bluuebunny/crossref_metadata_2025 huggingface dataset:
Bio-inspired design of ice-retardant devices based on benthic marine invertebrates: the effect of surface texture
Authors: Mehrabani Homayun , Ray Neil , Tse Kyle , Evangelista Dennis
Published: January 2018

Growth of ice on surfaces poses a challenge for both organisms and for devices that come into contact with liquids below the freezing point. Resistance of some organisms to ice formation and growth, either in subtidal environments (e.g. Antarctic anchor ice), or in environments with moisture and cold air (e.g. plants, intertidal) begs examination of how this is accomplished. Several factors may be important in promoting or mitigating ice formation. As a start, here we examine the effect of surface texture alone. We tested four candidate surfaces, inspired by hard-shelled marine invertebrates and constructed using a three-dimensional printing process. We screened biological and artificial samples for ice formation and accretion in submerged conditions using previous methods, and developed a new test to examine ice formation from surface droplets as might be encountered in environments with moist, cold air. It appears surface texture plays only a small role in delaying the onset of ice formation: a stripe feature (corresponding to patterning found on valves of blue mussels, Mytilus edulis, or on the spines of the Antarctic sea urchin Sterechinus neumayeri) slowed ice formation an average of 25% compared to a grid feature (corresponding to patterning found on sub-polar butterclams, Saxidomas nuttali). The geometric dimensions of the features have only a small (~6%) effect on ice formation. Surface texture affects ice formation, but does not explain by itself the large variation in ice formation and species-specific ice resistance observed in other work. This suggests future examination of other factors, such as material elastic properties and surface coatings, and their interaction with surface pattern.
A survey of dinosaur diversity by clade, age, place of discovery and year of description
Authors: Taylor Michael P
Published: January 2018

Dinosaur diversity is analyzed in terms of the number of valid genera within each major clade, Mesozoic age, place of discovery and year of description. Aves (Archaeopteryx + Neornithes) is excluded. Nomina nuda and nomina dubia are not counted. The results show 451 valid dinosaurian genera at the end of 2001, of which 282 are saurischian (112 sauropodomorphs and 170 theropods, including 93 coelurosaurs) and 169 ornithischian, including 11 pachycephalosaurs, 26 ceratopsians, 60 ornithopods, 12 stegosaurs, and 38 ankylosaurs. Thirty-eight genera arose in the Triassic, 124 in the Jurassic, and 289 in the Cretaceous, of which a disproportionately high number — 85 and 47 — are from the Campanian and Maastrichtian. The Kimmeridgian was the most productive age, with an average of 11.18 new genera per million years. The Kimmeridgian saw an unparalleled boom in sauropod diversity, with 20 new sauropod genera arising in its 3.4 million years, an average of one new sauropod every 170,000 years. Asia was the most productive continent with 149 genera, followed by North America (135), Europe (66), South America (52), Africa (39), Australasia (9), and finally Antarctica (1). Just three countries account for more than half of all dinosaur diversity, with 231 genera between them: the U.S.A (105), China (73), and Mongolia (53). The top six countries also include Argentina (44), England (30), and Canada (30), and together provide 335 dinosaur genera, nearly three quarters of the total. The rate of naming new dinosaurs has increased hugely in recent years, with more genera named in the last 19 years than in all the preceding 159 years. The results of these analyses must be interpreted with care, as diversity in ancient ecosystems is perceived through a series of preservational and human filters yielding observed diversity patterns that may be very different from the actual diversity.
Error correction and diversity analysis of population mixtures determined by NGS
Authors: Wood Graham R , Burroughs Nigel , Evans David J , Ryabov Eugene V
Published: January 2018

The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees; the methods are illustrated using honeybee viral samples. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed. Second, a package of methods for assessment of nucleotide diversity is assembled. A statistically based error correction method is presented, which works at the level of the nucleotide distribution rather than the level of individual nucleotides. The method relies on an error model and a sample of known viral genotypes that is used for model calibration. A compendium of existing and new diversity analysis tools is also presented, allowing hypotheses about diversity and mean diversity to be tested and associated confidence intervals to be calculated. Software in both Excel and Matlab and a guide are available at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/, the Warwick University Systems Biology Centre software download site.
Journal title abbreviations should be eliminated in the digital age
Authors: Bond Alexander L , Green Jessica R
Published: January 2018

Journal title abbreviations in articles’ lists of citations are troublesome for authors, editors, librarians, and researchers. While the origin of these abbreviations in the mid-17th century, and their propagation to modern times was likely the result of a desire to save space in articles, or as shorthand, we argue that in the digital age, such practices should be changed. We show that a journal’s choice to abbreviate journal titles in its literature cited section is purely arbitrary, and that the costs of abbreviating outweigh the benefits. Scientific journals in particular are prone to abbreviate journal titles, and this could hamper interdisciplinary research by creating an “in-group” mentality, however small.
Genetic reprogramming of human amniotic cells with episomal vectors: Neural rosettes as sentinels in candidate selection for validation assays
Authors: Wilson Patricia G , Payne Tiffany
Published: January 2018

The promise of genetic reprogramming has prompted initiatives to develop banks of induced pluripotent stem cells (iPSCs) from diverse sources. Sentinel assays for pluripotency could maximize available resources for generating iPSCs. Neural rosettes represent a primitive neural tissue that is unique to differentiating PSCs and commonly used to identify derivative neural/stem progenitors. Here, neural rosettes were used as a sentinel assay for pluripotency in selection of candidates to advance to validation assays. Candidate iPSCs were generated from independent populations of amniotic cells with episomal vectors. Phase imaging of living back up cultures showed neural rosettes in 2 of the 5 candidate populations. Rosettes were immunopositive for the Sox1, Sox2, Pax6 and Pax7 transcription factors that govern neural development in the earliest stage of development and for the Isl1/2 and Otx2 transcription factors that are expressed in the dorsal and ventral domains, respectively, of the neural tube in vivo. Dissociation of rosettes produced cultures of differentiation competent neural/stem progenitors that generated immature neurons that were immunopositive for Beta III-tubulin and glia that were immunopositive for GFAP. Subsequent validation assays of selected candidates showed induced expression of endogenous pluripotency genes, epigenetic modification of chromatin and formation of teratomas in immunodeficient mice that contained derivatives of the 3 embryonic germ layers. Validated lines were vector-free and maintained a normal karyotype for more than 60 passages. The credibility of rosette assembly as a sentinel assay for PSCs is supported by coordinate loss of nuclear-localized pluripotency factors Oct4 and Nanog in neural rosettes that emerge spontaneously in cultures of self-renewing validated lines. Taken together, these findings demonstrate value in neural rosettes as sentinels for pluripotency and selection of promising candidates for advance to validation assays.
Swabs to Genomes: A Comprehensive Workflow
Authors: Dunitz Madison I , Lang Jenna M , Jospin Guillaume , Darling Aaron E , Eisen Jonathan A , Coil David A
Published: January 2018

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
Exploring the knowledge and attitudes of Pakistani university students towards mental illnesses
Authors: Waqas Ahmed , Zubair Muhammad , Ghulam Hamza , Wajih ullah Muhammad , Tariq Zubair , Arshad Muhammad , Shabbir Muhammad Asim , Sarfaraz Ayeshah
Published: January 2018

Background: The objectives of the study were to explore the knowledge and attitudes of Pakistani university students toward mental illnesses. People with mental illnesses are challenged not only by their symptoms but also by the prejudices associated with their illness. Acknowledging the stigma of mental illness should be the first essential step toward devising an appropriate treatment plan.

Methods: A cross-sectional survey was conducted at the University of Punjab, Lahore, CMH Lahore Medical and Dental College, Lahore, and University of Sargodha, Sub-campus Lahore, from February to May, 2014. The self-administered questionnaire consisted of three sections: demographics, general knowledge of psychiatric illnesses, and a modified form of the Community Attitudes towards Mental Illnesses (CAMI) Scale. The questionnaire was distributed to 650 participants enrolled in different disciplines (Social Sciences, Medicine and Formal Sciences).

Results: Response rate was 81% (527/650 respondents). Mean age was 20.98 years. Most of the students (331, 62.8%) had an urban background and studied Social Sciences (238, 45.2%). 418 (79.3%) considered religion very important and most respondents considered psychiatrists (334, 63.4%) and spiritual leaders (72, 13.7%) to be best able to treat mental illnesses. 169 (32.1%) considered black magic to be a cause of mental illness. Only 215 (41%) had ever read an article on mental illnesses. Multiple regression analysis revealed study discipline, exposure, perceived causes of mental illnesses and superstitions to be significantly associated with attitudes towards mental illnesses (p < .05).

Conclusion: Although low awareness and exposure were found in this sample of Pakistani university students, their attitude towards mental illnesses was generally positive. Most respondents gave supernatural explanations for mental illnesses but only a few believed that spiritual leaders can play a role in treatment.
Design considerations when adopting the OpenEdx MOOC platform in campus-based courses: A comparative case study
Authors: Zary Laila , Hernwall Patrik
Published: January 2018

Massive Open Online Courses (MOOCs) are an innovation in higher education (Grajek, 2014). Faculty has challenges in designing MOOCs since most have mainly experience in developing campus-based courses. As MOOC platform are introduced in campus-based courses, it is important to investigate how this learning environment impacts on the design of MOOCs in relation to online environments. The aim of this study was therefore to investigate the influence of variations in the learning environment on the design of MOOCs.

A comparative case study approach was chosen to investigate two types of learning environments. The focus was on the similarities, differences and trends. The data collection was performed using semi-structured interviews. The answers were analyzed using a qualitative content analysis.

The pedagogical approach and learning content were the components that were mostly influenced. The targeted learners and the assessment of the learning activities were partly influenced. The learning environment didn’t impact on the course description, intended learning outcomes and aimed competencies.

The study contributed to knowledge on the influence of the learning environment on the design of MOOCs. Increasing understanding of the learning environment among faculty will contribute to a better design, implementation and evaluation of MOOCs and ultimately for the students’ benefit.
Investigation of the relationship between the PGI enzyme system and scarabs fitness response to temperature as a measure of environmental tolerance in invasive species
Authors: Lefort Marie-Caroline , Brown Samuel D. J. , Boyer Stéphane , Worner Susan SP , Armstrong Karen
Published: January 2018

In the field of invasion ecology, the determination of a species environmental tolerance, is a key parameter in the prediction of its potential distribution, particularly in the context of global warming. In poikilothermic species such as insects, temperature is often considered the most important abiotic factor that affects numerous life-history and fitness traits through its effect on metabolic rate. Therefore the response of an insect to challenging temperatures may provide key information as to its climatic and therefore spatial distribution. Variation in the phosphoglucose-6-isomerase (PGI) metabolic enzyme-system has been proposed in some insects to underlie their relative fitness, and is recognised as a key enzyme in their thermal adaptation. However, in this context it has not been considered as a potential mechanism contributing to a species invasive cability. The present study aimed to compare the thermal tolerance of an invasive scarab, Costelytra zealandica (White) with that of the closely related, and in part sympatrically occurring, congeneric non-invasive species C. brunneum (Broun), and to consider whether any correlation with particular PGI phenotypes was apparent. Third instar larvae of each species were exposed to one of three different temperatures (10, 15 and 20°C) over six weeks and their fitness (survival and growth rate) measured and PGI phenotyping performed via cellulose acetate electrophoresis. No relationship between PGI phenotypes and fitness was detected, suggesting that the PGI may not be contributing to the invasion success and pest status of C. zealandica.
Additive global cerebral blood flow normalization in arterial spin labeling perfusion imaging
Authors: Stewart Stephanie B , Koller Jonathan M , Campbell Meghan C , Perlmutter Joel S , Black Kevin J
Published: January 2018

To determine how different methods of normalizing for global cerebral blood flow (gCBF) affect image quality and sensitivity to cortical activation, pulsed arterial spin labeling (pASL) scans obtained during a visual task were normalized by either additive or multiplicative normalization of modal gCBF. Normalization by either method increased the statistical significance of cortical activation by a visual stimulus. However, image quality was superior with additive normalization, whether judged by intensity histograms or by reduced variability within gray and white matter.
An experimental test of a Bayesian method for inferring extinction with varying search efforts
Authors: Clements Christopher , Lee Tamsin , McCarthy Micheal A
Published: January 2018

Determining whether a species is extinct or extant is notoriously difficult, but is fundamental to both our understanding of biodiversity loss, and our ability to implement effective conservation measures. Many methods have been proposed in an attempt to infer quantitatively whether a species has gone extinct, with many seeking to do so by using sets of historic sighting events. Until recently, however, no methods have been proposed that explicitly take into account search effort (the proportion of a habitat searched when looking for a species), a key determinant of if/when historic sighting events have occurred. Here we present the first test of a recently proposed Bayesian approach for inferring the extinction status of a species from a set of historic sighting events where the search effort that has produced the sightings can be explicitly included in the calculation. We utilize data from a highly tractable experimental system, as well as simulated data, to test whether the method is robust to changing search efforts, and different levels of detectability of a species. We find that, whilst in general the method performs well, it is susceptible to both changes in search effort through time, as well as how detectable a species is. In addition, we show that the value of the prior expectation that the species is extant has a large impact on the accuracy of the methods, and that selecting correct priors is critical for accurate inference of extinction status.
A genetic manipulation of motor neuron excitability does not alter locomotor output in Drosophila larvae
Authors: McKiernan Erin C.
Published: January 2018

Are motor neurons just passive relayers of the signals they receive? Or, do motor neurons shape the signals before passing them on to the muscles, thereby influencing the timing of motor behavior? Few direct tests of the role of motor neuron intrinsic properties in shaping motor behavior have been carried out, and many questions remain about the role of specific ion channel genes in motor neuron function. In this study, two potassium channel transgenes were expressed in Drosophila larval motor neurons to increase their excitability. Mosaic animals were created in which some identified motor neurons expressed the transgenes while others did not. Motor output underlying crawling was compared in muscles innervated by control and experimental neurons in the same animals. Counterintuitively, no effect of the transgenic manipulation on motor output was seen. Future experiments are outlined to determine how the larval nervous system produces normal motor output in the face of altered motor neuron excitability.
Differences in healthcare expenditures for inflammatory bowel disease by insurance status, income, and clinical care setting
Authors: Park Michelle , Bhattacharya Jay , Park KT
Published: January 2018

Background: Socioeconomic factors and insurance status have not been correlated with differential use of healthcare services in inflammatory bowel disease (IBD). Aim: To describe IBD-related expenditures based on insurance and household income with the use of inpatient, outpatient, emergency, and office-based services, and prescribed medications in the United States (US). Methods: We evaluated the Medical Expenditure Panel Survey from 1996 to 2011 of individuals with Crohn’s disease (CD) or ulcerative colitis (UC). Nationally weighted means, proportions, and multivariate regression models examined the relationships between income and insurance status with expenditures. Results: Annual per capita mean expenditures for CD, UC, and all IBD were $10,364 (N=238), $7,827 (N=95), and $9,528, respectively, significantly higher than non-IBD ($4,314, N=276,372, p<0.05). Publicly insured patients incurred the highest costs ($18,067), over privately insured ($8,014, p<0.05) or uninsured patients ($5,129, p<0.05). Among all IBD patients, inpatient care composed the highest proportion of costs ($3,392, p<0.05). Inpatient costs were disproportionately higher for publicly insured patients. Public insurance had higher odds of total costs than private (OR 2.13, CI 1.08-4.19) or no insurance (OR 4.94, CI 1.26-19.47), with increased odds for inpatient and emergency care. Private insurance had higher costs associated with outpatient care, office-based care, and prescribed medicines. Low-income patients had lower costs associated with outpatient (OR 0.38, CI 0.15-0.95) and office-based care (OR 0.21, CI 0.07-0.62). Conclusions: In the US, high inpatient utilization among publicly insured patients is a previously unrecognized driver of high IBD costs. Bridging this health services gap between SES strata for acute care services may curtail direct IBD-related costs.
The simplest mathematical model of consciousness
Authors: Wallace Rodrick
Published: January 2018

Adaptation of the Arrhenius relation to cognitive process explains how an order of magnitude difference in the rate of metabolic free energy metabolism for neural tissues translates into many orders of magnitude increase in the rate of assembling sets of cognitive submodules into the temporary, tunable, 'global workspace' coalitions of consciousness, much faster than such closely analogous processes as wound healing, immune response, and gene expression. The model strongly contradicts Tononi's 'panpsychic' integrated information treatment of consciousness.
Long-term effects of the antibacterial agent triclosan on marine periphyton communities
Authors: Eriksson Martin , Johansson Henrik , Fihlman Viktor , Grehn Alexander , Sanli Kemal , Andersson Mats X , Blanck Hans , Arrhenius Åsa , Sircar Triranta , Backhaus Thomas
Published: January 2018

Triclosan (TCS) is a widely used antibacterial agent that has become a ubiquitous contaminant in freshwater, estuary and marine environments. Concerns for potential adverse effects of TCS have been described in several recent risk assessments. Effects on freshwater microbial communities have been quite well studied but studies addressing effects on marine microbial communities are scarce. Here we describe short- and long-term effects of TCS on marine periphyton (microbial biofilm) communities. Short-term effects on photosynthesis were estimated after 60 – 210 minutes exposure. Long-term effects on photosynthesis, chlorophyll fluorescence, pigment content, community tolerance and bacterial carbon utilization were studied after exposing periphyton for 17 days in flow-through microcosms to 0.316 - 10 000 nM TCS. Results from the short-term studies show that TCS is toxic to periphyton photosynthesis. EC50 values of 1080 and 3000 nM were estimated using 14CO2-incorporation and Pulse Amplitude Modulation (PAM), respectively. After long-term TCS exposure in flow-through microcosms photosynthesis estimated using PAM was, however, not inhibited by TCS concentrations up to 1000 nM, but instead increased with increasing TCS concentration. Similarly, the amount of photosynthetic pigments increased after an exposure of 31.6 nM TCS and higher; at 316 nM TCS the pigment amounts reached between 140 and 190% of the control level. Pollution-Induced Community Tolerance (PICT) was observed for algae and cyanobacteria at 100 nM TCS and higher. In spite of the widespread use of TCS as an antibacterial agent, the compound did not have any effects on bacterial carbon utilization after long-term exposure.
Stimulation of glucose uptake in murine soleus muscle and adipocytes by 5-(4-phenoxybutoxy)psoralen (PAP-1) may be mediated by Kv1.5 rather than Kv1.3
Authors: Ngala Robert A , Zaibi Mohamed S , Langlands Kenneth , Stocker Claire J , Arch Jonathan RS , Cawthorne Michael A
Published: January 2018

Kv1 channels are shaker-related potassium channels that influence insulin sensitivity. Kv1.3 -/- mice are protected from diet-induced insulin resistance and some studies suggest that Kv1.3 inhibitors provide similar protection. However, it is unclear whether blockade of Kv1.3 in adipocytes or skeletal muscle increases glucose uptake. There is no evidence that the related channel Kv1.5 has any influence on insulin sensitivity and its expression in adipose tissue has not been reported. PAP-1 is a selective inhibitor of Kv1.3, with 23-fold, 32-fold and 125-fold lower potencies as an inhibitor of Kv1.5, Kv1.1 and Kv1.2 respectively. Soleus muscles from wild-type and genetically obese ob/ob mice were incubated with 2-deoxy[1-14C]-glucose for 45 min and formation of 2-deoxy[1-14C]-glucose-6-phosphate was measured. White adipocytes were incubated with D-[U-14C]-glucose for 1h. TNFalpha and Il-6 secretion from white adipose tissue pieces were measured by enzyme-linked-immunoassay. In the absence of insulin, a high concentration (3 μM) of PAP-1 stimulated 2-deoxy[1-14C]-glucose uptake in soleus muscle of wild-type and obese mice by 30% and 40% respectively, and in adipocytes by 20% and 50% respectively. PAP-1 also stimulated glucose uptake by adipocytes at the lower concentration of 1 μM, but at 300 nM, which is still 150-fold higher than its EC50 value for inhibition of the Kv1.3 channel, it had no effect. In the presence of insulin, PAP-1 (3 μM) had a significant effect only in adipocytes from obese mice. PAP-1 (3 μM) reduced the secretion of TNFalpha by adipose tissue but had no effect on the secretion of IL-6. Expression of Kv1.1, Kv1.2, Kv1.3 and Kv1.5 was determined by RT-PCR. Kv1.3 and Kv1.5 mRNA were detected in liver, gastrocnemius muscle, soleus muscle and white adipose tissue from wild-type and ob/ob mice, except that Kv1.3 could not be detected in gastrocnemius muscle, nor Kv1.5 in liver, of wild-type mice. Expression of both genes was generally higher in liver and muscle of ob/ob mice compared to wild-type mice. Kv1.5 appeared to be expressed more highly than Kv1.3 in soleus muscle, adipose tissue and adipocytes of wild-type mice. Expression of Kv1.2 appeared to be similar to that of Kv1.3 in soleus muscle and adipose tissue, but Kv1.2 was undetectable in adipocytes. Kv1.1 could not be detected in soleus muscle, adipose tissue or adipocytes. We conclude that inhibition of Kv1 channels by PAP-1 stimulates glucose uptake by adipocytes and soleus muscle of wild-type and ob/ob mice, and reduces the secretion of TNFalpha by adipose tissue. However, these effects are more likely due to inhibition of Kv1.5 than to inhibition of Kv1.3 channels.
Endothelial cell-initiated extravasation of cancer cells visualized in zebrafish
Authors: Kanada Masamitsu , Zhang Jinyan , Yan Libo , Sakurai Takashi , Terakawa Susumu
Published: January 2018

The extravasation of cancer cells, a key step for distant metastasis, is thought to be initiated by disruption of the endothelial barrier by malignant cancer cells. An endothelial covering-type extravasation of cancer cells in addition to conventional cancer cell invasion-type extravasation was dynamically visualized in a zebrafish hematogenous metastasis model. The inhibition of VEGF-signaling impaired the invasion-type extravasation via inhibition of cancer cell polarization and motility regulated by an intracellular signaling. Paradoxically, the inhibition of VEGF-signaling showed the promotion, rather than the inhibition, of the endothelial covering-type extravasation of cancer cells, with structural changes in the endothelial walls. These findings may be a clue to the full understanding of the metastatic process as well as the metastatic acceleration by antiangiogenic reagents observed in preclinical studies.
Ethylene induces soil microbes to delay fruit ripening
Authors: Perry Guenevere , Williams Diane
Published: January 2018

The consumer demand for fresh fruits and vegetables increases every year, and farmers need a low cost novel method to reduce post-harvest loss and preserve the quality of fresh fruits and vegetables. This study identifies a method to induce soil bacteria to biosynthesize a nitrile compound that potentially enters the plants tissue and negatively affects climacteric ripening and delays the ripening process at 20-30˚C. This study used soil rich with soil microbes, to delay the ripening of climacteric fruit. The soil was treated with nitrogen, a heavy metal, and ethylene gas.

Ethylene induced the soil to delay the ripening of organic bananas and peaches. A prototype transportation container maintained fruit fresh for up to 72 h at 20-30˚C. The fruit retained color, firmness, texture, no bruising and minimal spotting. The soil also prevented fungal infection in all samples. GC-MS analysis suggests ethylene induced the soil microbes to release an acetonitrile compound into the gaseous environment. The nitrile is released in low concentrations, but mature plants (fruits) contain very low levels of indole-3-acetonitrile (IAN) or indole-3-acetic acid (IAA).

The nitrile may obstruct or modify the mature plants (fruit) late stages development process, thus delay the climacteric ripening process and retarding the physiological and phenotypic effects of fruit ripening. We believe this study may have strong applications for post-harvest biotechnology.
Language workbench user interfaces for data analysis
Authors: Benson Victoria M , Campagne Fabien
Published: January 2018

Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Workflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with workflows, and that do not require specialized user interfaces. However, some types of analyses can benefit from custom user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that can be expressed more succinctly with specialized user interfaces. Here, we show how Language Workbench (LW) technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that user interfaces developed in the Meta-Programming System (MPS) LW provide convenient means to configure a biomarker development project, to train models and view the validation statistics. We discuss several advantages of developing user interfaces for data analysis with a LW, including increased interface consistency, portability and extension by language composition. The language developed during this experiment is distributed as an MPS plugin (available at http://campagnelab.org/software/bdval-for-mps/
Hot spots and labyrinths: Why neuromodulation devices for episodic migraine should be personalized
Authors: Dahlem Markus A , Schmidt Bernd , Bojak Ingo , Boie Sebastian , Kneer Frederike , Hadjikhani Nouchine , Kurths Jürgen
Published: January 2018

Stimulation protocols for medical devices should be rationally designed. For episodic migraine with aura we outline model-based design strategies towards preventive and acute therapies using stereotactic neuromodulation. To this end, we regard a localized spreading depression (SD) wave segment as a central element in migraine pathophysiology. To describe nucleation and propagation features of the SD wave segment, we define the new concepts of cortical hot spots and labyrinths, respectively. In particular, we firstly focus exclusively on curvature-induced dynamical properties by studying a generic reaction-diffusion model of SD on the folded cortical surface. This surface is described with increasing level of details, including finally personalized simulations using patient's magnetic resonance imaging (MRI) scanner readings. At this stage, the only relevant factor that can modulate nucleation and propagation paths is the Gaussian curvature, which has the advantage of being rather readily accessible by MRI. We conclude with discussing further anatomical factors, such as areal, laminar, and cellular heterogeneity, that in addition to and in relation to Gaussian curvature determine the generalized concept of cortical hot spots and labyrinths as target structures for neuromodulation.Our numerical simulations suggest that these target structures are like fingerprints, they are individual features of each migraine sufferer. The goal in the future will be to provide individualized neural tissue simulations. These simulations should predict the clinical data and therefore can also serve as a test bed for exploring stereotactic neuromodulation.
Effects of five southern California macroalgal diets on consumption, growth, and gonad weight, in the purple sea urchin Strongylocentrotus purpuratus
Authors: Foster Matthew C , Byrnes Jarrett E , Reed Daniel C
Published: January 2018

Consumer growth and reproductive capacity are direct functions of diet. Strongylocentrotid sea urchins, the dominant herbivores in California kelp forests, strongly prefer giant kelp (Macrocystis pyrifera), but are highly catholic in their ability to consume other species. The biomass of Macrocystis fluctuates greatly in space and time and the extent to which urchins can use alternate species of algae or a mixed diet of multiple algal species to maintain fitness when giant kelp is unavailable is unknown. We experimentally examined the effects of single and mixed species diets on consumption, growth and gonad weight in the purple sea urchin Strongylocentrotus purpuratus. Urchins were fed single species diets consisting of one of four common species of macroalgae (the kelps Macrocystis pyrifera and Pterygophora californica, and the red algae Chondracanthus corymbiferus and Rhodymenia californica (hereafter referred to by genus) or a mixed diet containing all four species ad libitum over a 13-week period in a controlled laboratory setting. Urchins fed Chondracanthus, Macrocystis and a mixed diet showed the highest growth (in terms of test diameter, wet weight and jaw length) and gonad weight while urchins fed Pterygophora and Rhodymenia showed the lowest. Urchins consumed their preferred food, Macrocystis at the highest rate when offered a mixture, but consumed Chondracanthus or Macrocystis at similar rates when the two algae were offered alone. The differences in urchin feeding behavior and growth observed between these diet types suggest the relative availability of the algae tested here could affect urchin populations and their interactions with the algal assemblage. The fact that the performance of urchins fed Chondracanthus was similar or higher than those fed the preferred Macrocystis suggests purple sea urchins could sustain growth and reproduction during times of low Macrocystis abundance as is common following large wave events.
Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions
Authors: Barraquand Frédéric , Ezard Thomas H G , Joergensen Peter S , Zimmerman Naupaka , Chamberlain Scott A , Salguero-Gómez Roberto , Curran Timothy J , Poisot Timothée
Published: January 2018

Proficiency in mathematics and statistics is essential to modern ecological science, yet few studies have assessed the level of quantitative training received by ecologists. To do so, we conducted an online survey. The 937 respondents were mostly early-career scientists that studied biology as undergraduates. We found a clear self-perceived lack of quantitative training: 75% are not satisfied with their understanding of mathematical models; 75% feel the level of mathematics was “too low” in their ecology classes; 90% wanted more mathematics classes for ecologists; and 95% more statistics classes. Respondents thought that 30% of classes in ecology-related degrees should be focused on quantitative disciplines; likely more than what is taught in most universities. The main suggestion to improve quantitative training was to relate theoretical and statistical modeling to applied ecological problems. Improving quantitative training will require more mathematics classes for ecology-related degrees, and also more ecology classes containing mathematical and statistical examples.
Multitrophic functional diversity predicts ecosystem functioning in experimental assemblages of estuarine consumers
Authors: Lefcheck Jonathan S , Duffy J. Emmett
Published: January 2018

The use of functional traits to explain how biodiversity affects ecosystem functioning has attracted intense interest, yet few studies have a priori manipulated functional diversity, especially in multitrophic communities. Here, we manipulated multivariate functional diversity of estuarine grazers and predators within two levels of species richness to test how species richness and functional diversity predicted ecosystem functioning in a multitrophic food web. Community functional diversity was a better predictor than species richness for the majority of ecosystem properties, based on general linear mixed effects models. Combining inferences from 8 traits into a single multivariate index increased prediction accuracy of these properties relative to any individual trait. Structural equation modeling revealed that functional diversity of both grazers and predators was important in driving final biomass within and between trophic levels, with stronger effects observed for predators. We also show that different species drove different ecosystem responses, with evidence for both sampling effects and complementarity. Our study extends experimental investigations of functional trait diversity to a multilevel food web, and demonstrates that functional diversity can be more accurate and effective than species richness in predicting community biomass in a food web context.
Ethylene induced soil microbes to increase seed germination, reduce growth time, and improve crop yield in Pisum sativum L.
Authors: Perry Guenevere
Published: January 2018

The main scope of this project was to identify a novel induction method to improve the effectiveness of biological fertilizers for organic farmers. To eliminate additional variables the plants were not treated with chemical or biological pesticides. The biological fertilizer used in this study was induced with co-factors and ethylene under specific conditions. Ethylene induced the soil to release acetonitrile, a component of indole-3-acetonitrile a precursor to the plant hormone indole-3-acetic acid (IAA). It is known that plant growth promoting bacteria can produce IAA and directly/ indirectly modify plant development and growth.

In this preliminary study, the ethylene induced biological fertilizer (EIBF) improved germination rate, enhanced quality, reduced growth time, and improved crop yield of Pisum sativum L (green peas) with a single application. Many biological fertilizer require two to three applications a year to see improved growth.Green peas grown in ethylene induced soil improved pea quantity by 200% per plant compared to control samples. EIBF increased the crop yield by over 57%. The average biological fertilizer only improves crop by 20-30%. The peas harvested from the plants grown in EIBF were 4 times larger peas collected from plants grown in the control soil. The improvement and continued study of EBIF may have a global applications, impacting farming techniques in poor developing countries or organic farms.
A transgenic mouse model ubiquitously overexpressing Dnmt1s mRNA lacks increased protein levels
Authors: Grosser Christian , Vassen Lothar , Horsthemke Bernhard , Wagner Nicholas
Published: January 2018

Several types of cancer are characterized by global hypomethylation accompanied by regional hypermethylation and overexpression of DNA methyltransferase (cytosine-5) 1 (Dnmt1). In addition to the established role of Dnmt1 as maintenance methyltransferase, it has been suggested that Dnmt1 might also methylate certain target sites de novo. We created a transgenic mouse model to investigate whether the overexpression of the somatic form of Dnmt1, Dnmt1s, is sufficient to cause erroneous methylation and disease. Because ubiquitous Dnmt1 overexpression has been reported to be embryonic lethal, we designed a CAG promoter-driven Cre-loxP conditional transgene containing a floxed EGFP sequence followed by the Dnmt1s coding sequence. The EGFP sequence is excised and transgenic Dnmt1s expression is activated at specific time points or in specific tissues depending on the Cre deleter strain used for cross-ins. Pronucleus injections with the Dnmt1s transgene construct resulted in six founder lines as verified by PCR, Southern blot and EGFP fluorescence. We performed cross-ins with a CMV-Cre deleter strain to clarify if ubiquitous overexpression of Dnmt1s alone causes the previously observed embryonic lethality. Unexpectedly, these cross-ins yielded viable recombined offspring that ubiquitously overexpressed Dnmt1 mRNA at tissue-dependent levels of up to 229-fold. However, the recombined offspring did not significantly overexpress Dnmt1 protein and showed no apparent signs of disease or pathological phenotype. Here, we describe the establishment of our Dnmt1s-transgenic mouse model and propose possibilities for the absence of transgenic protein.
Systematic review of the statistical scope used in studies based on skeletal muscle autophagy and exercise
Authors: Brownlee Diane
Published: January 2018

Skeletal muscle reaction to exercise is an essential are of research due to its ongoing prevalence in disease research and general health. It is well documented that under exercise conditions, biogenesis and autophagy increase. One main component of this pathway are lysosomes, the essential cellular clearance machine. Statistical analyses used to analyze these data have been sustained over the years. The objective of this systematic review is to compare and contrast the different methods used for analyzing data in molecular exercise physiology. Upon investigating the research papers the majority of the papers used either a t-test or an ANOVA as their primary statistical analyses, used 41% and 64% of the time, respectively. All other statistical tests were used a maximum of 9% of the time. Another trend that was evident was the increased utilization of post hoc tests in the more recent papers compared to earlier papers. This could provide interesting evidence into the credibility of the results reported and provide more insight into the research in molecular exercise physiology.
The season for peace: reconciliation in a despotic species (Lemur catta)
Authors: Palagi Elisabetta , Norscia Ivan
Published: January 2018

However despotic a social group may be, managing conflicts of interest is crucial to preserve group living benefits, mainly based on cooperation. In fact, in despotic groups post-conflict management via reconciliation (the first post-conflict reunion between former opponents) can occur, even if at variable levels. In the despotic Lemur catta reconciliation was reported in one out of four captive groups. We used this species as a model to understand what variables influence the occurrence of the reconciliation in despotic groups. We analyzed 2339 PC-MC collected on eight groups (five in the Berenty forest, Madagascar; three hosted at the Pistoia Zoo, Italy). Since Lemur catta is characterized by rigid female dominance but show female-female coalitionary support, we expected to find reconciliation in the wild, other than in captivity. Consistently, we found the phenomenon to be present in one captive group and two wild groups, thus providing the first evidence of the presence of reconciliation in wild Lemur catta. Being this species a seasonal breeder (with mating occurring once a year), we expected that the season more than other variables (wild/captivity setting, rank, or individual features) would influence reconciliation levels. Via GLMM we found that the season was indeed the only variable significantly explaining reconciliation rates, lowest during mating and highest during the pregnancy period. We posit that reconciliation can be present in despotic species but not when the advantages of intra-group cooperation are annihilated by competition, as it occurs in seasonal breeders when reproduction is at stake. By comparing our results with literature, we conclude that in despotic social groups in which coalitions are observed, the right question is not if but when reconciliation can be present.
Ebola virus disease outbreak in Nigeria: transmission dynamics and rapid control
Authors: Althaus Christian L , Gsteiger Sandro , Musa Emmanuel O. , Shuaib Faisal , Low Nicola
Published: January 2018

International air travel has already spread Ebola virus disease (EVD) to major cities as part of the unprecedented epidemic that started in Guinea in December 2013. An infected airline passenger arrived in Nigeria on July 20, 2014 and caused an outbreak in Lagos and then Port Harcourt. After a total of 20 reported cases, including 8 deaths, Nigeria was declared EVD free on October 20, 2014. We quantified the impact of early control measures in preventing further spread of EVD in Nigeria and calculated the risk that a single undetected case will cause a new outbreak. We fitted an EVD transmission model to data from the outbreak in Nigeria and estimated the basic reproduction number R0 = 9.0 (95% confidence interval [CI]: 5.2-15.6). We also found that the net reproduction number Rt fell below unity 15 days (95% CI: 11-21 days) after the arrival of the index case. Using the estimated value of R0 in Nigeria, we calculated that the risk of an outbreak from a single undetected case was 89% (95% CI: 81-94%). Even though R0 can be high, our study illustrates the time window for successful containment of EVD outbreaks caused by infected air travelers.