bluuebunny/crossref_metadata_2025 huggingface dataset:
Periorbital and Orbital Aging: Senile Enophthalmos as a Cause of Upper Eyelid Ptosis
Authors: Guyuron Bahman , Harvey Donald
Published: June 2016

Background:

The aim of this study was to assess the effects of orbital aging over a prolonged period.

Methods:

The orbit and periorbital region were assessed in 21 adult patients over 6 to 24 years with medical-quality facial photographs. The anteroposterior and lateral photographs were evaluated for orbital changes, including enophthalmos and upper eyelid position. Quantitative analysis was performed on the anteroposterior photographs, and qualitative analysis was used to assess enophthalmos.

Results:

The mean age of the patients was 40 years at initial photography and 57 years at the time of secondary photography. At initial photography, eight of the 21 patients had ptosis: six had bilateral mild ptosis (<2 mm), one had bilateral moderate (2 to 3 mm) ptosis, and one had unilateral mild ptosis. At the second time point, only two patients did not have ptosis: four had unilateral mild, seven had bilateral mild, and eight had bilateral moderate ptosis. One patient had unilateral and two patients had bilateral enophthalmos at the initial photography. Nineteen of the 21 patients had relative enophthalmos at the second time point, and all 19 of the patients had eyelid ptosis (p < 0.00001).

Conclusions:

This study demonstrates the development of age-related enophthalmos and eyelid ptosis and the strong association between age-related enophthalmos and upper eyelid ptosis, which is commonly undetected.
Mid-Term Dental and Nerve-Related Complications of Infant Distraction for Robin Sequence
Authors: Steinberg Jordan P. , Brady Colin M. , Waters Brittany R. , Soldanska Magdalena , Burstein Fernando D. , Thomas Jack E. , Williams Joseph K.
Published: June 2016

Background:

Mandibular distraction is effective for relieving airway obstruction in Robin sequence; however, mid-term dental and nerve-related complications have not been adequately studied.

Methods:

Records were reviewed for patients with a single distraction in infancy using internal devices. Follow-up was 5 years or longer. Craniofacial dysmorphic syndromes and those affecting facial nerve function were excluded. Part I involved a review of dental records, whereas Part II involved assessment of inferior alveolar and marginal mandibular nerve function in returning patients with the use of 1,1,1,2-tetrafluoroethane cold stimulation and photography, respectively.

Results:

Eighty-five patients met inclusion criteria. Dental records were complete in 44 patients (median follow-up, 7.3 years; range, 5.4 to 13.2 years). First permanent molar injury was seen in 42 of 88 half-mouths (48 percent); 32 of 42 (76 percent) were restorable. Primary second molar damage and ankylosis were observed in 12 of 88 (14 percent) and one of 88 half-mouths (1 percent), respectively. Mandibular second premolar absence was noted unilaterally in eight of 36 patients (22 percent) and bilaterally in six of 36 patients (17 percent). A mean 1.2 ± 0.95 operative rehabilitations were required. Nerve testing was completed in 20 patients (median follow-up, 8.7 years; range, 5.5 to 13.2 years). Complete absence of cold sensation was noted in one of 40 half-mouths (2.5 percent), whereas lower lip depressor weakness was seen in six of 40 half-mouths (15 percent).

Conclusions:

Infant distraction is highly successful in averting tracheostomy; however, dental and nerve-related complications remain underreported. Regular follow-up with a pediatric dentist and early recognition of injury is essential. Although inferior alveolar nerve injury appears infrequent (2.5 percent), permanent lower lip depressor weakness is more common than previously reported (15 percent of sides).

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Peripheral Motor and Sensory Nerve Conduction following Transplantation of Undifferentiated Autologous Adipose Tissue–Derived Stem Cells in a Biodegradable U.S. Food and Drug Administration–Approved Nerve Conduit
Authors: Klein Silvan M. , Vykoukal Jody , Li De-Pei , Pan Hui-Lin , Zeitler Katharina , Alt Eckhard , Geis Sebastian , Felthaus Oliver , Prantl Lukas
Published: June 2016

Background:

Conduits preseeded with either Schwann cells or stem cells differentiated into Schwann cells demonstrated promising results for the outcome of nerve regeneration in nerve defects.

Methods:

The concept of this trial combines nerve repair by means of a commercially available nerve guidance conduit and preseeding with autologous, undifferentiated, adipose tissue-derived stem cells. Adipose tissue-derived stem cells were harvested from rats and subsequently seeded onto a U.S. Food and Drug Administration–approved type I collagen conduit. Sciatic nerve gaps 10 mm in length were created, and nerve repair was performed by the transplantation of either conduits preseeded with autologous adipose tissue-derived stem cells or acellular (control group) conduits. After 6 months, the motor and sensory nerve conduction velocity were assessed. Nerves were removed and examined by hematoxylin and eosin, van Gieson, and immunohistochemistry (S100 protein) staining for the quality of axonal regeneration.

Results:

Nerve gaps treated with adipose tissue-derived stem cells showed superior nerve regeneration, reflected by higher motor and sensory nerve conduction velocity values. The motor and sensory nerve conduction velocity were significantly greater in nerves treated with conduits preseeded with adipose tissue-derived stem cells than in nerves treated with conduits alone (p < 0.05). Increased S100 immunoreactivity was detected for the adipose tissue-derived stem cell group. In this group, axon arrangement inside the conduits was more organized.

Conclusions:

Transplantation of adipose tissue-derived stem cells significantly improves motor and sensory nerve conduction velocity in peripheral nerve gaps. Preseeded conduits showed a more organized axon arrangement inside the conduit in comparison with nerve conduits alone. The approach used here could readily be translated into a clinical therapy.

CLINCAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, V.
Muscle shortening velocity depends on tissue inertia and level of activation during submaximal contractions
Authors: Ross Stephanie A. , Wakeling James M.
Published: June 2016

In order to perform external work, muscles must do additional internal work to deform their tissue, and in particular, to overcome the inertia due to their internal mass. However, the contribution of the internal mass within a muscle to the mechanical output of that muscle has only rarely been studied. Here, we use a dynamic, multi-element Hill-type muscle model to examine the effects of the inertial mass within muscle on its contractile performance. We find that the maximum strain-rate of muscle is slower for lower activations and larger muscle sizes. As muscle size increases, the ability of the muscle to overcome its inertial load will decrease, as muscle tension is proportional to cross-sectional area and inertial load is proportional to mass. Thus, muscles that are larger in size will have a higher inertial cost to contraction. Similarly, when muscle size and inertial load are held constant, decreasing muscle activation will increase inertial cost to contraction by reducing muscle tension. These results show that inertial loads within muscle contribute to a slowing of muscle contractile velocities (strain-rates), particularly at the submaximal activations that are typical during animal locomotion.
The contribution of glycosaminoglycans to the mechanical behaviour of the posterior human sclera
Authors: Murienne Barbara J. , Chen Michelle L. , Quigley Harry A. , Nguyen Thao D.
Published: June 2016

We characterized the structural and mechanical changes after experimental digestion of sulfated glycosaminoglycans (s-GAGs) in the human posterior sclera, using ultrasound thickness measurements and an inflation test with three-dimensional digital image correlation (3D-DIC). Each scleral specimen was first incubated in a buffer solution to return to full hydration, inflation tested, treated in a buffer solution with chondroitinase ABC (ChABC), then inflation tested again. After each test series, the thickness of eight locations was measured. After enzymatic treatment, the average scleral thickness decreased by 13.3% (
p
< 0.001) and there was a stiffer overall stress–strain response (
p
< 0.05). The stress–strain response showed a statistically significant increase in the low-pressure stiffness, high-pressure stiffness and hysteresis. Thus, s-GAGs play a measurable role in the mechanical behaviour of the posterior human sclera.
The importance of burrowing, climbing and standing upright for laboratory rats
Authors: Makowska I. Joanna , Weary Daniel M.
Published: June 2016

Standard laboratory cages prevent rats (Rattus norvegicus) from performing many behaviours that they perform in the wild, but little is known about how this may affect their welfare. The aims of this study were (i) to record the propensity to burrow, climb and stand upright in 3-, 8- and 13-month old laboratory rats housed in semi-naturalistic environments and (ii) to compare the frequency of lateral stretching in semi-naturalistic versus standard-housed rats; we predicted standard-housed rats would perform more lateral stretches to compensate for the inability to stretch upright. Rats' propensity to burrow remained constant as they aged (approx. 30 bouts per day totalling 20–30 min), suggesting burrowing is important to rats. Climbing decreased from 76 to 7 bouts per day at 3 versus 13 months, probably because of declining physical ability. Upright standing decreased from 178 to 73 bouts per day, but continued to be frequently expressed even in older rats. Standard-housed rats stretched much more frequently than semi-naturalistic-housed rats (53 versus 6 bouts per day at 13 months), perhaps in compensation for inability to stretch upright and to relieve stiffness caused by low mobility associated with standard housing. These findings suggest that standard laboratory cages interfere with important natural behaviours, which is likely to compromise rat welfare.
Biophysically inspired model for functionalized nanocarrier adhesion to cell surface: roles of protein expression and mechanical factors
Authors: Ramakrishnan N. , Tourdot Richard W. , Eckmann David M. , Ayyaswamy Portonovo S. , Muzykantov Vladimir R. , Radhakrishnan Ravi
Published: June 2016

In order to achieve selective targeting of affinity–ligand coated nanoparticles to the target tissue, it is essential to understand the key mechanisms that govern their capture by the target cell. Next-generation pharmacokinetic (PK) models that systematically account for proteomic and mechanical factors can accelerate the design, validation and translation of targeted nanocarriers (NCs) in the clinic. Towards this objective, we have developed a computational model to delineate the roles played by target protein expression and mechanical factors of the target cell membrane in determining the avidity of functionalized NCs to live cells. Model results show quantitative agreement with
in vivo
experiments when specific and non-specific contributions to NC binding are taken into account. The specific contributions are accounted for through extensive simulations of multivalent receptor–ligand interactions, membrane mechanics and entropic factors such as membrane undulations and receptor translation. The computed NC avidity is strongly dependent on ligand density, receptor expression, bending mechanics of the target cell membrane, as well as entropic factors associated with the membrane and the receptor motion. Our computational model can predict the
in vivo
targeting levels of the intracellular adhesion molecule-1 (ICAM1)-coated NCs targeted to the lung, heart, kidney, liver and spleen of mouse, when the contributions due to endothelial capture are accounted for. The effect of other cells (such as monocytes, etc.) do not improve the model predictions at steady state. We demonstrate the predictive utility of our model by predicting partitioning coefficients of functionalized NCs in mice and human tissues and report the statistical accuracy of our model predictions under different scenarios.
Eutherians experienced elevated evolutionary rates in the immediate aftermath of the Cretaceous–Palaeogene mass extinction
Authors: Halliday Thomas John Dixon , Upchurch Paul , Goswami Anjali
Published: June 2016

The effect of the Cretaceous–Palaeogene (K–Pg) mass extinction on the evolution of many groups, including placental mammals, has been hotly debated. The fossil record suggests a sudden adaptive radiation of placentals immediately after the event, but several recent quantitative analyses have reconstructed no significant increase in either clade origination rates or rates of character evolution in the Palaeocene. Here we use stochastic methods to date a recent phylogenetic analysis of Cretaceous and Palaeocene mammals and show that Placentalia likely originated in the Late Cretaceous, but that most intraordinal diversification occurred during the earliest Palaeocene. This analysis reconstructs fewer than 10 placental mammal lineages crossing the K–Pg boundary. Moreover, we show that rates of morphological evolution in the 5 Myr interval immediately after the K–Pg mass extinction are three times higher than background rates during the Cretaceous. These results suggest that the K–Pg mass extinction had a marked impact on placental mammal diversification, supporting the view that an evolutionary radiation occurred as placental lineages invaded new ecological niches during the Early Palaeocene.
Cellular and molecular remodelling of a host cell for vertical transmission of bacterial symbionts
Authors: Luan Jun-Bo , Shan Hong-Wei , Isermann Philipp , Huang Jia-Hsin , Lammerding Jan , Liu Shu-Sheng , Douglas Angela E.
Published: June 2016

Various insects require intracellular bacteria that are restricted to specialized cells (bacteriocytes) and are transmitted vertically via the female ovary, but the transmission mechanisms are obscure. We hypothesized that, in the whiteflyBemisia tabaci, where intact bacteriocytes (and not isolated bacteria) are transferred to oocytes, the transmission mechanism would be evident as cellular and molecular differences between the nymph (pre-adult) and adult bacteriocytes. We demonstrate dramatic remodelling of bacteriocytes at the developmental transition from nymph to adulthood. This transition involves the loss of cell–cell adhesion, high division rates to constant cell size and onset of cell mobility, enabling the bacteriocytes to crawl to the ovaries. These changes are accompanied by cytoskeleton reorganization and changes in gene expression: genes functioning in cell–cell adhesion display reduced expression and genes involved in cell division, cell motility and endocytosis/exocytosis have elevated expression in adult bacteriocytes, relative to nymph bacteriocytes. This study demonstrates, for the first time, how developmentally orchestrated remodelling of gene expression and correlated changes in cell behaviour underpin the capacity of bacteriocytes to mediate the vertical transmission and persistence of the symbiotic bacteria on which the insect host depends.
How humans drive speciation as well as extinction
Authors: Bull J. W. , Maron M.
Published: June 2016

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using
net
species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation—and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature—considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.
Elevated virulence of an emerging viral genotype as a driver of honeybee loss
Authors: McMahon Dino P. , Natsopoulou Myrsini E. , Doublet Vincent , Fürst Matthias , Weging Silvio , Brown Mark J. F. , Gogol-Döring Andreas , Paxton Robert J.
Published: June 2016

Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination
in vivo
. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.
Light pollution is associated with earlier tree budburst across the United Kingdom
Authors: ffrench-Constant Richard H. , Somers-Yeates Robin , Bennie Jonathan , Economou Theodoros , Hodgson David , Spalding Adrian , McGregor Peter K.
Published: June 2016

The ecological impact of night-time lighting is of concern because of its well-demonstrated effects on animal behaviour. However, the potential of light pollution to change plant phenology and its corresponding knock-on effects on associated herbivores are less clear. Here, we test if artificial lighting can advance the timing of budburst in trees. We took a UK-wide 13 year dataset of spatially referenced budburst data from four deciduous tree species and matched it with both satellite imagery of night-time lighting and average spring temperature. We find that budburst occurs up to 7.5 days earlier in brighter areas, with the relationship being more pronounced for later-budding species. Excluding large urban areas from the analysis showed an even more pronounced advance of budburst, confirming that the urban ‘heat-island’ effect is not the sole cause of earlier urban budburst. Similarly, the advance in budburst across all sites is too large to be explained by increases in temperature alone. This dramatic advance of budburst illustrates the need for further experimental investigation into the impact of artificial night-time lighting on plant phenology and subsequent species interactions. As light pollution is a growing global phenomenon, the findings of this study are likely to be applicable to a wide range of species interactions across the world.
The oxidative cost of reproduction depends on early development oxidative stress and sex in a bird species
Authors: Romero-Haro A. A. , Sorci G. , Alonso-Alvarez C.
Published: June 2016

In the early 2000s, a new component of the cost of reproduction was proposed: oxidative stress. Since then the oxidative cost of reproduction hypothesis has, however, received mixed support. Different arguments have been provided to explain this. Among them, the lack of a life-history perspective on most experimental tests was suggested. We manipulated the levels of a key intracellular antioxidant (glutathione) in captive zebra finches (
Taeniopygia guttata
) during a short period of early life and subsequently tested the oxidative cost of reproduction. Birds were allowed to mate freely in an outdoor aviary for several months. We repeatedly enlarged or reduced their broods to increase or reduce, respectively, breeding effort. Birds whose glutathione levels were reduced during growth showed higher erythrocyte resistance to free radical-induced haemolysis when forced to rear enlarged broods. This supports the hypothesis predicting the occurrence of developing programmes matching early and adult environmental conditions to improve fitness. Moreover, adult males rearing enlarged broods endured higher plasma levels of lipid oxidative damage than control males, whereas adult females showed the opposite trend. As most previous studies reporting non-significant or opposite results used females only, we also discuss some sex-related particularities that may contribute to explain unexpected results.
Learning to cope: vocal adjustment to urban noise is correlated with prior experience in black-capped chickadees
Authors: LaZerte Stefanie E. , Slabbekoorn Hans , Otter Ken A.
Published: June 2016

Urban noise can interfere with avian communication through masking, but birds can reduce this interference by altering their vocalizations. Although several experimental studies indicate that birds can rapidly change their vocalizations in response to sudden increases in ambient noise, none have investigated whether this is a learned response that depends on previous exposure. Black-capped chickadees (
Poecile atricapillus
) change the frequency of their songs in response to both fluctuating traffic noise and experimental noise. We investigated whether these responses to fluctuating noise depend on familiarity with noise. We confirmed that males in noisy areas sang higher-frequency songs than those in quiet areas, but found that only males in already-noisy territories shifted songs upwards in immediate response to experimental noise. Unexpectedly, males in more quiet territories shifted songs downwards in response to experimental noise. These results suggest that chickadees may require prior experience with fluctuating noise to adjust vocalizations in such a way as to minimize masking. Thus, learning to cope may be an important part of adjusting to acoustic life in the city.
Ocean acidification alters fish–jellyfish symbiosis
Authors: Nagelkerken Ivan , Pitt Kylie A. , Rutte Melchior D. , Geertsma Robbert C.
Published: June 2016

Symbiotic relationships are common in nature, and are important for individual fitness and sustaining species populations. Global change is rapidly altering environmental conditions, but, with the exception of coral–microalgae interactions, we know little of how this will affect symbiotic relationships. We here test how the effects of ocean acidification, from rising anthropogenic CO
2
emissions, may alter symbiotic interactions between juvenile fish and their jellyfish hosts. Fishes treated with elevated seawater CO
2
concentrations, as forecast for the end of the century on a business-as-usual greenhouse gas emission scenario, were negatively affected in their behaviour. The total time that fish (yellowtail scad) spent close to their jellyfish host in a choice arena where they could see and smell their host was approximately three times shorter under future compared with ambient CO
2
conditions. Likewise, the mean number of attempts to associate with jellyfish was almost three times lower in CO
2
-treated compared with control fish, while only 63% (high CO
2
) versus 86% (control) of all individuals tested initiated an association at all. By contrast, none of three fish species tested were attracted solely to jellyfish olfactory cues under present-day CO
2
conditions, suggesting that the altered fish–jellyfish association is not driven by negative effects of ocean acidification on olfaction. Because shelter is not widely available in the open water column and larvae of many (and often commercially important) pelagic species associate with jellyfish for protection against predators, modification of the fish–jellyfish symbiosis might lead to higher mortality and alter species population dynamics, and potentially have flow-on effects for their fisheries.
Hierarchical structures of cactus spines that aid in the directional movement of dew droplets
Authors: Malik F. T. , Clement R. M. , Gethin D. T. , Kiernan M. , Goral T. , Griffiths P. , Beynon D. , Parker A. R.
Published: June 2016

Three species of cactus whose spines act as dew harvesters were chosen for this study:
Copiapoa cinerea
var.
haseltoniana
,
Mammillaria columbiana
subsp.
yucatanensis
and
Parodia mammulosa
and compared with
Ferocactus wislizenii
whose spines do not perform as dew harvesters. Time-lapse snapshots of
C. cinerea
showed movement of dew droplets from spine tips to their base, even against gravity. Spines emanating from one of the areoles of
C. cinerea
were submerged in water laced with fluorescent nanoparticles and this particular areole with its spines and a small area of stem was removed and imaged. These images clearly showed that fluorescent water had moved into the stem of the plant. Lines of vascular bundles radiating inwards from the surface areoles (from where the spines emanate) to the core of the stem were detected using magnetic resonance imaging, with the exception of
F. wislizenii
that does not harvest dew on its spines. Spine microstructures were examined using SEM images and surface roughness measurements (
R
a
and
R
z
) taken of the spines of
C. cinerea
. It was found that a roughness gradient created by tapered microgrooves existed that could potentially direct surface water from a spine tip to its base.

This article is part of the themed issue ‘Bioinspired hierarchically structured surfaces for green science’.
Influence of surface structure and chemistry on water droplet splashing
Authors: Koch Kerstin , Grichnik Roland
Published: June 2016

Water droplet splashing and aerosolization play a role in human hygiene and health systems as well as in crop culturing. Prevention or reduction of splashing can prevent transmission of diseases between animals and plants and keep technical systems such as pipe or bottling systems free of contamination. This study demonstrates to what extent the surface chemistry and structures influence the water droplet splashing behaviour. Smooth surfaces and structured replicas of
Calathea zebrina
(Sims) Lindl. leaves were produced. Modification of their wettability was done by coating with hydrophobizing and hydrophilizing agents. Their wetting was characterized by contact angle measurement and splashing behaviour was observed with a high-speed video camera. Hydrophobic and superhydrophilic surfaces generally showed fewer tendencies to splash than hydrophobic ones. Structuring amplified the underlying behaviour of the surface chemistries, increasing hydrophobic surfaces’ tendency to splash and decreasing splash on hydrophilic surfaces by quickly transporting water off the impact point by capillary forces. The non-porous surface structures found in
C. zebrina
could easily be applied to technical products such as plastic foils or mats and coated with hydrophilizing agents to suppress splash in areas of increased hygiene requirements or wherever pooling of liquids is not desirable.

This article is part of the themed issue ‘Bioinspired hierarchically structured surfaces for green science’.
Why re-entrant surface topography is needed for robust oleophobicity
Authors: Nosonovsky Michael , Bhushan Bharat
Published: June 2016

Surface patterns affect wetting properties of solid materials allowing manipulation of the phase state of an adjacent fluid. The best known example of this effect is the superhydrophobic composite (Cassie–Baxter) interface with vapour/air pockets between the solid and liquid. Mathematically, the effect of surface micropatterns can be studied by an averaging technique similarly to the method of separation of motions in dynamics. However, averaged parameters are insufficient for robust superhydrophobic and superoleophobic surfaces because additional topography features are important: hierarchical organization and re-entrant roughness. The latter is crucial for the oleophobicity because it enhances the stability of a composite interface. The re-entrant topography can be achieved by various methods. Understanding the role of re-entrant surface topography gives us new insights on the multitude of wetting scenarios beyond the standard Wenzel and Cassie–Baxter models.

This article is part of the themed issue ‘Bioinspired hierarchically structured surfaces for green science’.
Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications
Authors: Barthlott W. , Mail M. , Neinhuis C.
Published: June 2016

A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing.

This article is part of the themed issue ‘Bioinspired hierarchically structured surfaces for green science’.
Plant Chimeras: the good, the bad, and the ‘Bizzaria’
Authors: Frank Margaret H. , Chitwood Daniel H.
Published: June 2016

Chimeras – organisms that are composed of cells of more than one genotype – captured the human imagination long before they were formally described and used in the laboratory. These organisms owe their namesake to a fire-breathing monster from Greek mythology that has the head of a lion, the body of a goat, and the tail of a serpent. The first description of a non-fictional chimera dates back to the middle of the seventeenth century when the Florentine gardener Pietro Nati discovered an adventitious shoot growing from the graft junction between sour orange (Citrus aurantium) and citron (C. medica). This perplexing chimera that grows with sectors phenotypically resembling each of the citrus progenitors inspired discussion and wonder from the scientific community and was fittingly named the ‘Bizzaria’. Initially, the ‘Bizzaria’ was believed to be an asexual hybrid that formed from a cellular fusion between the grafted parents; however, in-depth cellular analyses carried out centuries later demonstrated that the ‘Bizzaria’, along with other chimeras, owe their unique sectored appearance to a conglomeration of cells from the two donors. Since this pivotal discovery at the turn of the twentieth century, chimeras have served both as tools and as unique biological phenomena that have contributed to our understanding of plant development at the cellular, tissue, and organismal level. Rapid advancements in genome sequencing technologies have enabled the establishment of new model species with novel morphological and developmental features that enable the generation of chimeric organisms. In this review, we show that genetic mosaic and chimera studies provide a technologically simple way to delve into the organismal, genetic, and genomic inner workings underlying the development of diverse model organisms. Moreover, we discuss the unique opportunity that chimeras present to explore universal principles governing intercellular communication and the coordination of organismal biology in a heterogenomic landscape.
fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets
Authors: Madrigal Pedro
Published: June 2016

Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomic science, as it allows both to evaluate the reproducibility across biological or technical replicates, and to compare different datasets to identify their potential correlations. Here I present fCCAC, an application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). I exemplify how this method can reveal shared covariance between histone modifications and DNA binding proteins, such as the relationship between the H3K4me3 chromatin mark and its epigenetic writers and readers.

Availability

R code is publicly available athttp://github.com/pmb59/fCCAC/.

Contact

pm12@sanger.ac.uk
C. eleganschromosomes connect to centrosomes by anchoring into the spindle network
Authors: Redemann Stefanie , Baumgart Johannes , Lindow Norbert , Fürthauer Sebastian , Nazockdast Ehssan , Kratz Andrea , Prohaska Steffen , Brugués Jan , Shelley Michael , Müller-Reichert Thomas
Published: June 2016

The mitotic spindle ensures the faithful segregation of chromosomes. To discover the nature of the crucial centrosome-to-chromosome connection during mitosis, we combined the first large-scale serial electron tomography of whole mitotic spindles in earlyC. elegansembryos with live-cell imaging. Using tomography, we reconstructed the positions of all microtubules in 3D, and identified their plus- and minus-ends. We classified them as kinetochore (KMTs), spindle (SMTs), or astral microtubules (AMTs) according to their positions, and quantified distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs are directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient.
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
Authors: Tørresen Ole K. , Star Bastiaan , Jentoft Sissel , Reinar William B. , Grove Harald , Miller Jason R. , Walenz Brian P. , Knight James , Ekholm Jenny M. , Peluso Paul , Edvardsen Rolf B. , Tooming-Klunderud Ave , Skage Morten , Lien Sigbjørn , Jakobsen Kjetill S. , Nederbragt Alexander J.
Published: June 2016

Background: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.

Results: By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21 % of the TRs across the assembly, 19 % in the promoter regions and 12 % in the coding sequences are heterozygous in the sequenced individual.

Conclusions: The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.
Tax policy and farm capital investment: Section 179 expensing and bonus depreciation
Authors: Williamson James M , Stutzman Sarah
Published: June 2016

Purpose

– The purpose of this paper is to estimate the impact of Internal Revenue Code cost recovery provisions – Section 179 and “bonus depreciation” – on farm capital investment.

Design/methodology/approach

– The authors construct a synthetic panel of data consisting of cohorts of similar farms based on state and production specialization using the USDA’s Agricultural Resource Management Survey for years 1996-2012. Employing panel data methods, the authors are able to control for time-invariant fixed effects, as well as the effects of past investment on current investment.

Findings

– The authors estimate statistically significant investment demand elasticities with respect to the Section 179 expensing deduction of between 0.28 and 0.50. A change in bonus depreciation, on average, had little impact on capital investment.

Practical implications

– The estimates suggest there is a modest effect of the cost recovery provisions on investment overall, but a stronger effect on farms that have more than $10,000 in gross cash farm income. There are other implications for the agricultural sector: the provisions may encourage technology adoption with its associated benefits, such as reduced cost of production and improved conservation practices. On the other hand, the policy could contribute to the growing concentration in production as large commercial farms expand their operated acreage to take advantage of increasingly efficient physical capital.

Originality/value

– To the authors’ knowledge, this is the first research to use a nationally representative dataset to estimate to impact of Section 179 and “bonus depreciation” on farm investment. The findings provide evidence of the provisions’ impact on farm capital purchases.
Land titles and formal credit in Thailand
Authors: Sakprachawut Soontaree , Jourdain Damien
Published: June 2016

Purpose

– The purpose of this paper is to investigate the effects of land titles and farmers’ characteristics on their participation in the formal credit market in a land reform area of Thailand.

Design/methodology/approach

– Data collected on 218 farm households in one land reform area of Western Thailand are analyzed with a generalized double-hurdle model to calculate the probability of farm households to take a loan and the size of the loans from a formal credit institute, the Bank for Agriculture and Agricultural Co-operatives.

Findings

– The results suggest that the absence of a title, whether fully or partially transferable, decreases significantly the participation to the formal credit market and the size of the loans. However, this effect was small. The findings also indicate that the farm assets, household head’s gender and age, and the labor force per hectare were significantly influencing the probability of participation to borrow money as well as the amount borrowed.

Practical implications

– The possibility given to farmers having title with partial transferability to provide alternative types of guarantees reduced the gap in loan-taking between the different types of land title. However, the presence of a land title, transferable or not, had a significant influence on farmers demand and success in obtaining credit.

Originality/value

– The paper investigates the possible effects of a unique partial land rights in Thailand that guarantees only security of use of the land but prohibits sale.
The impact of higher education commission of pakistan’s funding on the collection development budgets of university libraries
Authors: Khan Ghalib , Bhatti Rubina
Published: June 2016

Purpose

This study aims to investigate the annual financial management of university libraries in the province of Khyber Pakhtunkhwa (KPK), Pakistan, and its relationship with Higher Education Commission (HEC) grants to examine libraries’ share.

Design/methodology/approach

Using survey methods, this study explores the annual budget allocation of well-established university libraries in the province of KPK in the past five years and its relationship with HEC grants to determine libraries’ shares. The survey followed a qualitative design based on an interview technique of data collection. The scope of this study covers all those public sector universities which are chartered by the Government of KPK, recognized by HEC, and eligible for HEC grants on annual basis. Based on this formulation, 15 public sector universities were selected for the survey.

Findings

The data analysis of the present study revealed that no specific norms are followed by the university administrations in allocating funds for libraries out of HEC annual grants. University libraries in the province either do not have funding polices or are administered by the concerned establishments where Library and Information Science professionals have no role in the financial management of libraries. The study also found that university administrations in KPK either do not provide sufficient share to libraries out of HEC grants or specify an inadequate share which is in violation of the clear instructions of HEC ordinance 2002, Section 10(h).

Originality/value

This study is the first of its kind in Pakistan as it provides an insight into how much budget is allocated for collection development in the university libraries, compares it with HEC grants to calculate libraries’ share in percentage and suggests to the HEC to encourage university administration to allocate sufficient budget for libraries to improve collection development, service provision, acquisition, selection and patronage.
Can we shift more library costs to students?
Authors: Steele Kirstin
Published: June 2016

Purpose

The purpose of the study is to discuss Questia, a library database that is marketed directly to student users.

Design/methodology/approach

Opinion piece.

Findings

From a student’s perspective, Questia is very useful. It would not be a useful addition to undergraduate libraries, even if site licenses are available.

Research limitations/implications

It would be interesting to design a study to compare library skills of undergraduates who are subscribed to Questia with those who participate in traditional library instruction sessions.

Practical implications

It is suggested that Questia should be recommended to an undergraduate student who is struggling with basic research skills or who is especially pressed for time.

Originality/value

There are no scholarly articles discussing Questia after 2012.
Multisource system for NDT of welded elements exploited in aircraft industry
Authors: Chady Tomasz , Sikora Ryszard , Szwagiel Mariusz , Grzywacz Bogdan , Misztal Leszek , Waszczuk Pawel , Szydlowski Michal , Szymanik Barbara
Published: June 2016

Purpose

– The purpose of this paper is to describe a multisource system for nondestructive inspection of welded elements exploited in aircraft industry developed in West Pomeranian University of Technology, Szczecin in the frame of CASELOT project. The system task is to support the operator in flaws identification of welded aircraft elements using data obtained from X-ray inspection and 3D triangulation laser scanners.

Design/methodology/approach

– For proper defects detection a set of special processing algorithms were developed. For easier system exploitation and integration of all components a user friendly interface in LabVIEW environment was designed.

Findings

– It is possible to create the fully independent, intelligent system for welds’ flaws detection. This kind of technology might be crucial in further development of aircraft industry.

Originality/value

– In this paper a number of innovative solutions (new algorithms, algorithms’ combinations) for defects’ detection in welds are presented. All of these solutions are the basis of presented complete system. One of the main original solution is a combination of the systems based on 3D triangulation laser scanner and X-ray testing.
Finite element analysis of the active element displacement in a giant magnetostrictive transducer
Authors: Stachowiak Dorota
Published: June 2016

Purpose

– The purpose of this paper is to find the method for determining the displacement of the active element in a giant magnetostrictive transducer.

Design/methodology/approach

– The giant magnetostrictive transducer with the active element made of Terfenol-D has been considered. A structure with an axisymmetrical transducer has been proposed. In the proposed model the coupling of magnetic and mechanical field has been taken into account. Maxwell’s equations for electromagnetics and Navier’s equations for mechanical systems are formulated in weak form and coupled using a nonlinear magneto-mechanical constitutive law for Terfenol-D. In order to obtain the distribution of the magnetic and mechanical fields the finite element method was used. The elaborated nonlinear magnetostrictive model has been implemented by using a finite element weak formulation with COMSOL Multiphysics.

Findings

– The elaborated model for the giant magnetostrictive transducer allows to take into account the magneto-mechanical coupling as well as the material’s nonlinearity. The calculation results of the strain distributions caused by magnetostrictive forces have been presented. The output displacement of a transducer vs supply current for different compressive preload stresses has been calculated and measured. The simulation and measurements results are in close agreement.

Research limitations/implications

– Taking advantage of the geometrical structure of the prototype of the giant magnetostrictive transducer the computations are performed in an axial-symmetric domain with cylindrical coordinates (r, z, ϑ). The axisymmetric formulation describes the giant magnetostrictive transducers (GMT) without significant loss of accuracy. This approach leads to smaller numerical models and reduced computational time.

Practical implications

– The elaborated magneto-mechanical model can be used to the design and optimize the structure of GMT.

Originality/value

– The paper offers the magneto-mechanical model of the giant magnetostrictive transducer. The elaborated model can predict behavior of the magnetostrictive materials it can be used as a tool for the design process of the giant magnetostrictive transducer.