociative chemisorption of CH4 on Ni(111). IR-IR double resonance excitation in a molecular beam was used to prepare CH4 in three different vibrational symmetry components, A1, E, and F2, of the 2ν3 antisymmetric stretch overtone vibration as well as in the ν1+ν3 symmetric plus antisymmetric C–H stretch combination band of F2 symmetry. The quantum state specific dissociation probability S0 (sticking coefficient) was measured for each of the four vibrational states by detecting chemisorbed carbon on Ni(111) as the product of CH4 dissociation by Auger electron spectroscopy. We observe strong mode specificity, where S0 for the most reactive state ν1+ν3 is an order of magnitude higher than for the least reactive, more energetic 2ν3-E state. Our first principles quantum scattering calculations show that as molecules in the ν1 state approach the surface, the vibrational amplitude becomes localized on the reacting C–H bond, making them very reactive. This behavior results from the weakening of the reacting C–H bond as the molecule approaches the surface, decoupling its motion from the three non-reacting C–H stretches. Similarly, we find that overtone normal mode states with more ν1 character are more reactive: S0(2ν1) > S0(ν1 + ν3) > S0(2ν3). The 2ν3 eigenstates excited in the experiment can be written as linear combinations of these normal mode states. The highly reactive 2ν1 and ν1 + ν3 normal modes, being of A1 and F2 symmetry, can contribute to the 2ν3-A1 and 2ν3-F2 eigenstates, respectively, boosting their reactivity over the E component, which contains no ν1 character due to symmetry.
Molecular dynamics study of the interfacial thermal conductance of multi-walled carbon nanotubes and van der Waals force induced deformation
Authors: Rong Qingyuan , Shao Cheng , Bao Hua
Published: February 2017

Thermal boundary resistance (TBR) plays an important role in the thermal conduction of carbon nanotube (CNT)-based materials and CNT networks (e.g., thin films, arrays, and aerogels). Although individual CNTs have extremely high thermal conductivity, interfacial resistances can dominate the overall resistance and largely influence their thermal performance. Using molecular dynamics simulations, we systematically study the interfacial thermal conductance (ITC, the inverse of TBR) of multi-walled carbon nanotube (MWNT)-substrate interfaces and MWNT-MWNT junctions, and compare the CNT-CNT junctions with graphene-graphene junctions. The results show that for CNTs with the diameter of a few nanometers, the total ITCs first decrease and then stabilize with the increase of the number of walls, mainly due to the changes of mechanical strength and adhesive energy. Increasing the CNT diameter leads to a larger total ITC and it is mainly due to a larger contact area. The area normalized ITC of CNT-CNT junctions increases and then saturates with the number of walls, and it behaves non-monotonically with the diameter. Furthermore, a trapezoidal model of multi-layer graphene-graphene junctions is used to explain the number of wall dependence of ITC. We also find that with the same adhesive energy, total ITCs of CNT-CNT junctions and graphene-graphene junctions are similar, which allows us to roughly estimate ITCs of CNT-CNT junctions without performing numerical simulations.
Complex permittivity measurement using metamaterial split ring resonators
Authors: Chakyar Sreedevi P. , K. Simon Sikha , Bindu C. , Andrews Jolly , Joseph V. P.
Published: February 2017

A direct and efficient method for determining the complex permittivity of materials at microwave frequencies using a Split Ring Resonator (SRR) metamaterial structure is presented. A single SRR unit fabricated on a substrate arranged between transmitting and receiving probes acts as a test probe. Dielectric samples having at least one flat surface of area greater than or equal to the area of SRR structure are used as test samples. The relative permittivity and the loss tangent of the dielectric are evaluated from the resonant frequency shift and the bandwidth of the SRR resonator, by placing the sample over it. The LC resonance of the SRR test probe is theoretically related to the permittivity by considering its equivalent circuit in terms of the dielectric filled capacitances formed on the upper and lower surfaces of the SRR. The permittivity measurements are performed using test probes of different resonant frequencies, and the results are compared with the values obtained by the cavity perturbation method.
Mechanism and crucial parameters on GaN nanocluster formation in a silica matrix
Authors: Kioseoglou J. , Katsikini M. , Termentzidis K. , Karakostas I. , Paloura E. C.
Published: February 2017

The formation of wurtzite GaN nanoclusters in an amorphous silica matrix, via gallium and nitrogen ion implantation and rapid thermal annealing, is identified using Extended X Ray Absorption Fine Structure analysis. The mechanism and the crucial parameters that rule the formation of the nanoclusters are established by the use of molecular dynamics simulations. The dominant structural parameters are found to be the concentration of the silicon and oxygen vacancies that are formed during the implantation and the annealing temperature. It is concluded that annealing at 1400 K and 8% Ga/Si and 12% N/O ratios are needed for the formation of GaN nanoclusters. In addition to that, the GaN nanocluster formation is accomplished only when the vacancy concentrations of silicon and oxygen atoms are equal to 10% and 20%, respectively. Finally, the observation of various snapshots upon an increase of the annealing duration indicates the coalescence of smaller GaN nuclei towards larger ones, designating that the Ostwald ripening is a dominant mechanism.
Nontrivial surface state transport in Bi2Se3 topological insulator nanoribbons
Authors: Pan Haiyang , Zhang Kang , Wei Zhongxia , Wang Jue , Han Min , Song Fengqi , Wang Xuefeng , Wang Baigeng , Zhang Rong
Published: February 2017

Topological insulator nanostructures have the larger surface-to-volume ratios than the bulk materials, which enhances the surface state contribution to the electrical transport. Here, we report on the single-crystalline Bi2Se3 narrow nanoribbons synthesized by the chemical vapor deposition method. The surface state induced Aharonov-Bohm effect was observed in the parallel magnetic field. The weak antilocalization (WAL) at various temperatures can be well fitted by the 1D localization theory, and the fitting coherence length is larger than the cross section size of the nanoribbon. The amplitude of WAL after subtracting the bulk background is only dependent on the vertical component of the magnetic field at various angles, revealing the surface nature of WAL. All these signatures indicate the nontrivial surface state transport in our Bi2Se3 narrow nanoribbons.
Negative thermal quenching of below-bandgap photoluminescence in InPBi
Authors: Chen Xiren , Wu Xiaoyan , Yue Li , Zhu Liangqing , Pan Wenwu , Qi Zhen , Wang Shumin , Shao Jun
Published: February 2017

This paper reports a temperature-dependent (10–280 K) photoluminescence (PL) study of below-bandgap electron-hole recombinations and anomalous negative thermal quenching of PL intensity in InP1–xBix (x = 0.019 and 0.023). Four PL features are well resolved by curve-fitting of the PL spectra, of which the energies exhibit different temperature dependence. The integral intensities of the two high-energy features diminish monotonically as temperature rises up, while those of the two low-energy features decrease below but increase anomalously above 180 K. A phenomenological model is established that the residual electrons in the final state of the PL transition transfer into nonradiative state via thermal hopping, and the thermal hopping produces in parallel holes in the final state and hence enhances the radiative recombination significantly. A reasonable interpretation of the PL processes in InPBi is achieved, and the activation energies of the PL quenching and thermal hopping are deduced.
Evaluating the sensitivity of ecological indicators with a perspective of temporal scales
Authors: Zhang Chongliang , Chen Yong , Ren Yiping , Wan Rong
Published: February 2017

This simulation study tests the sensitivity of 12 candidate ecological indicators (EIs) that characterise fish abundance, body size and trophodynamics with respect to temporal scales. Size-spectrum models that explicitly account for trophic interactions are used to simulate community dynamics under different levels of fishing pressure, including a specific model of the fish community in Haizhou Bay, China, and trait-based models of generalised fishery systems. The sensitivity of EIs is characterised by (1) responsiveness, which refers to the dynamics of EI values with respect to the magnitude of changes in fishing effort, and (2) detectability, which measures the relative changes of EI with respect to reference baselines. The response of EIs is substantially non-linear over time. Most EIs are responsive to the reduction of fishing effort and have low detectability under high fishing pressure. Both characteristics of sensitivity tend to increase in the early years and level off in 2 decades, suggesting transient behaviours in EI dynamics. The results suggested the essential non-linear dynamics of EIs resulting from underlying trophic interactions and the potential misinterpretation of the temporal EIs dynamics. We highlight the necessity of considering temporal scales and fishing characteristics in applying EIs in fishery management.
Environmental and individual effects on the behaviour and spawning movements of Lethrinus nebulosus on a coral reef
Authors: Babcock R. C. , Pillans R. D. , Rochester W. A.
Published: February 2017

Spatial management of fish populations can potentially be optimised by incorporating responses to environmental variables, such as diel, tidal, lunar and seasonal factors, but individual variability in habitat use and behaviour may complicate such efforts. Acoustic tagging and tracking of 84 Lethrinus nebulosus in the Ningaloo Marine Park indicated that sizes of individual habitat utilisation kernels were similar across diel and tidal cycles, but varied greatly among individuals. Clearly differentiated diel and tidal habitat use patterns were evident in significant proportions of individuals, particularly in relation to tidal phase. For the majority of residents, home-range sizes were reasonably stable over periods of 2–4 years, but in some cases core areas did shift over time. At seasonal time scales, peaks of seasonal activity and home range area were recorded during spawning season (October–December). Long-distance return migrations to spawning locations were observed that were among the longest observed for any reef fish (over 130km). Suspected spawning-related movements were recorded almost exclusively in fish >500-mm fork length, and were semilunar, following quarter moons in October–December. Significant individual-level variability in movement and habitat use patterns, evident across multiple temporal scales, has important implications for the management of L. nebulosus populations.
Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1
Authors: Michael Alicia K. , Fribourgh Jennifer L. , Chelliah Yogarany , Sandate Colby R. , Hura Greg L. , Schneidman-Duhovny Dina , Tripathi Sarvind M. , Takahashi Joseph S. , Partch Carrie L.
Published: February 2017

Significance

Circadian rhythms depend upon the precise coordination of protein interactions within the transcription–translation feedback loop of the molecular clock. Period (PER) and cryptochrome (CRY) rhythmically repress activity of the circadian transcription factor, CLOCK:BMAL1 (brain and muscle Arnt-like protein 1), to establish daily patterns of gene expression. CRY1 binds to CLOCK:BMAL1 with and without PER to inhibit CLOCK:BMAL1 activity. Here we show that CRY1 interacts with the CLOCK PAS-B domain to dock the transcription factor into the secondary pocket of CRY1. Studies of a CRY1:CLOCK:BMAL1 complex highlight critical interfaces for the direct regulation of CLOCK:BMAL1 by cryptochromes. A molecular understanding of the clock mechanism is fundamental for the development and application of therapies for circadian-related disorders.
Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme
Authors: Li Yini , Zhou Mengying , Hu Qi , Bai Xiao-chen , Huang Weiyun , Scheres Sjors H. W. , Shi Yigong
Published: February 2017

Significance

As a prototypical initiator caspase, caspase-9 has been rigorously studied for 20 years. Although activation of the caspase-9 zymogen and catalytic activity of the mature caspase-9 both strictly depend on the Apaf-1 apoptosome, the underlying mechanism remains poorly understood. Previous mechanistic studies relied heavily on engineered caspase-9 in the absence of the Apaf-1 apoptosome. In this study, we tackle the problem through structure determination of the Apaf-1 apoptosome bound to caspase-9 and biochemical analysis of caspase-9 activity in the presence of the Apaf-1 apoptosome. The results demonstrate that the Apaf-1 apoptosome activates caspase-9 by two means: suppressing the inhibition mediated by the caspase recruitment domains (CARD) domain and stimulating the catalytic activity of the protease domain.
Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins
Authors: He Yi , Maisuradze Gia G. , Yin Yanping , Kachlishvili Khatuna , Rackovsky S. , Scheraga Harold A.
Published: February 2017

Significance

We study a set of proteins that exhibit low sequence identity, but high structural homology and functional similarity. It is demonstrated that a physics-based sequence comparison tool, the property factor method, is able to detect differences between the sequences of these proteins that correlate with differences in their structures and dynamics. It is shown that these sequence differences are not detected in this challenging system by conventional alignment methods. This result suggests that a significant amount of the information encoded in protein sequences is not captured by evolutionarily motivated comparison methods.
Screen for reactivation of MeCP2 on the inactive X chromosome identifies the BMP/TGF-β superfamily as a regulator of XIST expression
Authors: Sripathy Smitha , Leko Vid , Adrianse Robin L. , Loe Taylor , Foss Eric J. , Dalrymple Emily , Lao Uyen , Gatbonton-Schwager Tonibelle , Carter Kelly T. , Payer Bernhard , Paddison Patrick J. , Grady William M. , Lee Jeannie T. , Bartolomei Marisa S. , Bedalov Antonio
Published: February 2017

Significance

Rett syndrome is a neurodevelopmental disorder in girls who are heterozygous for a mutation in the X-linked gene MeCP2. Because cells in these individuals will be missing MeCP2 function only when the wild-type copy of the gene is on the inactive X, reactivation of the silenced copy of MeCP2 presents a potential therapeutic strategy. To identify genes that silence MeCP2 on the inactive X and that could therefore prove valuable as therapeutic targets, we carried out a screen for genes whose down-regulation reactivated a MeCP2 reporter on the inactive X. The 30 genes we have identified reveal a genetic circuitry required for maintenance of X-chromosome inactivation in differentiated cells and a large number of targets suitable for pharmacologic intervention.
ADP-ribosylhydrolase activity of Chikungunya virus macrodomain is critical for virus replication and virulence
Authors: McPherson Robert Lyle , Abraham Rachy , Sreekumar Easwaran , Ong Shao-En , Cheng Shang-Jung , Baxter Victoria K. , Kistemaker Hans A. V. , Filippov Dmitri V. , Griffin Diane E. , Leung Anthony K. L.
Published: February 2017

Significance

Viral outbreaks can be sudden and result in devastating social and economic consequences. Chikungunya virus (CHIKV) outbreaks of rash, arthritis, and neurologic disease have occurred in Africa, Asia, Europe, and the Americas. There are no licensed vaccines to prevent or drugs to treat CHIKV infection, and the mechanisms of disease generation are poorly understood. Here, we identify a macrodomain-containing CHIKV protein with enzymatic ADP-ribosylhydrolase activity that is critical for virulence in mammals and define the substrate specificity of this enzyme. Given the conservation of viral macrodomains in all alphaviruses and coronaviruses, our study may guide the design of small molecule chemical compounds that block hydrolase activity for treatment of a range of virus infections.
Effect of decompression drying treatment on physical properties of solid foods
Authors: Morikawa Takuya , Takada Norihisa , Miura Makoto
Published: February 2017

This study used a decompression drying instrument to investigate the effects of a drying treatment on the physical properties of solid foods. Commercial tofu was used as a model food and was treated at different temperature and pressure conditions in a drying chamber. Overall, high temperatures resulted in better drying. Additionally, pressure in the chamber influenced the drying conditions of samples. Differences in physical properties, such as food texture, shrinkage, and color were observed among some samples, even with similar moisture content. This was caused by differences in moisture distribution in the food, which seems to have manifested as a thin, dried film on the surfaces of samples. It caused inefficient drying and changes in physical properties. Control of the drying conditions (i.e. pressure and heat supply) has relations with not only physical properties, but also the drying efficiency of solid foods.
EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay
Authors: Volpi Stefano , Yamazaki Yasuhiro , Brauer Patrick M. , van Rooijen Ellen , Hayashida Atsuko , Slavotinek Anne , Sun Kuehn Hye , Di Rocco Maja , Rivolta Carlo , Bortolomai Ileana , Du Likun , Felgentreff Kerstin , Ott de Bruin Lisa , Hayashida Kazutaka , Freedman George , Marcovecchio Genni Enza , Capuder Kelly , Rath Prisni , Luche Nicole , Hagedorn Elliott J. , Buoncompagni Antonella , Royer-Bertrand Beryl , Giliani Silvia , Poliani Pietro Luigi , Imberti Luisa , Dobbs Kerry , Poulain Fabienne E. , Martini Alberto , Manis John , Linhardt Robert J. , Bosticardo Marita , Rosenzweig Sergio Damian , Lee Hane , Puck Jennifer M. , Zúñiga-Pflücker Juan Carlos , Zon Leonard , Park Pyong Woo , Superti-Furga Andrea , Notarangelo Luigi D.
Published: February 2017

We studied three patients with severe skeletal dysplasia, T cell immunodeficiency, and developmental delay. Whole-exome sequencing revealed homozygous missense mutations affecting exostosin-like 3 (EXTL3), a glycosyltransferase involved in heparan sulfate (HS) biosynthesis. Patient-derived fibroblasts showed abnormal HS composition and altered fibroblast growth factor 2 signaling, which was rescued by overexpression of wild-type EXTL3 cDNA. Interleukin-2–mediated STAT5 phosphorylation in patients’ lymphocytes was markedly reduced. Interbreeding of the extl3-mutant zebrafish (box) with Tg(rag2:green fluorescent protein) transgenic zebrafish revealed defective thymopoiesis, which was rescued by injection of wild-type human EXTL3 RNA. Targeted differentiation of patient-derived induced pluripotent stem cells showed a reduced expansion of lymphohematopoietic progenitor cells and defects of thymic epithelial progenitor cell differentiation. These data identify EXTL3 mutations as a novel cause of severe immune deficiency with skeletal dysplasia and developmental delay and underline a crucial role of HS in thymopoiesis and skeletal and brain development.
Estimating year-class strength of Icelandic summer-spawning herring on the basis of two survey methods
Authors: Gudmundsdottir Asta , Oskarsson Gudmundur J. , Sveinbjörnsson Sveinn
Published: February 2017

Gudmundsdottir, A., Oskarsson, G. J., and Sveinbjörnsson, S. 2007. Estimating year-class strength of Icelandic summer-spawning herring on the basis of two survey methods. – ICES Journal of Marine Science, 64: 1182–1190. Recruitment indices at age 1 and 2 were constructed for Icelandic summer-spawning herring using data from two inherently different survey methods on their nursery areas for the years 1988–2003. The surveys were a shrimp, bottom-trawl survey and a herring acoustic survey. Indices were compared with the year-class strength at age 2 derived from an assessment model (AMCI) used for the stock. A juvenile index at age 1 from the acoustic survey and at age 2 from the shrimp-trawl survey correlated significantly with the modelled recruitment, although only marginally with each other. One index was not considered markedly better than the other, and both have shortcomings even if the acoustic survey is believed better than the trawl survey for quantifying juvenile herring. The recruitment index at age 1 derived from the acoustic survey can be improved as an indicator of recruitment if that survey were to be extended to cover the nursery areas off western and southeastern Iceland, and the same areas covered each year.
Does sex really matter? Explaining intraspecies variation in ocean acidification responses
Authors: Ellis Robert P. , Davison William , Queirós Ana M. , Kroeker Kristy J. , Calosi Piero , Dupont Sam , Spicer John I. , Wilson Rod W. , Widdicombe Steve , Urbina Mauricio A.
Published: February 2017

Ocean acidification (OA) poses a major threat to marine ecosystems globally, having significant ecological and economic importance. The number and complexity of experiments examining the effects of OA has substantially increased over the past decade, in an attempt to address multi-stressor interactions and long-term responses in an increasing range of aquatic organisms. However, differences in the response of males and females to elevated
p
CO
2
have been investigated in fewer than 4% of studies to date, often being precluded by the difficulty of determining sex non-destructively, particularly in early life stages. Here we highlight that sex can significantly impact organism responses to OA, differentially affecting physiology, reproduction, biochemistry and ultimately survival. What is more, these impacts do not always conform to ecological theory based on differential resource allocation towards reproduction, which would predict females to be more sensitive to OA owing to the higher production cost of eggs compared with sperm. Therefore, non-sex-specific studies may overlook subtle but ecologically significant differences in the responses of males and females to OA, with consequences for forecasting the fate of natural populations in a near-future ocean.
An overview of city analytics
Authors: Higham Desmond J. , Batty Michael , Bettencourt Luís M. A. , Greetham Danica Vukadinović , Grindrod Peter
Published: February 2017

We introduce the 14 articles in the Royal Society Open Science themed issue on City Analytics. To provide a high-level, strategic, overview, we summarize the topics addressed and the analytical tools deployed. We then give a more detailed account of the individual contributions. Our overall aims are (i) to highlight exciting advances in this emerging, interdisciplinary field, (ii) to encourage further activity and (iii) to emphasize the variety of new, public-domain, datasets that are available to researchers.
Using computational theory to constrain statistical models of neural data
Authors: Linderman Scott W. , Gershman Samuel J.
Published: February 2017

Computational neuroscience is, to first order, dominated by two approaches: the “bottom-up” approach, which searches for statistical patterns in large-scale neural recordings, and the “top-down” approach, which begins with a theory of computation and considers plausible neural implementations. While this division is not clear-cut, we argue that these approaches should be much more intimately linked. From a Bayesian perspective, computational theories provide constrained prior distributions on neural data—albeit highly sophisticated ones. By connecting theory to observation via a probabilistic model, we provide the link necessary to test, evaluate, and revise our theories in a data-driven and statistically rigorous fashion. This review highlights examples of this theory-driven pipeline for neural data analysis in recent literature and illustrates it with a worked example based on the temporal difference learning model of dopamine.
Field manipulations of resources mediate the transition from intraspecific competition to facilitation
Authors: Svanfeldt Karin , Monro Keyne , Marshall Dustin J.
Published: February 2017

Population density affects individual performance, though its effects are often mixed. For sessile species, increases in population density typically reduce performance. Still, cases of positive density‐dependence do occur in sessile systems and demand explanation. The stress gradient hypothesis (SGH) predicts that under stressful conditions, positive effects of facilitation may outweigh the negative effects of competition.

While some elements of the SGH are well studied, its potential to explain intraspecific facilitation has received little attention. Further, there have been questions regarding whether the SGH holds if the stressor is a resource. Most studies of interactions between the environment and intraspecific facilitation have relied on natural environmental gradients; manipulative studies are much rarer.

To test the effects of intraspecific density and resources, we manipulated resource availability over natural population densities for the marine bryozoan Watersipora subtorquata.

We found negative effects of density on colony performance in low resource environments, but mainly positive density‐dependence in high resource environments. By adding resources, competition effects were reduced and the positive effects of facilitation were revealed.

Our results suggest that resource availability mediates the relative strength of competition and facilitation in our system. We also suggest that intraspecific facilitation is more common than may be appreciated and that environmental variation may mediate the balance between negative and positive density‐dependence.
Latent Fingermark Aging Patterns (Part III): Discontinuity Index as One Indicator of Degradation
Authors: De Alcaraz‐Fossoul Josep , Barrot Feixat Carme , Carreras‐Marin Clara , Tasker Jack , Zapico Sara C. , Gené Badia Manel
Published: February 2017

This article is the third in a series of reports exploring quantifiable visual parameters of the aging process of latent fingermarks. On this occasion, research is focused on the occurrence of ridge discontinuities (i.e. breakages) as a function of time. Experiment variables included type of secretion (eccrine and sebaceous), substrate (glass and plastic), and exposure to natural light (dark, shade, and direct light) over a 6 months period. Fingermarks were sequentially visualized with titanium dioxide powder, photographed, and the number of naturally occurring ridge discontinuities subsequently evaluated. A semi‐quantitative value, named Discontinuity Index, was used to better characterize this aging parameter. Results indicated that ridges of sebaceous depositions on glass were generally less affected by the environmental conditions compared with those on plastic surface. In addition, aging in darkness was not always the best condition for preservation, and the direct exposure to light seemed not to affect the degradation under certain conditions.
Development of a Patient‐centered Outcome Measure for Emergency Department Asthma Patients
Authors: Samuels‐Kalow Margaret E. , Rhodes Karin V. , Henien Mira , Hardy Emily , Moore Thomas , Wong Felicia , Camargo Carlos A. , Rizzo Caroline T. , Mollen Cynthia
Published: February 2017

Background

Measuring outcomes of emergency care is of key importance, but current metrics, such as 72‐hour return visit rates, are subject to ascertainment bias, incentivize overtesting and overtreatment at initial visit, and do not reflect the full burden of disease and morbidity experienced at home following ED care. There is increasing emphasis on including patient‐reported outcomes, but the existing patient‐reported measures have limited applicability to emergency care.

Objective

The objective was to identify concepts for inclusion in a patient‐reported outcome measure for ED care and assess differences in potential concepts by health literacy.

Methods

A three‐phase qualitative study was completed using freelisting and semistructured interviewing for concept identification, member checking for concept ranking, and cognitive interviewing for question development. Participants were drawn from three tertiary care EDs. Parents of patients (pediatric) or patients (adult) with asthma completed a demographic survey and an assessment of health literacy. Phase 1 participants also completed a freelisting exercise and qualitative interview regarding the definition of success following ED discharge. Phase 2 participants completed a member checking survey based on concepts identified in Phase 1. Phase 3 was a pilot of trial questions based on the highest‐ranked concepts from Phase 2.

Results

Phase 1 enrolled 22 adult patients and 37 parents of pediatric patients. Phase 2 enrolled 41 adult patients and 200 parents. Phase 3 involved 15 parents. Across all demographic/literacy groups, Phase 1 participants reported return to usual activity and lack of asthma symptoms as the most important markers of success. In Phase 2, symptom improvement, medication use and access, and asthma knowledge were identified as the most important components of the definition of post‐ED discharge success. Phase 3 resulted in five questions for the proposed measure.

Conclusions

A stepwise qualitative process can identify, rank, and formulate questions based on patient‐identified concepts for inclusion in a patient‐reported outcome measure for ED discharge. The four key concepts identified for inclusion: symptom improvement, medication access, correct medication use, and asthma knowledge are not measured by existing quality metrics.
Effect of quality of colostrum on health, growth and immunoglobulin G concentration in Holstein calves in a hot environment
Authors: Mellado Miguel , Torres Edir , Veliz Francisco G. , de Santiago Angeles , Macias‐Cruz Ulises , Garcia Jose E.
Published: February 2017

The aim of this study was to determine the effect of ingestion of pasteurized and subsequently frozen–thawed pooled colostrum (≥50 mg Ig/mL) with different bacterial counts and immunoglobulin concentration (IgC) on the occurrence of diarrhea and pneumonia in 306 neonatal Holstein calves in a hot environment. Calves were assigned to be fed colostrum with total bacterial counts (TBC) lower or greater than 100 000 colony‐forming units (cfu)/mL, total coliform counts (TCC) greater or lower than 10 000 cfu/mL, and IgC lower or higher than 85 mg Ig/mL. Calves fed colostrum with TBC ≥100 000 cfu/mL were more likely (risk ratio 1.34, confidence interval 1.05–1.71;P < 0.05) to present pneumonia than calves receiving colostrum with lower TBC (incidence 53.2 vs. 39.8%). Calves fed colostrum with high TCC had increased chances of suffering pneumonia (51.4 vs. 42.1%;P < 0.05) than calves fed colostrum with lower TCC. Calves fed colostrum with ≥85 mg Ig/mL tended to present higher daily weight gain (505 ± 113 vs. 484 ± 126 g;P = 0.09). TBC and TCC in colostrum did not influence the incidence rate of diarrhea. It was concluded that under the conditions of the present study, heavy contamination of on‐farm pasteurized frozen–thawed colostrum is seemingly unavoidable and this contamination poses a threat for pneumonia, but not for diarrhea.
How I manage patients with hairy cell leukaemia
Authors: Thompson Philip A. , Ravandi Farhad
Published: February 2017

Patients with hairy cell leukaemia (HCL) have highly favourable outcomes after purine analogue therapy. However, most patients subsequently relapse and require re‐treatment. A minority of patients develop purine analogue‐refractory disease. Targeted therapies have improved outcomes for such patients. Recently, the BRAF V600E mutation was identified in most patients with classical HCL, resulting in constitutive mitogen‐activated protein kinase pathway activation; impressive responses are achieved in heavily pre‐treated patients with BRAF inhibition. The CD22‐targeted immunoconjugate moxetumomab pasudotox and BTK inhibitor ibrutinib also achieve responses in relapsed and refractory patients. HCL variant and the IGHV4‐34 molecular variant of HCL lack BRAF mutation and have inferior outcomes with standard purine analogue therapy. The addition of rituximab to purine analogues achieves very high rates of minimal residual disease‐negative complete remission and improves outcomes for patients with HCL variant. Given the rarity of HCL, optimal integration of novel therapies into treatment algorithms will require well‐designed, collaborative studies.
Application of multi‐kinetic apatite fission track and (U‐Th)/He thermochronology to source rock thermal history: a case study from the Mackenzie Plain, NWT, Canada
Authors: Powell Jeremy W. , Schneider David A. , Issler Dale R.
Published: February 2017

Shale of the Upper Cretaceous Slater River Formation extends across the Mackenzie Plain of the Canadian Northwest Territories and has potential as a regional source rock because of the high organic content and presence of both oil‐ and gas‐prone kerogen. An understanding of the thermal history experienced by the shale is required to predict any potential petroleum systems. Our study integrates multi‐kinetic apatite fission track (AFT) and apatite (U‐Th)/He (AHe) thermochronometers from a basal bentonite unit to understand the timing and magnitude of Late Cretaceous burial experienced by the Slater River Formation along the Imperial River. We use LA‐ICP‐MS and EPMA methods to assess the chemistry of apatite, and use these values to derive the AFT kinetic parameter rmr0. Our AFT dates and track lengths, respectively, range from 201.5 ± 36.9 Ma to 47.1 ± 12.3 Ma, and 16.8 to 10.2 μm, and single crystal AHe dates are between 57.9 ± 3.5 and 42.0 ± 2.5 Ma with effective uranium concentrations from 17 ppm to 36 ppm. The fission track data show no relationship with the kinetic parameter Dpar and fail the χ2‐test indicating that the data do not comprise a single statistically significant population. However, when plotted against their rmr0 value, the data are separated into two statistically significant kinetic populations with distinct track length distributions. Inverse thermal history modelling of both the multi‐kinetic AFT and AHe datasets, reveal that the Slater River Formation reached maximum burial temperatures of ~65–90 °C between the Turonian and Paleocene, indicating that the source rock matured to the early stages of hydrocarbon generation, at best. Ultimately, our data highlight the importance of kinetic parameter choice for AFT and AHe thermochronology, as slight variations in apatite chemistry may have significant implications on fission track and radiation damage annealing in apatite with protracted thermal histories through the uppermost crust.
High‐dose oral colecalciferol loading in obesity: impact of body mass index and its utility prior to bariatric surgery to treat vitamin D deficiency
Authors: King R. J. , Chandrajay D. , Abbas A. , Orme S. M. , Barth J. H.
Published: February 2017

Obesity is associated with lower vitamin D levels compared with normal weight subjects, and if levels are not replaced prior to bariatric surgery, this can increase fracture risk as bone density typically falls post‐operatively. We analysed the effect of body mass index (BMI) on vitamin D levels in response to 300 000 IU of colecalciferol in patients with vitamin D deficiency (<30 nmol L−1). Patients were grouped according to their BMI as normal weight (20–24.9 kg m−2), overweight (25–29.9 kg m−2), obese class I (30–34.9 kg m−2) and obese class II and above (>35 kg m−2). The records were retrospectively analysed to investigate the effects of BMI on vitamin D (total 25‐hydroxy vitamin D [25(OH)D]), serum Ca2+ and parathyroid hormone (PTH) levels at 6, 12, 26 and 52 weeks compared with baseline. Compared with normal weight subjects, overweight and obese patients achieved lower mean peak total 25(OH)D levels (6 weeks post‐loading), which was most significant in the class II and above group (mean total 25(OH)D levels 96.5 ± 24.2 nmol L−1 and 72.42 ± 24.9 nmol L−1, respectively; P = 0.003). By 26 weeks, total 25(OH)D levels fell in all groups; however, there was now a significant difference between the normal weight subjects and all other groups (mean total 25(OH)D levels 84.1 ± 23.7 nmol L−1; 58 ± 20 nmol L−1, P = 0.0002; 62.65 ± 19.2 nmol L−1, P = 0.005; 59.2 ± 21 nmol L−1, P = 0.005, respectively). Far fewer patients in the overweight and obese groups maintained levels above the recommended level of 75 nmol L−1 52 weeks post‐loading (93%; 20%, P = 0.0003; 23%, P = 0.01; and 14%, P = 0.001, respectively). Alternative regimes for the treatment of vitamin D deficiency are needed in overweight and obese patients, especially those in whom bariatric surgery is planned.
Stimulation of N2O emission by manure application to agricultural soils may largely offset carbon benefits: a global meta‐analysis
Authors: Zhou Minghua , Zhu Bo , Wang Shijie , Zhu Xinyu , Vereecken Harry , Brüggemann Nicolas
Published: February 2017

Animal manure application as organic fertilizer does not only sustain agricultural productivity and increase soil organic carbon (SOC) stocks, but also affects soil nitrogen cycling and nitrous oxide (N2O) emissions. However, given that the sign and magnitude of manure effects on soil N2O emissions is uncertain, the net climatic impact of manure application in arable land is unknown. Here, we performed a global meta‐analysis using field experimental data published in peer‐reviewed journals prior to December 2015. In this meta‐analysis, we quantified the responses of N2O emissions to manure application relative to synthetic N fertilizer application from individual studies and analyzed manure characteristics, experimental duration, climate, and soil properties as explanatory factors. Manure application significantly increased N2O emissions by an average 32.7% (95% confidence interval: 5.1–58.2%) compared to application of synthetic N fertilizer alone. The significant stimulation of N2O emissions occurred following cattle and poultry manure applications, subsurface manure application, and raw manure application. Furthermore, the significant stimulatory effects on N2O emissions were also observed for warm temperate climate, acid soils (pH < 6.5), and soil texture classes of sandy loam and clay loam. Average direct N2O emission factors (EFs) of 1.87% and 0.24% were estimated for upland soils and rice paddy soils receiving manure application, respectively. Although manure application increased SOC stocks, our study suggested that the benefit of increasing SOC stocks as GHG sinks could be largely offset by stimulation of soil N2O emissions and aggravated by CH4 emissions if, particularly for rice paddy soils, the stimulation of CH4 emissions by manure application was taken into account.
Long‐term adherence to apomorphine infusion in patients with Parkinson disease: a 10‐year observational study
Authors: Kimber Thomas E. , Fang Jing , Huddy Lynda J. , Thompson Philip D.
Published: February 2017

Background

Patients with Parkinson disease (PD) commonly experience motor fluctuations and dyskinesias in response to oral dopaminergic medications. Affected patients may benefit from device‐assisted therapy, such as medication infusion or deep brain stimulation surgery. This is the first Australian study of the long‐term adherence to apomorphine infusion (AI) in patients with PD.

Aims

To assess the adherence to AI in patients with PD in a single centre over a 10‐year period and to find the reasons for discontinuation in patients who discontinued AI.

Methods

This is an observational study of patients with PD treated with AI between 2004 and 2014. Outcome measures included changes in motor function and quality of life following AI, change in dose of other dopaminergic medications following AI, duration of infusion, adverse effects, reasons for cessation of AI and subsequent treatment after cessation.

Results

Mean duration of AI was 21.65 months. No patient achieved apomorphine monotherapy, and the mean reduction in the levodopa‐equivalent dose of other dopaminergic medications after AI was 22.7%. The benefit of AI on motor function and quality of life was rated as ‘much improved’ or ‘better’ in 83% of patients. The most common reasons for discontinuation of AI were adverse effects and inadequate motor benefit. Most patients who discontinued AI were subsequently treated with another device‐assisted therapy.

Conclusion

AI is an effective therapy for severe motor response complications in PD, especially in the short and medium term. However, many patients cannot be maintained on AI in the longer term.
Exploratory study into the unmet supportive needs of people diagnosed with cirrhosis in Queensland, Australia
Authors: Valery Patricia C. , Clark Paul J. , McPhail Steven M. , Rahman Tony , Hayward Kelly , Martin Jennifer , Horsfall Leigh , Volk Michael L. , Skoien Richard , Powell Elizabeth
Published: February 2017

Background

Many patients with cirrhosis follow complex medication and dietary regimens, and those with decompensated cirrhosis suffer debilitating complications. These factors impact activities of daily living and quality of life.

Aims

To explore the concerns and challenges of people with cirrhosis and their use of support services and to also describe health professionals’ (HP) perspectives of patients’ concerns.

Methods

This is a cross‐sectional study at a tertiary liver clinic involving 50 patients and 54 HP. Data were collected using structured questionnaires. The study includes patients’ report of their challenges/problems now that they have cirrhosis (‘patient‐volunteered concerns’) and HP’ report of patients’ concerns. Both also ranked a list of 10 potential concerns.

Results

Patients were, on average, 58 years old (SD = 10.2), mostly male (78%), Caucasian (86%) and with compensated cirrhosis (60%). The patients’ most common volunteered concerns related to managing symptoms, emotional issues and disease. Most ranked ‘developing liver cancer’ (79%), ‘losing ability to do daily tasks for yourself’ (76%), ‘fear of dying’ (64%) and ‘fear of the unknown’ (64%) as priority concerns. Regarding the use of support services, 24% of patients had accessed a dietician, 20% a pharmacist and 18% a psychologist. From the HP’ perspective, the patients’ most significant challenges related to managing disease (65%) and symptoms (48%), access to healthcare (56%) and information/knowledge (48%).

Conclusions

Our findings demonstrate that cirrhosis (its symptoms, complications and treatment) is associated with significant concerns for patients. The discrepancies between the views of HP and patients suggest that we may not be measuring or addressing patients’ needs appropriately.
Dose adjustment of biologic therapies for psoriasis in dermatological practice: a retrospective study
Authors: Esposito M. , Gisondi P. , Conti A. , Giunta A. , del Giglio M. , Di Mercurio M. , Veneziano L. , Ferrucci G. , Bianchi L. , Chimenti S. , Girolomoni G.
Published: February 2017

Introduction

Despite the large routine use of biologic drugs in psoriasis treatment, the majority of studies do not take into consideration dose‐adjustment practice in ‘real‐life’ dermatological setting. In routine clinical practice, the disease management may include a large number of conditions requiring non‐standard dosage regimens, including dose escalation, dose reduction and/or off‐label treatment interruption.

Objective

The ONDA (Outcome of non‐standard dosing regimen in Psoriasis and Psoriatic Arthritis) study aim was to retrospectively analyse dose‐adjustment strategies among biologic therapies for psoriasis in dermatological practice during a 3‐year period.

Results

This retrospective, observational, multicentre study was carried out in 350 patients (68% male, 32% female) affected by plaque‐type psoriasis (Pso) with a coexistence of psoriatic arthritis in 164 patients (46.9%). At baseline mean PASI score was 14.9 (SD 7.2). Dose adjustment was demonstrated to be a common practice with 70/350 patients (20%) who needed a dose variation during the treatment time, in particular a dose increase in 20/70 patients (28.6%) and a dose reduction in 50/70 patients (71.4%). Dose increase was due to inefficacy on Pso parameters in 60% of cases and to inefficacy of PsA parameters in 40% of cases, while dose reduction (or temporary off‐label treatment interruption) was due to prolonged remission in 54% of cases, other reason in 18% of cases, patient choice or request in 14% of cases, occurrence of concomitant event in 12% of cases.

Conclusion

Dose adjustment is a common clinical practice, consisting of frequent dose reduction when a disease prolonged remission is obtained or dose increase to improve efficacy on Pso and PsA disease parameters.