bluuebunny/crossref_metadata_2025 huggingface dataset:
Lexical and morphosyntactic minimal pairs: Evidence for different processing and implications in language pathology treatment
Authors: Cilibrasi Luca , Stojanovik Vesna , Riddell Patricia M
Published: January 2018

Minimal pairs are defined as pair of words in a particular language which differ in only one phonological element and have a different meaning (Roach, 2000). Several authors argued their relevance in the treatment of phonological disorders (for instance, Barlow and Gierut, 2002). In this study we investigate the nature of minimal pairs showing that a subtype of them entails a peculiar form of processing. In many languages bound morphemes used to mark inflection generate minimal pairs. In English, the present third person singular morpheme -s and the past tense morpheme -ed generate in most cases minimal pairs, such as “asks / asked”. Several authors (Stemberger and MacWhinney, 1986, Bertram et al, 2000) have argued that inflected forms may be stored in the lexicon as units, i.e. together with the bound morpheme. If inflected forms are stored as units in the lexicon, discriminating lexical minimal pairs and morphosyntactic minimal pairs should not be different processes. Elements should be stored similarly in the lexicon, and then compared phonologically when the subject is presented with a minimal pair. In this study we addressed this question presenting 20 monolingual native speakers of English with lexical and morphosyntactic minimal pairs (30 per condition, frequency differences not significant), and with pairs of identical words (leading, thus, to 120 trials). Participants were asked to press “white” if words were different and “black” if words were identical. Conditions were matched on word length. Results show that subjects are significantly faster in discriminating words generating a lexical minimal pair, such as “back / badge” than words generating a morphosyntactic minimal pair, such as “asks / asked”, t (19) = -4.486, p < .001. A third condition was also present to deepen our understanding of the processing of morphosyntactic minimal pairs. In this condition subjects were presented with morphosyntactic minimal pairs generated by very infrequent verbs. Unexpectedly, minimal pairs generated by infrequent verbs revealed to be faster recognised (19) = 2.120, p < .05 than the other morphosyntactic minimal pairs. Even if this may be interpreted as a consequence of attention arousal for unexpected stimuli, the result is problematic if we assume inflected forms to be stored in the lexicon as units. Together, these results suggest that inflected forms are not stored as units and that the discrimination of morphosyntactic minimal pairs relies on the discrimination of inflectional morphemes. As such, we suggest that increasing the sensibility to morphosyntactic minimal pairs in people with a morphosyntactic disorder, such as children with Specific Language Impairment (SLI), should improve their language performance.
CATALISE: a multinational and multidisciplinary Delphi consensus study. Identifying language impairments in children
Authors: Bishop Dorothy V , Snowling Margaret J , Thompson Paul A , Greenhalgh Trisha ,   CATALISE consortium
Published: January 2018

Delayed or impaired language development is a common developmental concern, yet there is little agreement about the criteria used to identify and classify language impairments in children. Children's language difficulties are at the interface between education, medicine and the allied professions, who may all adopt different approaches to conceptualising them. Our goal in this study was to use an online Delphi technique to see whether it was possible to achieve consensus among professionals on appropriate criteria for identifying children who might benefit from specialist services. We recruited a panel of 59 experts representing ten disciplines (including education, psychology, speech-language therapy/pathology, paediatrics and child psychiatry) from English-speaking countries (Australia, Canada, Ireland, New Zealand, United Kingdom and USA). The starting point for round 1 was a set of 46 statements based on articles and commentaries in a special issue of a journal focusing on this topic. Panel members rated each statement for both relevance and validity on a seven-point scale, and added free text comments. These responses were synthesised by the first two authors, who then removed, combined or modified items with a view to improving consensus. The resulting set of statements was returned to the panel for a second evaluation (round 2). Consensus (percentage reporting 'agree' or 'strongly agree') was at least 80 per cent for 24 of 27 round 2 statements, though many respondents qualified their response with written comments. These were again synthesised by the first two authors. The resulting consensus statement is reported here, with additional summary of relevant evidence, and a concluding commentary on residual disagreements and gaps in the evidence base.
Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?
Authors: Silva Pedro J
Published: January 2018

1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability in a biological context requires it to be able to resist modification by xenobiotic-degrading enzymes like the P450 cytochromes. Quantum chemical computations described in this work show that 1,2-dihydro-1,2-azaborine is much more prone to modification by these enzymes than benzene, unless steric crowding of the ring prevents it from reaching the active site, or otherwise only allows reaction at the very sluggish C4-position. This novel heterocyclic compound is therefore expected to be of limited usefulness as an aryl bioisostere.
Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria
Authors: Davis II Edward W , Weisberg Alexandra J , Tabima Javier F , Grunwald Niklaus J. , Chang Jeff
Published: January 2018

Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, are important for disease management. Developments in molecular methods have contributed to increasing the resolution for accurate pathogen identification but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.
The Urban Wildlife Institute: Exploring Chicago's wildlife
Authors: Magle Seth
Published: January 2018

The Lincoln Park Zoo founded the Urban Wildlife Institute (UWI) in 2008, with the goal of conducting science to minimize conflict between humans and wildlife in cities around the world. UWI has since created a massive and unprecedented urban wildlife biodiversity monitoring network throughout the Chicagoland region. We will briefly summarize some of our findings on Chicago’s mammal, bat, arthropod, and bird populations, with special emphasis on our database of over 200,000 images of urban wildlife captured using motion-triggered cameras. Our research has not only uncovered new information about how urban animals select habitat and persist within urban landscapes, but has also helped connect the people of Chicago to the natural world through educational outreach and citizen science initiatives such as Partners in Fieldwork, and Chicago Wildlife Watch. UWI is working to ensure humans and wildlife can coexist in cities around the world, and also to remind growing urban populations that urban areas are ecosystems that are just as capable of inspiring wonder as the wildest jungles.
Microbe-ID: An open source toolbox for microbial genotyping and species identification
Authors: Tabima Javier F , Everhart Sydney E , Larsen Meredith M , Weisberg Alexandra J , Kamvar Zhian N , Tancos Matthew A , Smart Christine D , Chang Jeff H , Grünwald Niklaus J
Published: January 2018

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID ( www.microbe-id.org ) and provided a working implementation for the genus Phytophthora ( www.phytophthora-id.org ). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.
OSoMe: The IUNI observatory on social media
Authors: Davis Clayton A , Ciampaglia Giovanni Luca , Aiello Luca Maria , Chung Keychul , Conover Michael D , Ferrara Emilio , Flammini Alessandro , Fox Geoffrey C , Gao Xiaoming , Gonçalves Bruno , Grabowicz Przemyslaw A , Hong Kibeom , Hui Pik-Mai , McCaulay Scott , McKelvey Karissa , Meiss Mark R , Patil Snehal , Peli Kankanamalage Chathuri , Pentchev Valentin , Qiu Judy , Ratkiewicz Jacob , Rudnick Alex , Serrette Benjamin , Shiralkar Prashant , Varol Onur , Weng Lilian , Wu Tak-Lon , Younge Andrew J , Menczer Filippo
Published: January 2018

The study of social phenomena is becoming increasingly reliant on big data from online social networks. Broad access to social media data, however, requires software development skills that not all researchers possess. Here we present the IUNI Observatory on Social Media, an open analytics platform designed to facilitate computational social science. The system leverages a historical, ongoing collection of over 70 billion public messages from Twitter. We illustrate a number of interactive open-source tools to retrieve, visualize, and analyze derived data from this collection. The Observatory, now available at osome.iuni.iu.edu, is the result of a large, six-year collaborative effort coordinated by the Indiana University Network Science Institute.
Comparison of the performance of native and invasive plants of Senecio vulgairs L.
Authors: Cheng Dandan , Nguyen Viet - Thang , Ndihokubwayo Noel
Published: January 2018

According to the Evolution of Increased Competitive Ability (EICA) hypothesis and Enemy Release Hypothesis (ERH), comparing the plants from the same species, individuals from the invasive range will outperform those from the native range. However, not all recent studies support the prediction of these two hypotheses. In this study, we sought to test the prediction by comparing the performance of common groundsel ( Senecio vulgaris ) taken from native (Europe) and invasive (China) ranges. Those plants were grown in a greenhouse and in a common garden, and harvested with various vegetative and reproductive traits measured. We found that although the plants grown in the common garden grew and reproduced better than those grown in the greenhouse, the invasive plants outperformed the native plants in relation to most vegetation parameters (except plant height) and reproduction in both experiments; and generally, the invasive plants allocated more proportion of biomass to root than the native plants. However, the proportion of biomass allocated to reproductive organ and relative dry matter content were the same between the native and invasive plants, no matter among the plants grown in the greenhouse or in the common garden. Our study partially supported the predictions of the EICA and ERH and indicated that evolution might have happened to S. vulgaris invasive to China.
Schistosome tegumental ecto-apyrase (SmATPDase1) degrades exogenous pro-inflammatory and pro-thrombotic nucleotides.
Authors: Da'dara Akram A , Bhardwaj Rita , Ali Yasser MB , Skelly Patrick
Published: January 2018

Schistosomes are parasitic worms that can survive in the hostile environment of the human bloodstream where they appear refractory to both immune elimination and thrombus formation. We hypothesize that parasite migration in the bloodstream can stress the vascular endothelium causing this tissue to release chemicals alerting responsive host cells to the stress. Such chemicals are called damage associated molecular patterns (DAMPs) and among the most potent is the proinflammatory mediator, adenosine triphosphate (ATP). Furthermore, the ATP derivative ADP is a pro-thrombotic molecule that acts as a strong activator of platelets. Schistosomes are reported to possess at their host interactive tegumental surface a series of enzymes that could, like their homologs in mammals, degrade extracellular ATP and ADP. These are alkaline phosphatase (SmAP), phosphodiesterase (SmNPP-5) and ATP diphosphohydrolase (SmATPDase1). In this work we employ RNAi to knock down expression of the genes encoding these enzymes in the intravascular life stages of the parasite. We then compare the abilities of these parasites to degrade exogenously added ATP and ADP. . We find that only SmATPDase1-suppressed parasites are significantly impaired in their ability to degrade these nucleotides. Suppression of SmAP or SmNPP-5 does not appreciably affect the worms’ ability to catabolize ATP or ADP. These findings are confirmed by the functional characterization of the enzymatically active, full-length recombinant SmATPDase1 expressed in CHO-S cells. The enzyme is a true apyrase; SmATPDase1 degrades ATP and ADP in a cation dependent manner. Optimal activity is seen at alkaline pH. The Km of SmATPDase1 for ATP is 0.4 ±0.02 mM and for ADP, 0.252 ± 0.02 mM. The results confirm the role of tegumental SmATPDase1 in the degradation of the exogenous pro-inflammatory and pro-thrombotic nucleotides ATP and ADP by live intravascular stages of the parasite. By degrading host inflammatory signals like ATP, and pro-thrombotic signals like ADP, these parasite enzymes may minimize host immune responses, inhibit blood coagulation and promote schistosome survival.)
How molecular tools can help understanding species interactions to improve restoration outcomes
Authors: Boyer Stéphane , Waterhouse Benjamin R , Wratten Steve D
Published: January 2018

Preserving species interactions should be a key desired outcome in restoration ecology. With progress in environmental DNA techniques and the dramatic reduction in the cost of high-throughput DNA sequencing, large amounts of information can be gathered on how species interact with little to no disturbance to ecosystems. Here, we argue that the use of molecular tools to study ecological interactions will become increasingly important in restoration projects. We describe specific examples where recent advances in genetics allow for a better understanding of predator-prey, animal-plant, plant-microbe and trophic cascade interactions, which can inform restoration practice and substantially improve our capacity to restore functioning ecosystems.
A simple rat model of mild traumatic brain injury: device to reproduce anatomical and neurological changes of mild traumatic brain injury
Authors: Kim Ho Jeong , Han Soo Jeong
Published: January 2018

Mild traumatic brain injury typically involves temporary impairment of neurological function. Previous studies used the water pressure or rotational injury for designing the device to make a rat mild traumatic brain injury model. The objective of this study was to make a simple model of mild traumatic brain injury in rat. The device consisted of a free-fall impactor that was targeted onto the rat skull. The weight (175g) was freely dropped 30cm to rat’s skull bregma. We installed a safety device made of acrylic panel. To confirm a mild traumatic brain injury in 36 Sprague–Dawley rats, we performed the brain magnetic resonance image(MRI) within 24 hours after injury. We evaluated behavior and chemical changes in rats before and after mild traumatic brain injury. The brain MRI did not show high or low signal intensity in 34 rats. The mobility on grid floor was decreased after mild traumatic brain injury. Absolute number of foot-fault and foot-fault ratio were decreased after mild traumatic brain. But the difference of ratio was lesser than absolute number of foot-fault. These results show that the device is capable of reproducing mild traumatic brain injury in rat. Our device can reduce the potential to cause brain hemorrhage and reflect the mechanism of real mild traumatic brain injury compared with existing methods and behaviors. This model can be useful in exploring physiology and management of mild traumatic brain injury.
The relationship between information carrying words, memory and language skills in school age children with language impairment
Authors: Frizelle Pauline , Harte Jennifer , O'Sullivan Kathleen , Fletcher Paul , Gibbon Fiona E.
Published: January 2018

The receptive language measure information-carrying word (ICW) level is used extensively by speech and language therapists (SLTs) in the UK and Ireland. Despite this it has never been validated via its relationship to any other relevant measures. This study aims to validate the ICW measure by investigating the relationship between the receptive ICW score of children with language impairment (LI) and their performance on standardized memory and language assessments. Twenty-seven children with LI, aged between 5;07 and 8;11, completed a sentence comprehension task in which the instructions gradually increased in number of ICWs. The children also completed subtests from The Working Memory Test Battery for children and The Clinical Evaluation of Language Fundamentals – 4. Results showed that there was a significant positive relationship between both language and memory measures and children’s ICW score but that language was the greater contributor in children’s ability to do this task. ICW score is in fact a valid measure of the language ability of children with LI. However therapists should also be cognisant of its strong association with working memory when using this construct in assessment or intervention methods.
Antioxidant nutrition in Atlantic salmon (Salmo salar) parr and post-smolt, fed diets with high inclusion of plant ingredients and graded levels of micronutrients and selected amino acids
Authors: Hamre Kristin , Sissener Nini H. , Lock Erik-Jan , Olsvik Pål A , Espe Marit , Torstensen Bente E , Silva Joana , Johansen Johan , Waagbø Rune , Hemre Gro-Ingunn ghe
Published: January 2018

The shift from marine to plant based ingredients in fish feeds affects the dietary concentrations and bioavailability of micronutrients, amino acids and lipids and consequently warrants a re-evaluation of dietary nutrient recommendations. In the present study, an Atlantic salmon diet high in plant ingredients was supplemented with graded levels of nutrient premix (NP), containing selected amino acids, taurine, cholesterol, vitamins and minerals. This article presents the results on the antioxidant nutrients vitamin C, E and selenium (Se), and effects on tissue redox status. The feed ingredients appeared to contain sufficient levels of vitamin E and Se to cover the requirements to prevent clinical deficiency symptoms. The body levels of α-tocopherol (TOH) in parr and that of Se in parr and post-smolt showed a linear relationship with dietary concentration, while α-TOH in post-smolt seemed to be saturable with a breakpoint near 140 mg kg-1. Ascorbic acid (Asc) concentration in the basal feed was below the expected minimum requirement, but the experimental period was probably too short for the fish to develop visible deficiency symptoms. Asc was saturable in both parr and post-smolt whole body at dietary concentrations of 190 and 63-89 mg kg-1, respectively. Maximum whole body Asc concentration was approximately 40 mg kg-1 in parr and 14 mg kg-1 in post-smolt. Retention ranged from 41 to 10% in parr and from -206 to 12% in post-smolt with increasing NP supplementation. This indicates that the post-smolts had an extraordinarily high consumption of Asc. Analyses of glutathione (GSH) and glutathione disulphide (GSSG) concentrations and the calculated GSH based redox potentials in liver and muscle tissue, indicated only minor effects of diets on redox regulation. However, the post-smolt were more oxidized than the parr. This was supported by the high consumption of Asc and high expression of gpx1 and gpx3 in liver. Based on the present trials, the recommendations for supplementation of vitamin C and E in diets for Atlantic salmon are similar to current practices, e.g 150-200 mg kg-1 of α-TOH and 190 mg kg-1 Asc which was the saturating concentration in parr. Higher concentrations than what would prevent clinical deficiency symptoms are necessary to protect fish against incidents of oxidative stress and to improve immune and stress responses. There were no indications that the Se requirement exceeded the current recommendation of 0.3 mg kg-1.
Molecular docking of Sulfobacillus acidophilus barbiturase with s-triazine compounds
Authors: Basharat Zarrin , Yasmin Azra
Published: January 2018

Barbiturases have scarce structural information available and do not fit in the conventional group of proteins. It is contemplated that they play a role in catabolism of s-triazine herbicide compounds. Structure as well as interaction data information of barbiturase with s-triazine compounds is missing. Sequence data is a goldmine of biological information and acts as raw material for structure and docking analysis. De novo structure prediction of the Sulfobacillus acidophilus DSM 10332 barbiturase has been attempted in this data article. Molecular docking analysis was carried out with atrazine, simazine and hexazinone belonging to s-triazine class of herbicides. The analysis revealed key residues necessary for these interactions. The generated data could be used by environmental scientists working on the enzyme assisted herbicide degradation.
Hypothesis generating model-based wearable clinical trial
Authors: Kirkup Benjamin C
Published: January 2018

Wearable physiological sensors have the projected capability to detect unknown and unreported health conditions. Development requires rounds of discovery-oriented human subject research and confirmatory clinical trials. However, each study is a significant investment and difficult to justify in isolation. This impasse requires bootstrapping spiral device development through hypothesis-generating, model-based clinical trials. An unconventional clinical trial design addresses environmental health and infectious disease, through the day-to-day observation of diverse people who occupy a shared environment. The design utilizes a flexible suite of developmental diagnostic devices to detect the physiological impact of exposures. Through advanced data analysis, the devices provide information about deviations from normal parameters for each human subject. The correlation of these anomalies across the entire cohort generates hypotheses about exposures that impact health. These hypotheses can be investigated further in targeted studies and lead to simultaneous refinement of the devices.
Intrabasin Floral Differences in the Sonoran Desert; a case study from the Casa Grande Valley
Authors: Garcia Gabriela , Gabriele Sarah , Cowgill Benjamin , Rodriguez Xavier , Gay Robert J
Published: January 2018

Background: The purpose of this study was to determine what floral differences exist in North Mountain Park and Casa Grande Mountain Park which are both located on opposite sides of the Casa Grande Valley, Pinal County, Arizona and to attempt to explain any measured differences. Previous authors have proposed several explanations for floral variation within the Sonoran Desert including elevation, soil pH, and mineral content. This study explicitly tests several of these proposed mechanisms for determining community composition. Methods: The floral composition was measured in both North Mountain Park and Casa Grande Mountain Park through a series of transects which were sampled by multiple times in 2012 and 2013. Elevation data soil pH were also sampled. Results: The data recovered from North Mountain Park differed from the expected values in Casa Grande Mountain Park by 22%. This indicates a significant difference in the flora between these two localities that was not predicted by earlier studies. Elevation and soil pH differences between sampled localities were not significant. This suggests that mineral composition of the soil may play an important role within this basin in determining community composition. Discussion: Many factors that have been proposed in prior studies do not appear to play a significant role within the Casa Grande Valley in determining community composition. This indicates that the composition of a community is influenced by different factors in different locations within the Sonoran Desert. This makes determining overall controlling factors across an ecosystem difficult.
Effects of CO2 laser irradiation on matrix-rich biofilm development formation – An in vitro study
Authors: Zancope Bruna Raquel , Dainezi Vanessa B , Nobre-dos-Santos Marinês , Duarte, Jr Sillas , Pardi Vanessa , Murata Ramiro M
Published: January 2018

Background. CO2 laser has been used to morphologically and chemically modify the dental enamel surface as well as to turn it more resistant to demineralization. Despite a variety of experiments demonstrating the inhibitory effect of CO2 laser in reduce enamel demineralization, little is known about the effect of surface irradiated on bacterial growth. Thus, this in vitro study was preformed to evaluate the biofilm formation on enamel previously irradiated with a CO2 laser (λ = 10.6 µM). Methods. For this in vitro study, it was employed 96 specimens of bovine enamel, which were divided into 2 groups (n = 48): 1) Control-non-irradiated surface and 2) Irradiated enamel surface. Biofilms were grown on the enamel specimens by 1, 3 and 5 days under intermittent cariogenic condition in the irradiated and non irradiated surface. In each assessment time, the biofilm were evaluated by dry weigh, counting the number of viable colonies and in fifth day, were evaluated by polysaccharides analysis, quantitative real time PCR as well as by contact angle. In addition, the morphology of biofilms was characterized by fluorescence microscopy and field emission scanning electron microscopy (FESEM). Initially, the assumptions of equal variances and normal distribution of errors were conferred and the results are analyzed statistically by t-test and Mann Whitney test. Results. The mean of log CFU/ml obtained for the 1-day biofilm evaluation showed that there is statistical difference between the experimental groups. When biofilms were exposed to CO2 laser, CFU/mL and CFU/ Dry Weight in 3 day was reduced significantly compared with control group. The difference in the genes expression (gtfB and gbpB) and polysaccharides was not statically significant. Contact angle was increased relative to control when the surface was irradiated with CO2 laser. Similar morphology was also visible with both treatments, however irradiated group revealed evidence of melting and fusion in the specimens. Conclusion. In conclusion CO2 laser irradiation modify the energy surface and disrupt the initial biofilm formation.
Towards evenly distributed grazing patterns: Including social context in sheep management strategies
Authors: di Virgilio Agustina , Morales Juan Manuel
Published: January 2018

Background: A large proportion of natural grasslands around the world is exposed to overgrazing resulting in land degradation and biodiversity loss. Although there is an increasing effort in the promotion of sustainable livestock management, rangeland degradation still occurs because animals' foraging behaviour is highly selective at different spatial scales. The assessment of the ecological mechanisms modulating the spatial distribution of grazing and how to control it has critical implications for long term conservation of resources and the sustainability of livestock production. Considering the relevance of social interactions on animals’ space use patterns, our aim was to explore the potential effects of including animals’ social context into management strategies using domestic sheep grazing in rangelands as case study. Methods: We used GPS data from 19 Merino sheep (approximately 10% of the flock) grazing on three different paddocks (with sizes from 80 to 1000 Ha) during a year, to estimate resource selection functions of sheep grazing in flocks of different levels of heterogeneity. We assessed the effects of sheep class (i.e., ewes, wethers, and hoggets), age, body condition and time since release on habitat selection patterns. Results: We found that social rank was reflected on sheep habitat use, where dominant individuals (i.e., reproductive females) used more intensively the most preferred areas and low-ranked (i.e., yearlings) used less preferred areas. Our results showed that when sheep grazed on more heterogeneous flocks, grazing patterns were more evenly distributed at all the paddocks considered in this study. On the other hand, when high-ranked individuals were removed from the flock, low-ranked sheep shifted their selection patterns by increasing the use of the most preferred areas and strongly avoided to use less preferred sites (i.e., a highly selective grazing behaviour). Discussion: Although homogenization and segregation of flocks by classes are common practices to increase flock productivity, we are proposing an alternative that employs behavioural interactions in heterogeneous flocks to generate more evenly distributed grazing patterns. This practice can be combined with other practices such as rotational grazing and guardian dogs (to decrease mortality levels that may be generated by sheep grazing on more risky habitats).This does not imply any modifications of livestock stocking rates and densities or any additional investments for labour and materials. Considering livestock behaviour is critical for the design of sustainable management practices that balance landscape conservation and livestock productivity.
Saccharomyces cerevisiae found in the crop of a Neotropical Drosophila species fly collected in a natural forest remnant – comments on Hoang, Kopp & Chandler (2015)
Authors: Batista Marcos R. D. , Santos Ana R. O. , Chaves Rafael D. , Rosa Carlos A. , Klaczko Louis B.
Published: January 2018

Abstract Background. Hoang, Kopp & Chandler (2015) questioned the use of commercial Saccharomyces cerevisiae as a model for investigating Drosophila – yeast association, since this approach “may not be fully representative of host-microbe interactions as they operate in nature”. They also claimed: “S. cerevisiae is rarely found with natural populations of D. melanogaster or other Drosophila species”. Indeed, previous choice experiments found that Sophophora subgenus flies (including invasive species D. melanogaster) are more attracted to banana baits inoculated with apiculate yeasts such as Hanseniaspora uvarum over S. cerevisiae inoculated baits. Yet, the forest interior dwelling species (FIDS) D. tripunctata group flies choose preferentially S. cerevisiae inoculated baits over H. uvarum in a natural forest environment. Aim and Methods. Our objective was to carry out a pilot experiment to examine yeast species associated with Drosophila in a natural Atlantic Rainforest fragment, especially examining, the yeast found with FIDS of the D. tripunctata group. We sampled Drosophila in a natural population from a Neotropical forest fragment. Males were dissected for isolating yeast colonies from their crops and to use their genitalia for species identification. Yeast species were identified by sequencing the D1/D2 domains of the 26S rRNA gene. Results and Conclusion. We isolated five yeast species from crops of Drosophila species of tripunctata group, including one strain of S. cerevisiae (from D. paraguayensis), confirming a previous record of S. cerevisiae isolates from a few tripunctata group species. Thus, their contention that “the results from D. melanogaster–S. cerevisiae laboratory experiments may not be fully representative of host–microbe interactions in nature” is probably right, but because D. melanogaster is an invasive species that is preferentially attracted in forests to apiculate yeasts, yet S. cerevisiae may be associated with FIDS Drosophila such as D. paraguayensis.
A formal approach to the molecular fuzzy lock-and-key
Authors: Wallace Rodrick
Published: January 2018

The fuzzy lock-and-key (FLK) powers a vast array of sophisticated logic gates at inter- and intra-cellular levels. We invoke representations of groupoid tiling wreath products analogous to the study of nonrigid molecules - or of related fuzzy symmetry extensions - to build a Morse Function that can describe spontaneous symmetry breaking phase transitions driven by information catalysis. The Function can, however, also be used to construct an Onsager-like stochastic dynamics, linked to the phase transition approach by the rich stability criteria associated with stochastic differential equations. The two methods provide complementary ways of looking at the FLK. A limit condition emerging from the stochastic dynamics gives insight into a cellular 'generalized inflammation' requiring progressively higher commitment of metabolic free energy for maintenance of basic FLK processes. These results suggest that more systematic study may illuminate pathologies associated with the failure of the FLK, a centrally-important but enigmatic biological process.
The biomechanical, chemical, and physiological adaptations of the eggs of two Australian megapodes to their nesting strategies and their implications for extinct titanosaur dinosaurs
Authors: Grellet-Tinner Gerald , Lindsay Suzanne , Thompson Mike
Published: January 2018

Megapodes are galliform birds endemic to Australasia and unusual amongst modern birds in that they bury their eggs for incubation in diverse substrates and using various strategies. Alectura lathami and Leipoa ocellata are Australian megapodes that build and nest in mounds of soil and organic matter. Such unusual nesting behaviors have resulted in particular evolutionary adaptations of their eggs and eggshells. We used a combination of scanning electron microscopy, including electron backscatter diffraction and energy-dispersive X-ray spectroscopy, to determine the fine structure of the eggshells and micro-CT scanning to map the structure of pores. We discovered that the surface of the eggshell of A. lathami displays nodes similar to those of extinct titanosaur dinosaurs from Transylvania and Auca Mahuevo egg layer #4 (AM L#4). We propose that this pronounced nodular ornamentation is an adaptation to an environment rich in organic acids from their nest mound, protecting the egg surface from chemical etching and leaving the eggshell thickness intact. By contrast, L. ocellata nests in mounds of sand with less organic matter in semiarid environments and has eggshells with weakly defined nodes, like those of extinct titanosaurs from AM L#3 that also lived in a semiarid environment. We suggest the internode spaces in both megapode and titanosaur species act as funnels, which concentrate the condensed water vapor between the nodes. This water funneling in megapodes through the layer of calcium phosphate reduces the likelihood of bacterial infection by creating a barrier to microbial invasion. In addition, the accessory layer of both species possesses sulfur, which reinforces the calcium phosphate barrier to bacterial and fungal contamination. Like titanosaurs, pores through the eggshell are Y-shaped in both species, but A. lathami displays unique mid-shell connections tangential to the eggshell surface and that connect some adjacent pores, like the eggshells of titanosaur of AM L#4 and Transylvania. The function of these inter-connections is not known, but likely helps the diffusion of gases in eggs buried in environments where occlusion of pores is possible.
A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units
Authors: Jackson Matthew A , Bell Jordana T , Spector Tim D , Steves Claire J
Published: January 2018

A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions.
Bioavailability of D-methionine relative to L-methionine for nursery pigs using the slope-ratio assay
Authors: Kong Changsu , Ahn Jong Young , Kim Beob G
Published: January 2018

This experiment was conducted to determine the bioavailability of D-methionine (Met) relative to L-Met for nursery pigs using the slope-ratio assay. A total of 50 crossbred barrows with an initial BW of 13.5 kg (SD = 1.0) were used in an N balance study. A Met-deficient basal diet (BD) was formulated to contain an adequate amount of all amino acids for 10 to 20 kg pigs except for Met. The two reference diets were prepared by supplementing the BD with 0.4 or 0.8 g L-Met/kg at the expense of corn starch, and an equivalent concentration of D-Met was added to the BD for the two test diets. The pigs were adapted to the experimental diets for 5 d and then total but separated collection of feces and urine was conducted for 4 d according to the marker-to-marker procedure. Nitrogen intakes were similar across the treatments. Fecal N output was not affected by Met supplementation regardless of source and consequently apparent N digestibility did not change. Conversely, there was a negative linear response (P < 0.01) to Met supplementation with both Met isomers in urinary N output, which resulted in increased retained N (g/4 d) and N retention (% of intake). No quadratic response was observed in any of the N balance criteria. The estimated bioavailability of D-Met relative to L-Met from urinary N output (g/4 d) and N retention (% of intake) as dependent variables using supplemental Met intake (g/4 d) as an independent variable were 87.6 and 89.6%, respectively, but approximate 95% fiducial limits for the relative bioavailability estimates included 100%. In conclusion, with an absence of statistical significance, the present study indicated that the mean relative bioequivalence of D- to L-Met was 87.6% based on urinary N output or 89.6% based on N retention.
A new direction for prenatal chromosome microarray testing: software-targeting for detection of clinically significant chromosome imbalance without equivocal findings
Authors: Ahn Joo Wook , Bint Susan , Irving Melita D , Kyle Phillipa M , Akolekar Ranjit , Mohammed Shehla N , Mackie Ogilvie Caroline
Published: January 2018

Purpose. To design and validate a prenatal chromosome microarray testing strategy that moves away from size-based detection thresholds, towards a more clinically relevant analysis, providing higher resolution than G-banded chromosomes but avoiding the detection of imbalances of unclear prognosis that cause parental anxiety.

Methods. All prenatal samples fulfilling our criteria for karyotype analysis (n=342) were tested by chromosome microarray and only copy number variants of established deletion/duplication syndrome regions and any other imbalance >3Mb were detected and reported. A retrospective full-resolution analysis of 249 of these samples was carried out to ascertain the performance of this testing strategy.

Results. Using our prenatal analysis, 23/342 (6.7%) samples were found to be abnormal. Of the remaining samples, 249 were anonymized and reanalyzed at full-resolution; a further 46 regions of imbalance were detected in 44 of these traces (17.7%). None of these additional imbalances were of clear clinical significance.

Conclusion. This prenatal chromosome microarray strategy detected all CNVs of clear prognostic value and did not miss any imbalances of clear clinical significance. This strategy avoided both the problems associated with interpreting imbalances of uncertain prognosis and the parental anxiety that are a result of such findings.
Lack of tonotopic organization of the auditory cortex in schizophrenia
Authors: Ragole Thomas , Slason Erin , Teale Peter , Reite Martin , Rojas Donald C.
Published: January 2018

Background: Disorganization of tonotopy in the auditory cortex has been described in schizophrenia. Subjects with schizophrenia show little to no spatial organization of responses to different tone frequencies in the auditory cortex. Previous studies have called into question the use of MEG and the M100 response to assess tonotopy. This study seeks to replicate prior results of tonotopic disorganization in schizophrenia compared to healthy controls.

Methods: The tonotopic organization for 400 Hz and 4,000 Hz sound in 19 patients with schizophrenia and 11 comparison subjects was determined using MEG by examining the M100 auditory-evoked magnetic field dipole in primary auditory cortex. The equivalent current dipole locations were then mapped and compared.

Results: The previous result of a lack of tonotopy in subjects with schizophrenia was partly replicated. In control subjects, the 400 Hz tone auditory evoked field was found anterior to the 4000 Hz in the primary auditory cortex.

Conclusions: The lack of tonotopic organization of the auditory cortex is replicable in patients with schizophrenia and suggests that the architecture underlying tonotopy in the auditory cortex is disordered. This result suggests possible alteration in the organization of the auditory cortex, which may in turn influence higher order cognitive processes by altering the perception of incoming auditory stimuli.
Morphometrics of a wild Asian elephant exhibiting disproportionate dwarfism
Authors: de Silva Shermin , Weerathunga U. Sameera , Pushpakumara T. V.
Published: January 2018

Dwarfism is a condition characterized by shorter stature, at times accompanied by differential skeletal growth proportions relative to the species-typical physical conformation. Causes vary and are well-documented in humans as well as certain mammalian species in captive or laboratory conditions, but rarely observed in the wild. Here we report on a single case of apparent dwarfism in a free-ranging adult male Asian elephant (Elephas maximus) in Sri Lanka, comparing physical dimensions to those of other males in the same population, males in other populations, and previous records. The subject was shorter than typical mature males, with a shoulder height of approximately 195cm and a body length of 218cm. This ratio of body length to height also deviates from what is typically observed, which is nearly 1:1. The subject also exhibits a slight elongation of the skull. We discuss how this phenotype compares to cases of dwarfism in other non-human animals.
Marine biodiversity and ecosystem functioning: what’s known and what’s next?
Authors: Gamfeldt Lars , Lefcheck Jonathan S , Byrnes Jarrett E K , Cardinale Bradley J , Duffy J. Emmett , Griffin John N
Published: January 2018

Marine ecosystems are experiencing rapid and pervasive loss of species. Understanding the consequences of species loss is critical to effectively managing these systems. Over the last several years, numerous experimental manipulations of species richness have been performed, yet existing quantitative syntheses have focused on a just a subset of processes measured in experiments and, as such, have not summarized the full data available from marine systems. Here, we present the results of a meta-analysis of 174 marine experiments from 42 studies that have manipulated the species richness of organisms across a range of taxa and trophic levels and analysed the consequences for various ecosystem processes (categorised as production, consumption or biogeochemical fluxes). Our results show that, generally, mixtures of species tend to enhance levels of ecosystem function relative to the average component species in monoculture, but have no or negative effect on functioning relative to the ‘highest-performing' species. These results are largely consistent with those from other syntheses, and extend conclusions to ecological functions that are most commonly measured in the marine realm (e.g. nutrient release from sediment bioturbation). For experiments that manipulated three or more levels of richness, we attempted to discern the functional form of the BEF relationship. We found that, for response variables categorised as consumption, a power-function best described the relationship, which is also consistent with previous findings. However, we identified a linear relationship between richness and production. Combined, our results suggest that losses of species will, on average, tend to alter the functioning of marine ecosystems. We outline several research frontiers that will allow us to more fully understand how, why, and when diversity may drive the functioning of marine ecosystems.