bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of histomorphology and DNA preservation produced by fixatives in the veterinary diagnostic laboratory setting
Authors: Dark Michael J. , Craft William F. , Conway Julia A.
Published: January 2018

Histopathology is the most useful tool for diagnosis of a number of diseases, especially cancer. To be effective, histopathology requires that tissues be fixed prior to processing. Formalin is currently the most common histologic fixative, offering many advantages: it is cheap, readily available, and pathologists are routinely trained to examine tissues fixed in formalin. However, formalin fixation substantially degrades tissue DNA, hindering subsequent use in diagnostics and research. We therefore evaluated three alternative fixatives, TissueTek® Xpress® Molecular Fixative, modified methacarn, and PAXgene®, all of which have been proposed as formalin alternatives, to determine their suitability for routine use in a veterinary diagnostic laboratory. This was accomplished by examining the histomorphology of sections produced from fixed tissues as well as the ability to amplify fragments from extracted DNA. Tissues were sampled from two dogs and four cats, fixed for 24-48 hours, and processed routinely. While all fixatives produced acceptable histomorphology, formalin had significantly better morphologic characteristics than the other three fixatives. Alternative fixatives generally had better DNA amplification than formalin, although results varied somewhat depending on the tissue examined. While no fixative is yet ready to replace formalin, the alternative fixatives examined may be useful as adjuncts to formalin in diagnostic practices.
Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior
Authors: Balakrishnan Christopher N , Mukai Motoko , Gonser Rusty A , Wingfield John C , London Sarah E , Tuttle Elaina M , Clayton David F
Published: January 2018

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, over 89% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with 16,846, 15,805, and 16,646 unique BLAST hits in song, white-throated and white-crowned sparrows, respectively. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as a primary determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.
Biogeographic patterns in the cartilaginous fauna (Pisces: Elasmobranchii and Holocephali) in the southeast Pacific Ocean
Authors: Bustamante Carlos , Vargas-Caro Carolina , Bennett Michael B
Published: January 2018

The abundance and species richness of the cartilaginous fish community of the continental shelf and slope off central Chile is described, based on fishery-independent trawl tows made in 2006 and 2007. A total of 194,705 specimens comprising 20 species (9 sharks, 10 skates, 1 chimaera ) were caught at depths of 100 – 500 m along a 1,000 km transect between 29.5° S and 39° S. Sample site locations were grouped to represent eight geographical zones within this latitudinal range. Species richness fluctuated from 1 to 6 species per zone. There was no significant latitudinal trend for sharks, but skates showed an increased species richness with increasing latitude. Standardised catch per unit effort increased with increasing depth for sharks, but not for skates, but the observed trend for increasing CPUE with latitude was not significant for either sharks or skates. A change in community composition occurred along the depth gradient with the skates, Psammobatis rudis, Zearaja chilensis and Dipturus trachyderma dominating communities between 100 and 300 m, but small-sized, deep-water dogfishes, such as Centroscyllium spp . dominated the catch between 300 and 500 m. Cluster and ordination analysis identified one widespread assemblage, grouping 58% of sites, and three shallow-water assemblages. Assemblages with low diversity ( coldspots ) coincided with highly productive fishing grounds for demersal crustaceans and bony fishes. The community distribution suggested that the differences between assemblages may be due to compensatory changes in mesopredator species abundance, as a consequence of continuous and unselective species removal. Distribution patterns and the quantitative assessment of sharks, skates and chimaeras presented here complement extant biogeographic knowledge and further the understanding of deep-water ecosystem dynamics in relation to fishing activity in the south-east Pacific Ocean.
Ploidy of Bacillus subtilis, Bacillus megaterium, and three new isolates of Bacillus and Paenibacillus
Authors: Böttinger Benjamin , Zerulla Karolin , Soppa Jörg
Published: January 2018

Bacteria were long assumed to be monoploid, maintaining one copy of a circular chromosome. In recent years it became obvious that the majority of species in several phylogenetic groups of prokaryotes are oligoploid or polyploid, e.g. in halophilic and methanogenic archaea, proteobacteria, and cyanobacteria. The present study aimed at investigating the distribution of ploidy in an additional group of prokaryotes, i.e. in the gram-positive genus Bacillus. First, the numbers of origins and termini of the two laboratory strains Bacillus subtilis and Bacillus megaterium were quantified using an optimized real time PCR approach. B. subtilis was found to be mero-oligoploid in exponential phase with, on average, 5.9 origins and 1.2 termini. In stationary phase the average numbers of origins per cell was considerably smaller. B. megaterium was found to be polyploid in exponential phase with about 12 copies of the origin and terminus. Again, the ploidy level was down-regulated in stationary phase. To verify that oligo-/polyploidy is not confined to strains with a long history of growth in the laboratory, three strains were newly isolated from soil, which were found to belong to the genera of Bacillus and Paenibacillus. All three strains were found to be oligoploid with a growth-phase dependent down-regulation of the ploidy level in stationary phase. Taken together, these results indicate that oligo-/polyploidy might be more widespread in Bacillus and related genera than assumed until now and that monoploidy is not typical.
The relationship between managed bees and the prevalence of parasites in bumblebees
Authors: Graystock Peter , Goulson Dave , Hughes William O
Published: January 2018

Honey bees and, more recently, bumblebees have been domesticated and are now managed commercially primarily for crop pollination, mixing with wild pollinators during foraging on shared flower resources. There is mounting evidence that managed honey bees or commercially produced bumblebees may affect the health of wild pollinators such as bumblebees by increasing competition for resources and the prevalence of parasites in wild bees. Here we screened 764 bumblebees from around five greenhouses that either used commercially produced bumblebees or did not, as well as bumblebees from 10 colonies placed at two sites either close to or far from a honey bee apiary, for the parasites Apicystis bombi, Crithidia bombi, Nosema bombi, N. ceranae, N. apis and deformed wing virus. We found that A. bombi and C. bombi were more prevalent around greenhouses using commercially produced bumblebees, while C. bombi was 18% more prevalent in bumblebees at the site near to the honey bee apiary than those at the site far from the apiary. Whilst these results are from only a limited number of sites, they support previous reports of parasite spillover from commercially produced bumblebees to wild bumblebees, and suggest that the impact of stress from competing with managed bees or the vectoring of parasites by them on parasite prevalence in wild bees needs further investigation. It appears increasingly likely that the use of managed bees comes at a cost of increased parasites in wild bumblebees, which is not only a concern for bumblebee conservation, but which may impact other pollinators as well.
Levodopa-stimulated dopamine release in Tourette syndrome
Authors: Black Kevin J , Piccirillo Marilyn L. , Koller Jonathan M. , Hseih Tiffany , Wang Lei , Mintun Mark A.
Published: January 2018

BACKGROUND: Several lines of evidence suggest that dopamine (DA)-influenced neuronal pathways may malfunction in Tourette Syndrome (TS). A dopamine-responsive abnormality of brain function in TS could be either presynaptic or postsynaptic. Some PET studies support the hypothesis of presynaptic abnormalities in levodopa uptake, dopamine synthesis, or dopamine release. Alternatively, presynaptic dopaminergic function could be normal in TS but dopamine-sensitive abnormalities could exist in striatum, pallidum, thalamus, or cortex. METHODS: In this study we directly tested the presynaptic hypothesis using a new approach. We used positron emission tomography (PET) and [11C]raclopride (RAC*) to measure synaptic dopamine release in response to levodopa and placebo infusions (with carbidopa) in 5 neuroleptic-naïve adults with TS and 5 matched control subjects. The primary analysis examined RAC* binding potential (BPND) in predefined volumes of interest (VOIs). A secondary analysis compared BPND voxel by voxel over the entire brain. RESULTS: (1) Overall, baseline RAC* BPND did not differ significantly between groups, though nucleus accumbens BPND was higher in TS (16%, p=0.051). (2) Across regions, DA release declined from before to during infusion (p=0.014), including with placebo. (3) This decline was smaller in TS (p=0.080). (4) Levodopa’s effect on BPND differed significantly in right midbrain (p=0.002, corrected), where levodopa displaced RAC* by 59% in control subjects but increased BPND by 74% in TS subjects, and in parahippocampal gyrus (p=0.02, corrected). DISCUSSION: Our finding that a before/after RAC* design is confounded by time and/or expectation effects has implications for other RAC* PET studies. The smaller magnitude of the decrease with time in TS may be attributable to impaired habituation to the scan environment. Levodopa’s opposite effect on RAC* binding in TS dopaminergic midbrain was not predicted, but may signify an abnormal response to dopaminergic stimulation in TS. These findings invite confirmation in a larger sample.
dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
Authors: Puritz Jonathan , Hollenbeck Christopher M. , Gold John R.
Published: January 2018

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for organisms with large effective population sizes and high levels of genetic polymorphism but for which no genomic resources exist. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is most likely due to the fact that dDocent quality trims instead of filtering and incorporates both forward and reverse reads in assembly, mapping, and SNP calling, thus enabling use of reads with Indel polymorphisms. The pipeline and a comprehensive user guide can be found at (http://dDocent.wordpress.com).
Assessing the impact of human trampling on vegetation: a systematic review and meta-analysis of experimental evidence
Authors: Pescott Oliver L. , Stewart Gavin
Published: January 2018

Vegetation trampling resulting from recreation can adversely impact natural habitats, leading to the loss of vegetation and the degradation of plant communities. A considerable primary literature exists on this topic, therefore it is important to assess whether this accumulated evidence can be used to reach general conclusions concerning vegetation vulnerability to inform conservation management decisions. Experimental trampling studies on a global scale were retrieved using a systematic review methodology and synthesised using random effects meta-analysis. The relationships between vegetation recovery and each of initial vegetation resistance, trampling intensity, time for recovery, Raunkiaer life-form (perennating bud position), and habitat were tested using random effects multiple meta-regressions and subgroup analyses. The systematic search yielded 304 studies; of these, nine reported relevant randomized controlled experiments, providing 188 vegetation recovery effect sizes for analysis. The synthesis indicated there was significant heterogeneity in the impact of trampling on vegetation recovery. This was related to resistance and recovery time, and the interactions of these variables with Raunkiaer life-form, but was not strongly dependent on the intensity of the trampling experienced. The available evidence suggests that vegetation dominated by hemicryptophytes and geophytes recovers from trampling to a greater extent than vegetation dominated by other life-forms. Variation in effect within the chamaephyte, hemicryptophyte and geophyte life-form sub-groups was also explained by the initial resistance of vegetation to trampling, but not by trampling intensity. Intrinsic properties of plant communities appear to be the most important factors determining the response of vegetation to trampling disturbance. Specifically, the dominant Raunkiaer life-form of a plant community accounts for more variation in the resilience of communities to trampling than the intensity of the trampling experienced, suggesting that simple assessments based on this trait could guide decisions concerning sustainable access to natural areas. Methodological and reporting limitations must be overcome before more disparate types of evidence can be synthesised; this would enable more reliable extrapolation to non-study situations, and a more comprehensive understanding of how assessments of intrinsic plant traits can be used to underpin conservation management decisions concerning access.
A wireless marker system to enable evoked potential recordings using a wireless EEG system (EPOC) and a portable computer
Authors: Thie Johnson
Published: January 2018

As wireless EEG devices have become affordable at low cost, have a small form factor and quick setup time, they can be deployed at universities and schools for teaching purposes. However they have not been applied for evoked potential recording since they lack an option to receive stimulus markers. Meanwhile evoked potential recording is required for functional assessment of the sensory systems such as auditory and visual. This paper describes a wireless system that embeds information about the stimulus in the EEG channels. The transmitter unit is connected to the stimulus device to detect the stimulus and transmit the stimulus information to the receiver unit. The receiver unit attached to two of the EEG electrodes decodes the information and generates a pulse across the electrodes. The pulse width conveys the information about the stimulus. Hence the stimuli are synchronised with the EEG data allowing users to evaluate the evoked potentials in the offline processing. The wireless marker system was verified with audio stimuli consisting of 1000Hz and 1200Hz tones and reliably generated pulses with 100ms and 200ms width respectively. The delay between the onset of the tone and the onset of the pulse was 19.3 +/- 0.1ms. Since the variability of the delay was under 1ms and so negligible, the evoked potentials could be evaluated reliably. The evoked potential could be shifted back by 19.3ms to compensate for the delay. The system was also verified with a black-and-white checkerboard pattern stimuli and reliably generated pulses with 100ms width when the pattern reversed. The delay between the onset of the reversal and the onset of the pulse was 6.4ms. Similarly the variability of the delay was negligible.
Modeling and simulation of hemodynamic effects during different cardiopulmonary resuscitation (CPR) technologies
Authors: Jenkins David , Zeng Hc
Published: January 2018

Cardiopulmonary Resuscitation (CPR) is a simple and effective medical treatment for sudden cardiac arrest patients. Because of those existing interferences in the experiments, most of the animal experiments and the CPRs in vivo studies get contradictory conclusions. In this report, according to the current theories of CPR, we got a CPR model; simulated various CPR technologies, and compared their hemodynamic variables. Compared the simulation results and animal experimental data, this report showed that when the External counterpulsation technique applied in CPR, the cardiac output, as well as the diastolic and the aortic pressure would be improved, which was consistent with the results of animal experiments.
Augmented reality in healthcare education: an integrative review
Authors: Zhu Egui , Hadadgar Arash , Masiello Italo , Zary Nabil
Published: January 2018

Background. Developing healthcare competencies in students and professionals poses great educational challenges. A possible solution is to provide learning opportunities that utilize augmented reality (AR), where virtual learning experiences can be embedded within a real physical context. The aim of this study was to provide a comprehensive overview of the current state of AR in terms of user acceptance, the AR applications currently developed and the effect of AR on the development of competencies in healthcare. Methods. We conducted an integrative review, which is the broadest type of research review method allowing for the inclusion of various research designs. This allows us to more fully understand a phenomenon of interest. Our review included multi-disciplinary research publications in English reported until 2012. Results. We found 2 529 research papers from ERIC, CINAHL, Medline, PubMed, Web of Science and Springer-link. Three qualitative, twenty quantitative and two mixed-method studies were included. Using thematic analysis, we have described characteristics for research, technology and education. This study showed that AR was applied across a wide range of topics in healthcare education. Furthermore, acceptance for AR as a learning technology was reported among the learners, as well as its potential for improving different types of competencies. Discussion. AR is still considered a novelty in the literature, with most of the studies reporting early prototypes. Additionally, the designed AR applications lacked an explicit pedagogical theoretical framework. Instead, the learning strategies adopted were of the traditional style ‘see one, do one and teach one’ and do not integrate clinical competencies to ensure patients’ safety.
Classifying acoustic signals into phoneme categories: average and dyslexic readers make use of complex dynamical patterns
Authors: Hasselman Fred
Published: January 2018

Aetiologies of developmental dyslexia often assume a deficit in auditory processing may be causally entailed in the specific learning disorder. The purpose of this study is to compare a number of assumed auditory features that are supposed to evidence the account given by such aetiologies under conditions of strong inference. To do so, the relevant acoustic features were extracted from the same set of artificial speech stimuli that lie on a /bAk/-/dAk/ continuum. Features were tested on their ability to enable a simple classifier (Quadratic Discriminant Analysis) to reproduce the observed classification performance of average and dyslexic readers in a speech perception experiment. The ‘classical’ features examined were based on component process accounts of developmental dyslexia such as the supposed deficit in Envelope Rise Time detection and the deficit in the detection of rapid changes in the distribution of energy in the frequency spectrum (formant transitions). Studies examining these temporal processing deficit hypotheses remarkably do not employ measures that quantify the temporal dynamics of stimuli. It is shown that measures based on quantification of the dynamics of complex, interaction-dominant systems enable QDA to classify the stimuli almost identically as dyslexic and average reading participants. It seems unlikely that participants used any of the features that are traditionally associated with accounts of (impaired) speech perception that assume classifying speech stimuli amounts to a linear additive interaction of component processes that each parse the acoustic signal independent of one another.
The impact of maths support tutorials on mathematics confidence and academic performance in a cohort of HE Animal Science students
Authors: van Veggel Nieky , Amory Jonathan
Published: January 2018

Students embarking on a bioscience degree course, such as Animal Science, often do not have sufficient experience in mathematics. However, mathematics form an essential and integral part of any bioscience degree and are essential to enhance employability. This paper presents the findings of a project looking at the effect of mathematics tutorials on a cohort of first year animal science and management students. The results of a questionnaire, focus group discussions and academic performance analysis indicate that small group tutorials enhance students’ confidence in maths and improve students’ academic performance. Furthermore, student feedback on the tutorial programme provides a deeper insight into student experiences and the value students assign to the tutorials.
Pairwise antagonism assay of clinical Acinetobacter isolates
Authors: Summers Amy M , Heitkamp Rae A , Cheng Sylvia , Kirkup Benjamin C
Published: January 2018

Many bacteria antagonize each other in nature; laboratory evidence of these interactions dates from 1925 (Gratia). However, antagonism assays are typically performed between a small number of 'sensitive' strains screening a range of potential 'killers' in the hunt for natural antibiotics, or a single 'killer' against a broad range of 'pathogens.' By contrast, several recent studies have performed pairwise assays across a range of organisms; including marine Vibrio (Cordero et al 2012) and fresh water Bacillus (Perez-Gutierrez et al 2012) strains. These studies have revealed some critical new microbial ecology by using the complete suite of antagonisms among strains. Environmental strains are often viewed as more microdiverse than clinical strains, in part because clinical strains experience purifying selection by the immune system and rapid population expansions. To explore the frequency and distribution of antagonism in clinical isolates, a pairwise antagonism dataset is being collected from clinical Acinetobacter. Significant method development has gone into finding a method robust and sensitive. Overnight cultures, grown in trypticase soy broth at 37°C, are spread on trypticase soy agar to create a confluent bacterial lawn. Using a 96-well pin replicator, 94 isolates of Acinetobacter and two negative control checks are inoculated on the lawn. The plates are incubated at 37°C for 18 to 24 hours and the assay scored for the presence or absence of a colony growing on the bacterial lawn and the presence or absence of a clearing around the inoculation points. The revealed suite of antagonisms is rich and diverse. 8,836 interactions were scored; of them, at least 5,640 are suggestive of antagonism. In a preliminary dataset, almost every strain already participates as an antagonist against some other strain. This is much higher than the frequencies reported in other environmental collections; and does not suggest a single ecological niche for the clinical strains. This data is collected in the context of antimicrobial susceptibilities and limited clinical metadata, providing a contrast to the environmental data which has been generated for the environmental strains. As we continue to collect antagonism data on clinical Acinetobacter isolates, we will learn more about the naturally occurring antimicrobial chemicals that these organisms produce and secrete.
Clinical trials and Myokines
Authors: Ylva Hellsten
Published: January 2018

Background: Cardiovascular disease is a major cause of death in the western world. Regular physical activity is known to be highly beneficial for improving cardiovascular health status. Methods:The current abstract is based on the authors own data and a literature review. The authors own studies have all been accepted by the local ethics committee. In intervention studies the effect of physical training on cardiovascular risk parametres as well as on specific biochemical systems in the cardiovascular system have been studied. Changes in plasma myokine concentrations have been assessed in acute exercise and training interventions in different populations. Results: The conducted studies within the cardiovascular area clearly show that regular physical activity is highly beneficial for vascular function and for reducing blood pressure both in aged individuals and in individuals with life style related disease. An ongoing study at The University of Copenhagen conducted in collaboration with Martin Daumer will show to what extent estrogen loss in connection with menopause in women can be replaced by physical activity and thereby retard the progressive risk for cardiovascular disease commonly seen in women after menopause. Many studies have documented that myokines are elevated in response to exercise but more systematic investigations of how specific myokines are altered in response to various types of intensities and duration of exercise and in different subsets of the population is required to more solidly assess their usefulness as markers of physical health status. Discussion/conclusion: Based on data from our own studies and studies in the literature, physical activity should be recommended for prevention of cardiovascular disease and should be a primary recommendation in treatment of patients with cardiovascular disease to improve overall cardiovascular health. Use of myokines as markers of health status may be useful but selection of the best markers should await further evidence from systematic studies. 
Triclosan causes toxic effects to algae in marine biofilms, but does not inhibit the metabolic activity of marine biofilm bacteria
Authors: Johansson C. Henrik , Janmar Lisa , Backhaus Thomas
Published: January 2018

Effects of the antimicrobial agent triclosan to natural periphyton communities (biofilms, comprising primarily microalgae and bacteria) were assessed in two independent experiments during spring and summer. For that purpose a semi-static test system was used in which periphyton was exposed to a concentration range of 5 – 9 054 nmol/L triclosan. Effects on algae were analyzed as content and composition of photosynthetic pigments. The corresponding EC50 values were 39.25 and 302.45 nmol/L for the spring and summer experiment respectively. Effects on periphytic bacteria were assessed as effects on carbon utilization patterns, using Biolog Ecoplates. No inhibition of either total carbon utilization or functional diversity was observed, indicating a pronounced triclosan tolerance of the marine bacteria. In contrast, a small stimulation of the total carbon utilization was observed at triclosan concentrations exceeding 100 nmol/L.
Bio::DB::NextProt: A Perl Module for neXtProt Database Information Retrieval
Authors: Leprevost Felipe V
Published: January 2018

The neXtProt database is a comprehensive knowledge platform recently adopted by the Chromosome-centric Human Proteome Project as the main reference database. The primary goal of the project is to identify and catalog every human protein encoded in the human genome. For such, computational approaches have an important role as data analysis and dedicated software are indispensable. Here we describe Bio::DB::NextProt, a Perl module that provides an object-oriented access to the neXtProt REST Web services, enabling the programatically retrieval of structured information. The Bio::DB::NextProt module presents a new way to interact and download information from the neXtProt database. Every parameter available through REST API is covered by the module allowing a fast, dynamic and ready-to-use alternative for those who need to access neXtProt data. Bio::DB::NextProt is an easy-to-use module that provides automatically retrieval of data, ready to be integrated into third-party software or to be used by other programmers on the fly. The module is freely available from from CPAN (metacpan.org/release/Bio-DB-NextProt) and GitHub (github.com/Leprevost/Bio-DB-NextProt) and is released under the perl\_5 license.
Equilibrium switching and mathematical properties of nonlinear interaction networks with concurrent antagonism and self-stimulation
Authors: Rabajante Jomar , Talaue Cherryl O.
Published: January 2018

Concurrent decision-making model (CDM) of interaction networks with more than two antagonistic components represents various biological systems, such as gene interaction, species competition and mental cognition. The CDM model assumes sigmoid kinetics where every component stimulates itself but concurrently represses the others. Here we prove generic mathematical properties (e.g., location and stability of steady states) of n-dimensional CDM with either symmetric or asymmetric reciprocal antagonism between components. Significant modifications in parameter values serve as biological regulators for inducing steady state switching by driving a temporal state to escape an undesirable equilibrium. Increasing the maximal growth rate and decreasing the decay rate can expand the basin of attraction of a steady state that contains the desired dominant component. Perpetually adding an external stimulus could shut down multi-stability of the system which increases the robustness of the system against stochastic noise. We further show that asymmetric interaction forming a repressilator-type network generates oscillatory behavior.
Fast and accurate estimation of the covariance between pairwise maximum likelihood distances
Authors: Gil Manuel
Published: January 2018

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account in any process that compares or combines distances to increase precision. In this paper, we present a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei and Jin, 1989) which links the covariance to path lengths. We prove it here under a simple symmetric substitution model. In a simulation, we show that our estimator outperforms previously published ones in terms of the mean squared error.
Protein kinase C in the wood frog, Rana sylvatica: reassessing the tissue-specific regulation of PKC isozymes during freezing
Authors: Dieni Christopher A. , Storey Kenneth B.
Published: January 2018

The wood frog, Rana sylvatica, survives whole-body freezing and thawing each winter. The extensive adaptations required at the biochemical level are facilitated by alterations to signaling pathways, including the insulin/Akt and AMPK pathways. Past studies investigating changing tissue-specific patterns of the second messenger IP3 in adapted frogs have suggested important roles for protein kinase C (PKC) in response to stress. In addition to their dependence on second messengers, phosphorylation of three PKC sites by upstream kinases (most notably PDK1) is needed for full PKC activation, according to current generally-accepted models. The present study uses phospho-specific immunoblotting to investigate phosphorylation states of PKC- as they relate to distinct tissues, PKC isozymes, and phosphorylation sites- in control and frozen frogs. In contrast to past studies where second messengers of PKC increased during the freezing process, phosphorylation of PKC tended to generally decline in most tissues of frozen frogs. All PKC isozymes and specific phosphorylation sites detected by immunoblotting decreased in phosphorylation levels in hind leg skeletal muscle and hearts of frozen frogs. Most PKC isozymes and specific phosphorylation sites detected in livers and kidneys also declined; the only exceptions were the levels of isozymes/phosphorylation sites detected by the phospho-PKCα/βII (Thr638/641) antibody, which remained unchanged from control to frozen frogs. Changes in brains of frozen frogs were unique; no decreases were observed in the phosphorylation levels of any of the PKC isozymes and/or specific phosphorylation sites detected by immunoblotting. Rather, increases were observed for the levels of isozymes/phosphorylation sites detected by the phospho-PKCα/βII (Thr638/641), phospho-PKCδ (Thr505), and phospho-PKCθ (Thr538) antibodies; all other isozymes/phosphorylation sites detected in brain remained unchanged from control to frozen frogs. The results of this study indicate a potential important role for PKC in cerebral protection during wood frog freezing. Our findings also call for a reassessment of the previously-inferred importance of PKC in other tissues, particularly in liver; a more thorough investigation is required to determine whether PKC activity in this physiological situation is indeed dependent on phosphorylation, or whether it deviates from the generally-accepted model and can be “overridden” by exceedingly high levels of second messengers, as has been demonstrated with certain PKC isozymes (e.g. PKCδ).
Structure, ontogeny and evolution of the patellar tendon in emus (Dromaius novaehollandiae) and other palaeognath birds
Authors: Regnault Sophie , Pitsillides Andrew A , Hutchinson John R.
Published: January 2018

The patella (kneecap) exhibits multiple evolutionary origins in birds, mammals, and lizards, and is thought to increase the mechanical advantage of the knee extensor muscles. Despite appreciable interest in the specialized anatomy and locomotion of palaeognathous birds (ratites and relatives), the structure, ontogeny and evolution of the patella in these species remains poorly characterized. Within Palaeognathae, the patella has been reported to be either present, absent, or fused with other bones, but it is unclear how much of this variation is real, erroneous or ontogenetic. Clarification of the patella’s form in palaeognaths would provide insight into the early evolution of the patella in birds, in addition to the specialized locomotion of these species. Findings would also provide new character data of use in resolving the controversial evolutionary relationships of palaeognaths. In this study, we examined the gross and histological anatomy of the emu patellar tendon across several age groups from five weeks to 18 months. We combined these results with our observations and those of others regarding the patella in palaeognaths and their outgroups (both extant and extinct), to reconstruct the evolution of the patella in birds. We found no evidence of an ossified patella in emus, but noted its tendon to have a highly unusual morphology comprising large volumes of adipose tissue contained within a collagenous meshwork. The emu patellar tendon also included increasing amounts of a cartilage-like tissue throughout ontogeny. We speculate that the unusual morphology of the patellar tendon in emus results from assimilation of a peri-articular fat pad, and metaplastic formation of cartilage, both potentially as adaptations to increasing tendon load. We corroborate previous observations of a ‘double patella’ in ostriches, but in contrast to some assertions, we find independent (i.e. unfused) ossified patellae in kiwis and tinamous. Our reconstructions suggest a single evolutionary origin of the patella in birds and that the ancestral patella is likely to have been a composite structure comprising a small ossified portion, lost by some species (e.g. emus, moa) but expanded in others (e.g. ostriches).
Surveying for bird carcasses resulting from window collisions: a standardized protocol
Authors: Hager Stephen B. , Cosentino Bradley J.
Published: January 2018

Collisions with building windows are thought to be a significant source of mortality for urban birds. Past studies on bird-window collisions have used a variety of survey methods to estimate the magnitude of mortality, and few have constructed methods in light of the biases related to scavengers and worker abilities that lead to imperfect detection of carcasses. Adoption of a systematic carcass survey protocol in future studies would reduce site-specific biases and among-site survey variability, which in turn would improve the accuracy of mortality estimates at all scales. We present here a standardized carcass survey protocol that serves two basic functions: (a) it is simple and inexpensive to implement, and (b) it accounts for the removal of carcasses by scavengers and detection of carcasses by field workers. Consistent with these goals, we added a variety of approaches with particular aspects of the protocol for researchers to chooose from depending on the goals of their study. The following topics are addressed in the protocol: 1. Preparing for surveys, 2. Supplies, 3. Frequency of surveys throughout the study, 4. When during the day to complete surveys, 5. Field worker behavior during surveys, 6. The pre-survey carcass ‘clean-up’, 7. How to conduct carcass surveys, 8. Carcass collection and containment, 9. Identifying species of bird carcasses, 10. Data collection and management, and 11. Duration of carcass surveys.
Effect of obesity and exercise on the expression of the novel myokines, Myonectin and Irisin
Authors: Peterson Jonathan M , Mart Ryan , Bond Cherie E
Published: January 2018

Metabolic dysfunction in skeletal muscle is a major contributor to the development of type 2 diabetes. Endurance exercise training has long been established as an effective means to directly restore skeletal muscle glucose and lipid uptake and metabolism. However, in addition to the direct effects of skeletal muscle on glucose and lipids, there is renewed interest in the ability of skeletal muscle to coordinate metabolic activity of other tissues, such as adipose tissue and liver. The purpose of this study was to examine the effects of endurance exercise on the expression level of two novel muscle-derived secreted factors, or myokines, Myonectin and Fibronectin type III domain containing 5 (Fndc5), the precursor for Irisin. Methods: We used the diaphragm muscle from both the obese Zucker rat (OZR) and lean Zucker Rat (LZR) with 9 weeks of aerobic training on a motorized treadmill. We examined the gene expression of 12 commonly used reference genes and performed quantitative real-time PCR analysis on the gene expression of Myonectin and Fndc5. Results: Of the 12 commonly used PCR reference genes tested we were able to establish that Hypoxanthine phosphoribosyltransferase 1 (HPRT1) and lactate dehydrogenase A (Ldha) remained stable in the diaphragm muscle regardless of obesity or exercise training. Interestingly, we also concluded that the commonly used reference genes: beta-Actin, beta-2-microglobulin, Non-POU domain containing, octamer-binding, Peptidylprolyl isomerase H, 18S ribosomal rna, TATA box binding protein and Transferrin receptor were all found to be altered by the combination of exercise and obesity. Our study showed that the diaphragm muscle of the OZR had significantly higher expression levels of both myonectin and Fndc5. Exercise training had no effect on the expression level of Fndc5, but significantly lowered the gene expression of myonectin in both the LZR and OZR groups. Conclusion: Contrary to prior findings regarding the regulation of Fndc5 and myonectin we show that myonectin and Fndc5 expression are both increased in the OZR model of obesity. Further, long-term exercise training decreases myonectin levels, which is opposite, the effect reported with short-term exercise. However, this report confirms earlier work showing that Fndc5 gene expression is not altered by chronic exercise.
Meta-analysis of resting-state fMRI in depression: generating spatial hypotheses for potential clinical applications
Authors: Sundermann Benedikt , Olde lütke Beverborg Mona , Pfleiderer Bettina
Published: January 2018

Information derived from functional magnetic resonance imaging (fMRI) during wakeful rest has been introduced as a candidate diagnostic biomarker in unipolar major depressive disorder (MDD). Multiple reports of resting state fMRI in MDD describe group effects. Such prior knowledge can be adopted to pre-select potentially discriminating features, for example for diagnostic classification models with the aim to improve diagnostic accuracy. Purpose of this analysis was to consolidate spatial information about alterations of spontaneous brain activity in MDD to serve such feature selection and as a secondary aim to improve understanding of disease mechanisms. 32 studies were included in final analyses. Coordinates extracted from the original reports were assigned to two categories based on directionality of findings. Meta-analyses were calculated using the non-additive activation likelihood estimation approach with coordinates organized by subject group to account for non-independent samples. Results were compared with established resting state networks (RSNs) and spatial representations of recently introduced temporally independent functional modes (TFMs) of spontaneous brain activity. Converging evidence revealed a distributed pattern of brain regions with increased or decreased spontaneous activity in MDD. The most distinct finding was hyperactivity/ hyperconnectivity presumably reflecting the interaction of cortical midline structures (posterior default mode network components associated with self-referential processing and the subgenual anterior cingulate cortex) with lateral frontal areas related to externally-directed cognition. One particular TFM seems to better comprehend the findings than classical RSNs. Alterations that can be captured by resting state fMRI show considerable overlap with those identifiable with other neuroimaging modalities though differing in some aspects.
The interface between priming memory and the working memory
Authors: Smith Graeme E.
Published: January 2018

There is an interface between priming memory and working memory that acts to limit the amount of data in working memory, and also allows priming memory to be actively maintained so that memories stay intact while they are in working memory. This interface converts from functional clusters to chunks automatically as part of the transfer from priming to working memory. As a result, memories in working memory can be rehearsed in order to actively maintain them. This represents more than a change in state, it represents a radical change in the way memories are accessed. Priming memory without this stage can only be extended it cannot be refreshed and so there is a limit of about 3 seconds to how long it will last before it begins to degrade. With priming, an actively maintained and refreshed signal can last almost indefinitely.
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology
Authors: Wittwer Lucas D , Piližota Ivana , Altenhoff Adrian M , Dessimoz Christophe
Published: January 2018

Orthology inference and other sequence analyses across multiple genomes typically start by performing exhaustive pairwise sequence comparisons, a process referred to as “all-against-all”. As this process scales quadratically in terms of the number of sequences analysed, this step can become a bottleneck, thus limiting the number of genomes that can be simultaneously analysed. Here, we explored ways of speeding-up the all-against-all step while maintaining its sensitivity. By exploiting the transitivity of homology and, crucially, ensuring that homology is defined in terms of consistent protein subsequences, our proof-of-concept decreased the time complexity by ~75% while recovering >99.6% of all homologs identified by the full all-against-all procedure on empirical sequences from bacteria and fungi. In comparison, state-of-the-art k-mer approaches are orders of magnitude faster but only recover 3-14% of all homologous pairs. We also outline ideas to further improve the speed and recall of the new approach. An open source implementation is provided as part of the OMA standalone software at http://omabrowser.org/standalone .
Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origin
Authors: Evangelista Dennis , Cam Sharlene , Huynh Tony , Kwong Austin , Mehrabani Homayun , Tse Kyle , Dudley Robert
Published: January 2018

The capacity for aerial maneuvering was likely a major influence on the evolution of flying animals. Here we evaluate consequences of paravian morphology for aerial performance by quantifying static stability and control effectiveness of physical models for numerous taxa sampled from within the lineage leading to birds (Paraves). Results of aerodynamic testing are mapped phylogenetically to examine how maneuvering characteristics correlate with tail shortening, fore- and hind-wing elaboration, and other morphological features. In the evolution of Paraves we observe shifts from static stability to inherently unstable aerial platforms; control effectiveness also migrated from tails to the forewings. These shifts suggest that some degree of aerodynamic control and and capacity for maneuvering preceded the evolution of strong power stroke. The timing of shifts also suggests features normally considered in light of development of a power stroke may play important roles in control.