bluuebunny/crossref_metadata_2025 huggingface dataset:
Enzyme systems for effective dag removal from cattle hides
Authors: Navone Laura , Speight Robert E.
Published: October 2018

The effective removal of recalcitrant manure balls (dags) composed of dung, hair, soil, urine, sugars and straw from the hides of cattle remains a significant issue for the livestock industry. Dags must be removed to reduce the likelihood of microbial meat contamination and irreversible damage during leather processing. Current removal methods require extensive washing over many hours per animal resulting in high water use, costs and stress to the animal. Enzymes can be highly effective catalysts for the breakdown of biomass but previous research into the enzymatic removal of dags has had limited success. This work investigates the latest commercial enzyme preparations and classes of enzymes never previously tested for dag removal in new formulations. Cellulase, xylanase, laccase and α-amylase enzymes were applied to target the lignocellulosic and starch components of the dags. Protease enzymes that targeted the interaction between the dag and the hair, were also investigated as a novel approach for dag removal from cattle. Our results show that the application of a protease with keratinolytic activity is crucial for dag removal, weakening the framework of hairs at the point of attachment between the hair and the dag, as well as potentially degrading adhesive protein that may hold the structure together. The addition of a reducing agent and surfactant to the treatment facilitated optimal decomposition of the dag structure. Implementation of these enzymatic dag removal systems could significantly reduce the time, water use, animal stress and costs of cleaning cattle in the red meat industry.
The influences of climate, habitat and fire on the distribution of cockatoo grass (Alloteropsis semialata) (Poaceae) in the Wet Tropics of northern Australia
Authors: Bateman Brooke L. , Johnson Christopher N.
Published: October 2018

Cockatoo grass [Alloteropsis semialata (R.Br.) A. Hitchc.] is considered a keystone species in northern Australian ecosystems as it provides a food resource for many species, including several endangered vertebrates. This study examined both local and regional environmental factors influencing cockatoo grass distribution and abundance in the Wet Tropics of north Queensland, Australia. Local distribution and abundance were investigated in the sclerophyll ecotone between open woodland and tall open forest, because little is known about cockatoo grass distribution within this habitat; also, the endangered northern bettong (Bettongia tropica) is restricted to this habitat and depends on cockatoo grass for its survival. Regional-scale modelling of distribution was undertaken to examine the climatic tolerances of cockatoo grass in Queensland. Density of cockatoo grass was negatively related to litter cover, soil moisture, and the presence of two dominant grass species, Themeda triandra [Forssk.(R.Br.) Stapf] and Cleistochloa subjuncea (C.E.Hubb.). Soil nutrients (N, C, S, and C : N ratio) were positively related to density of cockatoo grass. A late dry season experimental burn demonstrated that cockatoo grass had high survival to fire, with increased density and flowering in response to fire. Regional-scale modelling using climate variables indicated that cockatoo grass is more suited to the drier end of the sclerophyll habitat range. Cockatoo grass in the woodland-forest ecotone in the Wet Tropics appears to be influenced by several environmental features associated with the ground layer. The species benefits from the reduction in litter cover and competing grass species that result from management actions such as prescribed burning. Understanding of the factors limiting this species, both at a local and regional scale, can be used to guide management of this ecotone habitat for both cockatoo grass and the survival of other species that depend on it.
Multiple Pleistocene refugia in the widespread Patagonian tree Embothrium coccineum (Proteaceae)
Authors: Vidal-Russell Romina , Souto Cintia P. , Premoli Andrea C.
Published: October 2018

Embothrium coccineum J.R.Forst. & G.Forst is an endemic tree of the Patagonian temperate forest. The objective of this study is to evaluate the impact of last glaciation events on the genetic structure of this widespread and ecologically tolerant species, to postulate possible refugial areas. Phylogeographic analyses were performed using chloroplast DNA sequences (trnL-trnF spacer and ndhC-trnV spacer) from individuals collected in 34 populations along the total range of the species, and these results were compared with a similar study in Nothofagus. A total of 22 haplotypes were found, three of which were widely distributed while 13 were found at only one location. Historical demography suggests a long period of stable effective population size, decreasing gradually towards the Last Glacial Maximum (LGM), followed by an increase in population size that stabilised 2500 years ago. The phylogeographic analyses reflect recent events of colonisation after the LGM from multiple refugia. In the northern area of its distribution probably the species survived in several pockets within the Andes mountain range and in Cordillera de la Costa in Chile. In the south, it is suggested that Embothrium survived the glacial period at the edge of the glaciers. These findings are in agreement with the fossil pollen record that shows 10 000-year-old grains in the south, suggesting colonisation from nearby areas when ice retreated. Embothrium is a coloniser that naturally occurs as scattered individuals within mixed forests. Hence, the shallow phylogeographic structure reported here reflects a Pleistocene signature highly impacted by drift resulting in the randomly fixation of new variants reducing the cpDNA structure.
Investigating the Avidin-Biotin Interaction on Chiral Soft Structure Platforms
Authors: Krishna K. Vijaya , Verma Sandeep
Published: October 2018

The synthesis of a novel biotin-cholesterol conjugate is described together with its propensity to self-assemble and exhibit interesting optical behaviour, when examined under cross-polarized light. The avidin-biotin interaction performed with this conjugate reveals loss of birefringence suggesting that such constructs could possibly be applied for optical tracking of important biological interactions.
Combinatorial Solid-Phase Synthesis of 6-Aryl-1,3,5-triazines via Suzuki Coupling
Authors: Lee Jae Wook , Ha Hyung-Ho , Vendrell Marc , Bork Jacqueline T. , Chang Young-Tae
Published: October 2018

A synthetic methodology to prepare collections of trisubstituted aryl 1,3,5-triazines with broad structural diversity via Suzuki coupling has been developed. We first optimized the combinatorial derivatization of the triazine core using Suzuki cross-coupling. Second, in order to further expand the methodology for the preparation of negatively charged triazines, we adapted this approach to polymer-supported amino acids and prepared aryl triazines with different charge distribution. With a collection of 160 aryl triazine derivatives in good purities and without any purification step, we proved the viability of this orthogonal scheme for the preparation of triazine libraries using amine/amino acid-captured solid supports and Suzuki cross-coupling.
Recent Studies on Flash Vacuum Thermolysis in Tandem with UV-Photoelectron Spectroscopy and Quantum Calculations
Authors: Chrostowska Anna , Leśniak Stanisław
Published: October 2018

Flash vacuum thermolysis (FVT) is a particular method that allows the synthesis of stable compounds or the generation of short-lived species. Its coupling with spectroscopic characterisation provides very useful tools for mechanistic investigations. One of the most efficient and especially well suited techniques for this purpose is ultraviolet–photoelectron spectroscopy (UV-PES), which in tandem with FVT provides the ionisation energies of in situ formed molecules in the gas phase. The experimental data thus obtained in real-time are supported by quantum chemical calculations for consistency of the assignments of PES spectra and constitute fundamental information about electronic structure and bonding. The FVT/UV-PES technique has been known for more than 40 years, but one advantage in the present age is the greater confidence in electronic structure computations for predicting ionisation energies, thus providing the necessary tool for unambiguous interpretation of experimental data. This mini-review aims to give some representative, original examples, chosen from a French–Polish collaboration that illustrates the efficiency and wide applicability of the FVT/UV-PES tandem methodology. The selected examples on the FVT of thione and imine derivatives will be presented.
Research and practice: environmental action for improving water quality in cotton catchments since 1990
Authors: Kennedy I. R. , Rose M. T. , Crossan A. , Burns M.
Published: October 2018

In the modern era, agriculture must seek to be environmentally sustainable, an obligation now considered as a social contract. This demands that its activities do no significant harm, where the natural resources sustaining it are fully safeguarded, but of necessity in the context of profitable agriculture. The requirement to minimise the environmental impact of the necessary agrochemicals and pesticides in waterways is especially demanding. In the past 20 years, the Australian cotton industry has approached this obligation in various ways, needing extensive planning, learning from past experiences, but it can be legitimately claimed, with significant success. This success has been achieved at some cost, requiring large numbers of personnel, time and resources. This review aims to document the strategies that have been employed, how these required effective research management and how the research data generated was applied. To the extent that this complex program of participatory action has succeeded, while also acknowledging some dramatic failures, other areas of agriculture can also benefit by identification of the key factors contributing to success.
Deep drainage in a Grey Vertosol under furrow-irrigated cotton
Authors: Ringrose-Voase Anthony J. , Nadelko Anthony J.
Published: October 2018

Deep drainage under irrigated cotton is not only a waste of a scare resource but also has the potential to cause groundwater levels to rise and cause salinity. Drainage is difficult and expensive to measure directly, so most estimates have relied on modelling or chloride mass-balance calculations. However, direct, accurate measurements of drainage are required to understand drainage processes in cracking clay soils and to provide some certainty about other estimates. A variable-tension lysimeter was installed at 2.1 m depth in a Grey Vertosol under a furrow-irrigated, cotton–wheat rotation. The collection trays were installed without disturbing the overlying soil. A vacuum was applied to the trays and was continuously adjusted to match the matric potential in the surrounding soil at the same depth, thus maintaining the same hydraulic gradient as in the surrounding soil.
The lysimeter was used to measure drainage and other components of the water balance from 2006 to 2011, including three cotton crops, one wheat crop and a long fallow. During this period, two types of drainage were observed. Matrix drainage occurred after an extended period during which rainfall exceeded evapotranspiration. This caused a wetting front to move through the soil over a period of months until it reached the lysimeter and was measured as drainage. Matrix drainage extended over a period of 1 month but at a low rate of ~0.5 mm/day.
During the cotton season, the earlier irrigations generally caused a sharp peak in drainage of up to 3.5 mm day–1 ~25 h after irrigation. However, the water content and soil-water potential at 2.1 m were largely unaffected, and in some cases, the hydraulic gradient was upwards while drainage was occurring. This suggests this drainage is caused by irrigation flowing rapidly through the profile bypassing the soil matrix. Later in the season, when soil-water deficits developed in the subsoil at 0.5–1.0 m between irrigations, the peaks in drainage rate became much smaller.
Bypass drainage appears to account for most of the drainage during the measurement period. Apart from lowering the water use efficiency, it is also more unpredictable and difficult to manage. In addition, bypass drainage is less efficient at removing salt from the soil profile, so that a higher leaching fraction may be required to prevent excessive salt accumulation.
Black root rot of cotton in Australia: the host, the pathogen and disease management
Authors: Pereg Lily L.
Published: October 2018

Black root rot is a seedling disease caused by the soil-borne fungal pathogen Thielaviopsis basicola, a species with a worldwide distribution. Diseased plants show blackening of the roots and a reduced number of lateral roots, stunted or slow growth, and delayed flowering or maturity. It was first detected in cotton in Australia in 1989, and by 2004, T. basicola reached all cotton-growing regions in New South Wales and Queensland and the disease was declared as an Australian pandemic. This review covers aspects of the disease that have implications in black root rot spread, severity and management, including the biology and ecology of T. basicola, host range and specificity, chemical and biological control of T. basicola in cotton cropping systems, and crop rotations and host resistance. This review is of special interest to Australian readers; however, the incorporation of ample information on the biology of the pathogen, its interactions with plants and it relation to disease management will benefit readers worldwide.
Variance, inter-trait correlation, heritability and trait-marker association of herbage yield, nutritive values, and morphological characteristics in Italian ryegrass (Lolium multiflorum Lam.)
Authors: Wang J. , Cogan N. O. I. , Pembleton L. W. , Forster J. W.
Published: October 2018

Italian ryegrass (Lolium multiflorum Lam.) is one of the most important temperate forage grasses on a global basis. The present study estimated trait variance, inter-trait correlation and broad-sense heritability (H2) for herbage yield, nutritive values and morphological characteristics of Italian ryegrass, and analysed associations between these traits and single nucleotide polymorphism (SNP) markers. A field-based, spaced-plant nursery experiment was conducted to assess 960 genotypes from seven cultivars and breeding lines, in a randomised complete block design with four replicates. Significant correlations, broad ranges of variation and significant genotypic variance components were identified for 18 measured phenotypic traits. Moderate H2 estimates (0.36–0.52) were obtained for nutritive values, compared with low to high H2 estimates (0.20–0.69) for yield over five cuttings, and moderate to high H2 estimates (0.40–0.78) for morphological traits. Within- and among-cultivar variation ranged from 40.0% to 95.1% and 4.9% to 60.0%, respectively, depending on different traits. Association analysis identified 65 significant SNP–trait gene associations involving multiple genomic regions, which warrant further validation. The implications of trait correlation and heritability for selection and improvement are discussed.
Corrigendum to: Atmospheric variation of nitrous acid at different sites in Europe
Authors: Acker Karin , Möller Detlev
Published: October 2018

Environmental context. Nitrous acid (HNO2) is an important source of the hydroxyl radical (OH.), the most important daytime oxidising species that contributes to the formation of ozone as well as of other secondary pollutants in the troposphere. Understanding the sources and sinks of HNO2 is of crucial interest for accurately modelling the chemical composition of the troposphere and predicting future trace gas concentrations.
Abstract. Nitrous acid and several other atmospheric components and variables were continuously measured during complex field experiments at seven different suburban and rural sites in Europe. HNO2 is mainly formed by heterogeneous processes and is often accumulated in the nighttime boundary layer. Our results confirm that the photolysis of HNO2 is an important source of the hydroxyl radical, not only in the early morning hours but also throughout the entire day, and is often comparable with the contribution of ozone and formaldehyde photolysis. At all research sites unexpectedly high HNO2 mixing ratios were observed during the daytime (up to several hundred ppt, or pmol mol-1). Moreover, surprisingly, the HNO2 mixing ratio at the three mountain sites often showed a broad maximum or several distinct peaks at midday and lower mixing ratios during the night. Assuming a quickly established photo-equilibrium between the known significant gas phase reactions, only a few ppt HNO2 should be present around noon. The ratio of known sources to sinks indicates a missing daytime HNO2 source of 160-2600 ppt h-1 to make up the balance. Based on these values and on production mechanisms proposed in the literature we hypothesise that the daytime mixing ratio levels may only be explained by a fast electron transfer onto adsorbed NO2.
A global model study of ozone enhancement during the August 2003 heat wave in Europe
Authors: Guerova G. , Jones N.
Published: October 2018

Environmental context. During the 2003 European summer, record high temperatures were measured and some regions experienced 14 consecutive days with maximum temperatures above 35°C, thus triggering a heat wave. The prolonged heat and strong insolation facilitated the build up of exceptionally long-lasting and spatially extensive episodes of high ozone concentrations close to the surface. Ozone is a very reactive pollutant with known effects on both human and vegetation health. It is important to build robust models that can predict its concentration in a similar manner to which weather prediction models operate.
Abstract. The European summer of 2003 was characterised by intense heat, prolonged isolation and suppressed ventilation of the boundary layer which, combined with large anthropogenic emissions and strong fires, resulted in a build up of an unprecedentedly high and long-lasting photochemical smog over large parts of the continent. In this work, a global chemistry and transport model GEOS-Chem is compared with surface O3 concentrations observed in 2003 in order to examine the extent to which the model is capable of reproducing such an extreme event. The GEOS-Chem reproduces the temporal variation of O3 at the Jungfraujoch mountain site, Switzerland, including the enhanced concentrations associated with the August 2003 heat wave (r = 0.84). The spatial distribution of the enhanced surface O3 over Spain, France, Germany and Italy is also captured to some extent (r = 0.63), although the largest concentrations appear to be located over the Italian Peninsula in the model rather than over Central Europe as suggested by the surface O3 observations. In general, the observed differences between the European averaged O3 concentrations in the summer of 2003 to those in 2004 are larger in the observations than in the model, as the model reproduces relatively well the enhanced levels in 2003 but overestimates those observed in 2004. Preliminary contributions of various sources to the O3 surface concentrations over Europe during the heat wave indicate that anthropogenic emissions from Europe contribute the most to the O3 build up near the surface (40 to 50%, i.e. 30 ppb). The contribution from anthropogenic emissions from the other major source regions of the northern hemisphere, in particular North America, tends to be smaller than those of other years. The model indicates that the large fires that occurred in that year contributed up to 5% (3 ppb) to surface O3 in close proximity to the fire regions and less elsewhere in Europe. Biogenic volatile organic compounds (VOCs) emitted by grass and forest areas contributed up to 10% (5–6 ppb) of surface O3 over France, Germany and northern Italy, which represents a contribution that is twice as large than that found in 2004. These results in terms of contributions from various sources, particularly biogenic emissions, should be seen as preliminary, as the response of vegetation to such extreme events may not be well represented in the model.
Efficacy of soluble sodium tripolyphosphate amendments for the in-situ immobilisation of uranium
Authors: Wellman Dawn M. , Pierce Eric M. , Valenta Michelle M.
Published: October 2018

Environmental context. Contamination of groundwater and sediments by heavy metals and radioactive metals is a significant problem within the United States Department of Energy complex as a result of past nuclear operations. One way to remediate these metals is through reaction with phosphate compounds, which can immobilise the metals by forming highly stable metal phosphate compounds. Long-chain, water-soluble phosphate compounds provide a means to inject phosphate into subsurface contaminant plumes, to precipitate metal ions from solution. Results presented here illustrate that application of a soluble sodium tripolyphosphate to sediment contaminated with uranium will rapidly reduce the concentration of uranium in the pore water to concentrations near or below drinking water limits under water-saturated and unsaturated conditions.
Abstract. A series of conventional water-saturated and pressurised unsaturated flow column experiments were conducted to evaluate the effects of using soluble polyphosphate amendments for in-situ, subsurface remediation of uranium. Experiments were conducted under mildly alkaline, calcareous conditions, representative of conditions commonly encountered at sites across the arid western United States. Results presented here illustrate that application of a soluble polyphosphate amendment to sediment contaminated with uranium will rapidly reduce the concentration of uranium released to the porewater to near or below drinking water limits under water-saturated and -unsaturated conditions. Column experiments conducted in the absence of polyphosphate illustrate sustained release of aqueous uranium at concentrations well above drinking water standards in excess of over 25 pore volumes under water-saturated conditions and over 50 pore volumes under unsaturated conditions. In the presence of tripolyphosphate, the concentration of aqueous uranium released from the sediment was below drinking water limits within 10 to 35 pore volumes under water-saturated and unsaturated conditions, respectively. Moreover, results indicate the necessity of conducting site-specific dynamic tests to tailor phosphate-based remediation technology to site specific geochemical and hydrological conditions.
Interactions of hydrophobic metal complexes and their constituents with aquatic humic substances
Authors: Boullemant Amiel , Gagné Jean-Pierre , Fortin Claude , Campbell Peter G. C.
Published: October 2018

Environmental context. Lipophilic metal complexes, because they can readily cross biological membranes, are especially bioavailable. However, in natural waters these complexes do not necessarily exist in a free state, i.e. they may bind to the organic matter (humic substances) that is present in natural waters. It follows that the in situ bioavailability of lipophilic metal complexes will tend to be less than that measured in simple laboratory experiments.
Abstract. The ability of dissolved humic substances (HS: fulvic and humic acids) to complex cationic metals is well known, but their interactions with neutral lipophilic metal complexes are little understood. In the present study, we have examined the behaviour of two such complexes (

Cd 
L
2
0

-->Cd L02: L = DDC = diethyldithiocarbamate, or L = XANT = ethylxanthate) in the presence of Suwannee River Humic and Fulvic acids. Interactions between the neutral complexes and the humic substances were assessed by excitation-emission matrix (EEM) fluorescence spectroscopy at pH 5.5 and 7.0, and by equilibrium dialysis experiments (500 Da cut-off). The EEM measurements were carried out by titrating the humic substances (6.5 mg C L–1) with Cd, in the absence or presence of ligand L (1 µM DDC or 100 µM XANT). Given the very high stability constants for the complexation of cadmium by DDC and XANT and the excess ligand concentration, virtually all (>96%) of the Cd added to the L + HS matrix was calculated to be present as the neutral

Cd
L
2
0

-->CdL20 complex over the entire pH range tested. For both humic substances, addition of DDC or XANT alone led to shifts in the fluorescence spectra at both pH values, indicating that the DDC– and XANT– anions likely interact by electrostatic or hydrogen bonding within the humic molecules. The subsequent addition of Cd to these L + HS systems resulted in a disproportionately large enhancement of the fluorescence intensities of individual EEM peaks, this fluorescence enhancement being only slightly decreased by the shift from pH 7.0 to 5.5. We interpret this enhancement as evidence that the two neutral complexes associate with the humic substances, presumably by forming ternary complexes (Ln-Cd-HS). Hydrophobic interactions between the humic substances and the neutral complexes may also contribute, but to a lesser extent, as demonstrated by partitioning calculations based on the lipophilicity of the neutral complexes. The association of the neutral complexes with Suwannee River Humic Acid was confirmed by dialysis experiments.
How and why patients use acupuncture: an interpretive phenomenological study
Authors: Jakes Dan , Kirk Ray
Published: October 2018

INTRODUCTION: The usual drivers of health care provision, namely efficacy and cost, might be expected to drive down the use of Complementary and Alternative Medicines (CAMs), given the relative paucity of evidence of efficacy for many CAMs. Usage of CAMs remains extensive and little attention has been given to explaining this paradox. This paper explores how patients integrate acupuncture, as a CAMs exemplar, within their personal schemes of health care. METHODS: An interpretive phenomenological approach underpinned the inquiry, which gathered data from in-depth interviews with 12 participants who had recently consulted acupuncturists. Thematic analysis was conducted using a constant comparison methodology. FINDINGS: Participants mostly accessed acupuncture for musculoskeletal and pain-related conditions. Usage was often initially motivated by dissatisfaction with conventional health care, perceptions that the source of the problem had not been addressed, and sometimes was due to negative experiences with medical professionals. Previous positive outcomes with acupuncture motivated more extensive use, as did personal health ideologies. Acupuncture was viewed to be appropriate for treating chronic and quality of life health issues, while treatment-associated cost was identified as a barrier to access. CONCLUSIONS: CAMs usage has been explained variously by 'push' and 'pull' factors; however, this study has shown that reasons for patient use of acupuncture may be complex and change over time. This qualitative study suggests that acupuncture fulfils specific health needs unmet in conventional health care, but also that patients view CAMs treatment as part of a broader and more pluralistic scheme of health care. KEYWORDS: Acupuncture; alternative medicine; alternative therapies; attitude to health complementary therapies
Viewpoint: Health literacy and patient portals
Authors: Gu Yulong , Orr Martin , Warren Jim
Published: October 2018

Health literacy has been described as the capacity to obtain, process, and understand basic health information and services needed to make appropriate health decisions. Improving health literacy may serve to promote concordance with therapy, engage patients in their own health care, and improve health outcomes. Patient portal technology aims at enabling patients and families to have easy access to key information in their own medical records and to communicate with their health care providers electronically. However, there is a gap in our understanding of how portals will improve patient outcome. The authors believe patient portal technology presents an opportunity to improve patient concordance with prescribed therapy, if adequate support is provided to equip patients (and family/carers) with the knowledge needed to utilise the health information available via the portals. Research is needed to understand what a health consumer will use patient portals for and how to support a user to realise the technology?s potential.
Genetic diversity and biogeography of the south polar water bear Acutuncus antarcticus (Eutardigrada : Hypsibiidae) – evidence that it is a truly pan-Antarctic species
Authors: Cesari Michele , McInnes Sandra J. , Bertolani Roberto , Rebecchi Lorena , Guidetti Roberto
Published: October 2018

Antarctica is an ice-dominated continent and all its terrestrial and freshwater habitats are fragmented, which leads to genetic divergence and, eventually, speciation. Acutuncus antarcticus is the most common Antarctic tardigrade and its cryptobiotic capabilities, small size and parthenogenetic reproduction present a high potential for dispersal and colonisation. Morphological (light and electron microscopy, karyology) and molecular (18S rRNA and cytochrome c oxidase subunit I (COI) genes) analyses on seven populations of A. antarcticus elucidated the genetic diversity and distribution of this species. All analysed populations were morphologically indistinguishable and made up of diploid females. All specimens presented the same 18S rRNA sequence. In contrast, COI analysis showed higher variability, with most Victoria Land populations presenting up to five different haplotypes. Genetic distances between Victoria Land specimens and those found elsewhere in Antarctica were low, while distances between Dronning Maud Land and specimens from elsewhere were high. Our analyses show that A. antarcticus can still be considered a pan-Antarctic species, although the moderately high genetic diversity within Victoria Land indicates the potential for speciation events. Regions of Victoria Land are considered to have been possible refugia during the last glacial maximum and a current biodiversity hotspot, which the populations of A. antarcticus mirror with a higher diversity than in other regions of Antarctica.
Molecular phylogeny informs generic and subgeneric concepts in the Schizoptera Fieber genus group (Heteroptera : Schizopteridae) and reveals multiple origins of female-specific elytra
Authors: Leon S. , Weirauch C.
Published: October 2018

Wing dimorphism occurs in many genera of Schizopteridae Reuter, 1891 and other litter bugs (Heteroptera:Dipsocoromorpha), in both males and females. In the largest litter bug genus, Schizoptera Fieber, and closely related taxa, sexual wing dimorphism is observed in several species whereby males are macropterous, but females possess elytra, or hardened forewings – a feature that is rare outside of beetles and that we here refer to as female-specific elytra. Phylogenetic hypotheses for Schizoptera are unavailable, but are essential to reveal if female-specific elytra evolved once or multiple times within the genus and to test if the presence of elytra can reverse states to macropterous wings. In addition, generic and subgeneric concepts of this speciose genus-group have not been tested in a phylogenetic framework, and relationships with other schizopterid genera remain largely unknown. Our molecular phylogeny of Schizoptera and related genera documents that this genus is currently polyphyletic, and we raise the subgenus Kophaegis to generic rank to render Schizoptera monophyletic (Orthorhagus was recently elevated to genus). Relationships within Schizoptera reveal several well supported clades, some of them corresponding to currently recognised subgenera. To examine the value of previously used diagnostic features, we optimise 11 morphological characters on the molecular phylogeny and update generic and subgeneric diagnoses. Tracing transitions between macropterous and elytrous wing types, we show that female-specific elytra evolved at least seven times within Schizopteridae, four of those times within the Schizoptera genus-group, and that elytra reversed to macropterous wings at least twice. We propose that Schizopteridae may be an excellent model to study the selective pressures that have given rise to sexually dimorphic traits.
Unexpected diversity in the relictual European spiders of the genus Pimoa (Araneae : Pimoidae)
Authors: Mammola Stefano , Hormiga Gustavo , Arnedo Miquel A. , Isaia Marco
Published: October 2018

Pimoidae is a small family of araneoid spiders, hitherto represented in Europe by two species with disjunct distribution in the Alps and in the Cantabrian Mountains of northern Spain. Here we report the description of two additional European species of Pimoa, discovered within the range of the only former alpine species, P. rupicola: P. graphitica sp. nov. and P. delphinica sp. nov. The new species are distinguished from the latter by genitalic characters as well as by molecular characters. On the basis of the re-examination of old and recent abundant material collected in caves and other subterranean habitats, we revise the distribution patterns of the genus Pimoa in the Alps and outline the species distribution ranges. Molecular data suggest the existence of gene flow between populations of the two new species when in sympatry. The different species probably originated in the alpine region as a result of range contractions following dramatic climatic changes in the Alps since the mid Miocene. We interpreted the present-day overlapping distribution in light of a possible postglacial expansion. Finally, we provide insights on the natural history and life cycles of the new species and discuss their phylogenetic relationships within Pimoidae.
A review of the status of Coptotermes (Isoptera : Rhinotermitidae) species in Australia with the description of two new small termite species from northern and eastern Australia
Authors: Lee Timothy R. C. , Evans Theodore A. , Cameron Stephen L. , Ho Simon Y. W. , Namyatova Anna A. , Lo Nathan
Published: October 2018

Integrative taxonomy, including molecular, morphological, distributional and biological data, is applied in a review of the taxonomy of the Australian species of the pest termite genus Coptotermes. The validity of the previously described species is discussed, and two new species, Coptotermes nanus, sp. nov. and Coptotermes cooloola, sp. nov., are described from the Kimberley region of Western Australia and south-east Queensland respectively. Their delimitation is based on morphological and distributional data, and the results of generalised mixed Yule-coalescent analysis of mitochondrial DNA sequence data. Images of the external view of the two new species are provided, as well as a key, based on soldier characters, for all Australian species of Coptotermes.
When molecules and morphology work together: lines of evidence for the validity of Caridina buehleri Roux (Crustacea : Decapoda : Atyidae) and for C. gueryi Marquet, Keith & Kalfatak as its junior synonym
Authors: de Mazancourt Valentin , Marquet Gerard , Klotz Werner , Keith Philippe , Castelin Magalie
Published: October 2018

The taxonomy of the freshwater shrimps Caridina (Atyidae) is very complex and confused mostly because the morphological characters that have traditionally been used for species delimitation and identification are highly plastic. There is thus a need for an integrative approach to their taxonomy. In total, 42 specimens belonging to either Caridina buehleri Roux, 1934 or Caridina gueryi Marquet, Keith & Kalfatak, 2009 were examined. We combined here morphological data from 12 specimens from the whole distributional range of the species, including type specimens with 16S mtDNA analyses from seven freshly sampled specimens, to verify the specific status of Caridina buehleri from Papua New-Guinea, Central Sulawesi, Western Samoa and the Solomon Islands, and C. gueryi from Vanuatu. The comparison of 24 morphological characters showed that morphological variations of character traits between C. gueryi and C. buehleri are widely overlapping and that no morphological feature can effectively split specimens into two clear groups. Molecular characters corroborated these results, as specimens from both groups were only separated by a 2% p-distance, a genetic distance that is coherent with their potentially high dispersal abilities. We thus consider C. gueryi as a junior synonym of C. buehleri. Finally, C. buehleri is characterised mainly by a styliform and characteristically indented rostrum and a long stylocerite. Detailed re-descriptions of the type specimens of C. buehleri and C. gueryi are given, as well as their geographical and ecological distribution.
Morphological and molecular characterisation of a new genus and new species of Parabathynellidae (Crustacea : Syncarida) in Queensland, Australia
Authors: Little J. , Camacho A. I.
Published: October 2018

A new genus and species in the family Parabathynellidae Noodt, 1965, Lockyerenella danschmidti, gen. et sp. nov., is described from Queensland, Australia. The species displays several distinctive character states within the Parabathynellidae, and a unique combination of character states. Interestingly, L. danschmidti is the only known species of Parabathynellidae in Australia (and in the world) to possess a long and robust seta on the last segment of the antenna, which is present in both males and females. The new genus is morphologically distinct from the known genera, but is more similar to Queensland species of Notobathynella Schminke, 1973 and Arkaroolabathynella Abrams & King, 2013 from South Australia, than to species from other areas of the continent. This is the first work to couple genetics to the morphological description of a stygofauna species in Queensland. Phylogenetic relationships between L. danschmidti and related genera from elsewhere on the continent were evaluated through the analysis of combined mitochondrial and nuclear DNA sequence data. This analysis revealed at least one new genus within the Parabathynellidae, confirming our morphological hypothesis.
Extracellularly oxidative activation and inactivation of matured prodrug for cryptic self-resistance in naphthyridinomycin biosynthesis
Authors: Zhang Yue , Wen Wan-Hong , Pu Jin-Yue , Tang Man-Cheng , Zhang Liwen , Peng Chao , Xu Yuquan , Tang Gong-Li
Published: October 2018

Significance

The shielding strategy for self-resistance in antibiotic biosynthesis from bacteria has been known to employ reversible group-transfer reactions that usually do not directly act on the antibiotic pharmacophore. Typically, the phosphorylation-modified, glycosylation-modified, acetylation-modified, and prepeptide-modified prodrug need to be activated by removing the protection group during or following export and, thereby, employing the hydrolysis reaction as the final step. Herein, we discover an unprecedented oxidative activation and overoxidative inactivation of a matured prodrug; significantly, the oxidation reaction directly deals with the drug warhead and occurs outside the host cells. This cryptic self-resistance mechanism sheds light on antibiotic resistance and the complex biology of extracellular environment.
Flow stimuli reveal ecologically appropriate responses in mouse visual cortex
Authors: Dyballa Luciano , Hoseini Mahmood S. , Dadarlat Maria C. , Zucker Steven W. , Stryker Michael P.
Published: October 2018

Significance

The visual system of the mouse is now widely studied as a model for development and disease in humans. Studies of its primary visual cortex (V1) using conventional grating stimuli to construct linear–nonlinear receptive fields suggest that the mouse must have very poor vision. Using stimuli resembling the flow of images across the retina as the mouse moves through the grass, we find that most V1 neurons respond reliably to very much finer details of the visual scene than previously believed. Our findings suggest that the conventional notion of a unique receptive field does not capture the operation of the neural network in mouse V1.
Volume Ratio of Glomerular Tufts to Bowman Capsules and Renal Outcomes in Nephrosclerosis
Authors: Haruhara Kotaro , Tsuboi Nobuo , Sasaki Takaya , Amano Hoichi , Tanaka Mai , Koike Kentaro , Kanzaki Go , Okabayashi Yusuke , Miyazaki Yoichi , Ogura Makoto , Yokoo Takashi
Published: October 2018

BACKGROUND

The concomitant appearance of glomerular collapse and enlargement is characteristic of the histological findings in nephrosclerosis. However, no previous study quantitatively examined the clinicopathological significance of this feature in patients with biopsy-proven nephrosclerosis.

METHODS

Renal biopsy specimens and follow-up data from nephrosclerosis patients with estimated glomerular filtration rates >30 ml/min/1.73 m2 at diagnosis were retrospectively reviewed. Mean volumes for glomerular tufts (GV) and Bowman capsules (BV) were separately calculated, based on the measurement of all areas of glomerular tufts and Bowman capsules in a cross-section of biopsy specimens. The G/B ratio was defined as the ratio of GV to BV. The doubling of serum creatinine levels (DSC) and the initiation of renal replacement therapies (end-stage renal disease (ESRD)) were examined as renal outcome indices.

RESULTS

A total of 67 patients with biopsy-proven nephrosclerosis were included. Clinicopathological findings at biopsy, other than GV, were comparable among all patients, irrespective of G/B ratio. Overall, 25 patients (37%) developed DSC and 9 (13%) developed ESRD during the median observation periods of 7.8 and 8.5 years, respectively. Renal survival curve analyses indicated a significantly worse prognosis for patients with a low G/B ratio, as compared with those with a high G/B ratio. Cox hazard analyses for DSC identified low G/B ratio as a significant predictor, but not low GV or BV.

CONCLUSIONS

These results suggest that the quantitative evaluation of G/B ratio may detect subtle abnormalities in the glomerulus, indicating the subsequent renal outcomes of nephrosclerosis patients.
Thalia: semantic search engine for biomedical abstracts
Authors: Soto Axel J , Przybyła Piotr , Ananiadou Sophia
Published: October 2018

Although the publication rate of the biomedical literature has been growing steadily during the last decades, the accessibility of pertinent research publications for biologist and medical practitioners remains a challenge. This article describes Thalia, which is a semantic search engine that can recognize eight different types of concepts occurring in biomedical abstracts. Thalia is available via a web-based interface or a RESTful API. A key aspect of our search engine is that it is updated from PubMed on a daily basis. We describe here the main building blocks of our tool as well as an evaluation of the retrieval capabilities of Thalia in the context of a precision medicine dataset.

Availability and implementation

Thalia is available at http://nactem.ac.uk/Thalia_BI/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Diarrheal Etiology and Impact of Coinfections on Rotavirus Vaccine Efficacy Estimates in a Clinical Trial of a Monovalent Human–Bovine (116E) Oral Rotavirus Vaccine, Rotavac, India
Authors: Praharaj Ira , Platts-Mills James A , Taneja Sunita , Antony Kalpana , Yuhas Krista , Flores Jorge , Cho Iksung , Bhandari Nita , Revathy R , Bavdekar Ashish , Rongsen-Chandola Temsunaro , McMurry Timothy , Houpt Eric R , Kang Gagandeep
Published: October 2018

Background

Rotavirus vaccine efficacy (VE) estimates in low-resource settings are lower than in developed countries. We detected coinfections in cases of severe rotavirus diarrhea in a rotavirus VE trial to determine whether these negatively impacted rotavirus VE estimates.

Methods

We performed TaqMan Array Card assays for enteropathogens on stools from rotavirus enzyme immunoassay–positive diarrhea episodes and all severe episodes (Vesikari score ≥11), from a phase 3 VE trial of Rotavac, a monovalent human–bovine (116E) rotavirus vaccine, carried out across 3 sites in India. We estimated pathogen-specific etiologies of diarrhea, described associated clinical characteristics, and estimated the impact of coinfections on rotavirus VE using a test-negative design.

Results

A total of 1507 specimens from 1169 infants were tested for the presence of coinfections. Rotavirus was the leading cause of severe diarrhea even among vaccinated children, followed by adenovirus 40/41, Shigella/enteroinvasive Escherichia coli, norovirus GII, sapovirus, and Cryptosporidium species. Bacterial coinfections in rotavirus-positive diarrhea were associated with a longer duration of diarrhea and protozoal coinfections with increased odds of hospitalization. Using the test-negative design, rotavirus VE against severe rotavirus gastroenteritis increased from 49.3% to 60.6% in the absence of coinfections (difference, 11.3%; 95% confidence interval, –10.3% to 30.2%).

Conclusions

While rotavirus was the dominant etiology of severe diarrhea even in vaccinated children, a broad range of other etiologies was identified. Accounting for coinfections led to an 11.3% increase in the VE estimate. Although not statistically significant, an 11.3% decrease in VE due to presence of coinfections would explain an important fraction of the low rotavirus VE in this setting.
Transcriptional activation of fucosyltransferase (FUT) genes using the CRISPR-dCas9-VPR technology reveals potent N-glycome alterations in colorectal cancer cells
Authors: Blanas Athanasios , Cornelissen Lenneke A M , Kotsias Maximilianos , van der Horst Joost C , van de Vrugt Henri J , Kalay Hakan , Spencer Daniel I R , Kozak Rad P , van Vliet Sandra J
Published: October 2018

Aberrant fucosylation in cancer cells is considered as a signature of malignant cell transformation and it is associated with tumor progression, metastasis and resistance to chemotherapy. Specifically, in colorectal cancer cells, increased levels of the fucosylated Lewisx antigen are attributed to the deregulated expression of pertinent fucosyltransferases, like fucosyltransferase 4 (FUT4) and fucosyltransferase 9 (FUT9). However, the lack of experimental models closely mimicking cancer-specific regulation of fucosyltransferase gene expression has, so far, limited our knowledge regarding the substrate specificity of these enzymes and the impact of Lewisx synthesis on the glycome of colorectal cancer cells. Therefore, we sought to transcriptionally activate the Fut4 and Fut9 genes in the well-known murine colorectal cancer cell line, MC38, which lacks expression of the FUT4 and FUT9 enzymes. For this purpose, we utilized a physiologically relevant, guide RNA-based model of de novo gene expression, namely the CRISPR-dCas9-VPR system. Induction of the Fut4 and Fut9 genes in MC38 cells using CRISPR-dCas9-VPR resulted in specific neo-expression of functional Lewisx antigen on the cell surface. Interestingly, Lewisx was mainly carried by N-linked glycans in both MC38-FUT4 and MC38-FUT9 cells, despite pronounced differences in the biosynthetic properties and the expression stability of the induced enzymes. Moreover, Lewisx expression was found to influence core-fucosylation, sialylation, antennarity and the subtypes of N-glycans in the MC38-glycovariants. In conclusion, exploiting the CRISPR-dCas9-VPR system to augment glycosyltransferase expression is a promising method of transcriptional gene activation with broad application possibilities in glycobiology and oncology research.
Prescribed k-Curvature Problems on Complete Noncompact Riemannian Manifolds
Authors: Fu Jixiang , Sheng Weimin , Yuan Lixia
Published: October 2018

To study the prescribed $k$-curvature problem of 2nd-order symmetric curvature tensors on complete noncompact Riemannian manifolds, we consider a class of fully nonlinear elliptic partial differential equations. It is proved that on a Riemannian manifold with negative sectional curvature and Ricci curvature bounded from below, the equation is solvable provided that all the eigenvalues of the tensor are negative. The result is applicable to the prescribed $k$-curvature problems of modified Schouten tensor and Bakry–Émery Ricci tensor.