bluuebunny/crossref_metadata_2025 huggingface dataset:
Multivariate statistical approaches for uncovering spatio-temporal and treatment-derived differences in the molecular physiology of a model coral-dinoflagellate mutualism: a meta-analysis
Authors: Mayfield Anderson B , Chen Chii-Shiarng
Published: January 2018

Background: Multivariate statistical approaches (MSA), such as principal components analysis and multidimensional scaling, seek to uncover meaningful patterns within datasets by considering multiple response variables in a concerted fashion. Although these techniques are readily used by ecologists to visualize and explain differences between study sites, they could theoretically be employed to differentiate organisms within an experimental framework while simultaneously identifying response variables that drive documented experimental differences.

Methods: A meta-analysis employing various MSA was conducted to re-analyze data from two studies that sought to understand the response of the common, Indo-Pacific reef coral Seriatopora hystrix to temperature changes.

Results: Gene expression and physiological data partitioned experimental specimens by time of sampling, treatment temperature, and site of origin upon employing MSA.

Discussion: These findings 1) signify that S. hystrix and its dinoflagellate endosymbionts display physiological and molecular signatures that are characteristic of sampling time, site of colony origin, and/or temperature regime and 2) promote the utility of MSA for documenting biologically meaningful shifts in the physiological and/or sub-cellular response of marine invertebrates exposed to environmental change.
Integration of the MODFLOW Lak7 package in the FREEWAT GIS modelling environment
Authors: Cannata Massimiliano , Neumann Jakob , Cardoso Mirko , Rossetto Rudy , Foglia Laura , Borsi Iacopo
Published: January 2018

The MODFLOW Lake Package is integrated into the FREEWAT GIS environment in order to simulate surface water - groundwater interaction using state of the art techniques for numerical simulations, thus allowing the improved consideration of surface water bodies for water resources management. Surface water bodies, both stationary and flowing, can strongly affect groundwater elevations and flow patterns which in turn may affect the qualitative and quantitative state of groundwater resources. With the advancement of numerical simulation techniques and increased model complexity, FREEWAT facilitates the usage of the lake package through existing QGIS tools to edit model layer geometry as well as an intuitive and simple user interface for the specification of constant and time variable lake properties as defined through MODFLOW.
An Open source GIS-based tool for economic loss estimation due to flood events
Authors: Sterlacchini Simone , Zazzeri Marco , Cappellini Giacomo , Pastormerlo Michele , Bonazzi Alessandro
Published: January 2018

Two complementary GIS-based functions are designed and implemented to assess the expected degree of loss due to the occurrence of flood events. Each function processes institutional thematic layers and allows decision makers first to quantify the physical and the economic exposure of the elements at risk in a given study region and then to assess the expected degree of economic loss in relation to the flood water depth chosen for the analysis. The functions are implemented using QGIS with GRASS Python API extension and the workflow is exposed as a QGIS plug-in. The GUI is built over QT multi-platform framework and, therefore, the results are consistently integrated into the QGIS system.
First record of Bertrana striolata (Arachnida: Araneae: Araneidae) in Amazonian Ecuador
Authors: Cisneros-Heredia Diego F , Carrazco Iván
Published: January 2018

We present the first record of the orb-weaver spider Bertrana striolata from Amazonian lowlands (east of the Andes) in Ecuador, based on a specimen collected at the Tiputini Biodiversity Station, province of Orellana, Ecuador. In Ecuador, B. striolata was previously known from a single locality on the Pacific lowlands (4 km NE of the town of Pedro Vicente Maldonado, 550 m, province of Pichincha). To the best of our knowledge, this record also corresponds to the second locality of the species in the country, and the first record for the province of Orellana.
The open geohazard widget to perform environmental risk analysis
Authors: Cipolloni Carlo , Krivic Matija , Novak Matevž , Pantaloni Marco
Published: January 2018

In the framework of European project eENVplus (hhtp://www.eenvplus.eu) the Geological Survey of Italy and Geological Survey of Slovenia in collaboration with some technical partners developed a pilot to perform several geohazard analyses in the cross-border area. Several web processing services to perform hazard probability map have been developed using open-source software and a javaScript client widget based on Cesium1.11 to manage the pilot has been designed as well. The final data have been prepared in INSPIRE compliance format to be in line with European legislation and directive and data are provided with an open licence.
Natural compounds as potential PI3K-AKT1 signaling pathway inhibitors by means of pharmacophore modeling
Authors: Dotolo Serena , Gaeta Angelo , Facchiano Angelo
Published: January 2018

AKT1, a modulator of PI3K-AKT1 pathway, is dysregulated in several human diseases, and understanding deeper its role in the complexity of biological systems remains an important goal. The research has been focused on development and study of potential synthetic-natural allosteric inhibitors for AKT1, and recent studies have shown how some natural compounds may play this role (1). We are interested in a screening of small bioactive molecules, in order to identify the potential “lead compounds”, for next experimental assays, searching those potentially able to inhibit AKT1 and its signaling mechanisms, trying to re-establish the normal balance and safeguarding of human health. The workflow executed is the following: 1) search in PDB database of a model structure for AKT1 (comparing different structures and choosing the most suitable for our purposes), through algorithm BLAST. 2) pharmacophore modeling by means of ZINCpharmer web-server, to investigate all purchasable compounds of the ZINC database, using the Pharmer as efficient and exact pharmacophore search technology (2). 3) screening of possible natural AKT1 inhibitors, using the pharmacophore generated by ZINCpharmer, choosing only the best candidates for next steps. 4) molecular validation of selected compounds, to analyze the ligand-protein interactions. 5) study of physical-chemical properties of selected compounds to trace their origin. 6)prediction of their biosynthetic pathways and Pharmacokinetics/Pharmacodynamics models, by means of ADMET/toxicity predictor server in order to direct the design of next experimental assays. Our attention is focused on the study of natural compounds that can show many health benefits, through the realization and analysis of “pharmacophore modeling”, essential step in drug discovery (3). We selected the PDB structure 3O96 as the reference complex (protein-ligand), and we analyzed it by means of ZINCpharmer, to generate three different “pharmacophore models” with three different list of natural compounds. It is performed a thorough screening of compounds applying other filters, to find some good candidates as possible natural AKT1 allosteric inhibitors. The compounds that match a well-defined pharmacophore have been analyzed through direct molecular docking, for selecting only the best candidates and studying the protein-ligand interactions. Selected compounds have been investigated in more details, to trace their origin, by their chemical-physical properties. This information can help us to predict some plausible enzyme-catalyzed reaction pathways, investigated with PathPred server and KEGG compound database, in order to highlight the most important reactions for biosynthesis of compounds and obtain PharmacoKinetics/PharmacoDynamics (PK/PD) models through ADME predictor server and to realize of next experimental assays.

(Abstract truncated at 3,000 characters - the full version is available in the pdf file)
A cellular automata to simulate the growth and death of a cell culture
Authors: Guerrisi Giuseppe , Giordano Deborah , Marabotti Anna , Raiconi Giancarlo , Tagliaferri Roberto
Published: January 2018

Motivation: The term “cell culture” is generally referred to the process by which some cells, often derived from multicellular organisms or tissues, or tumoral cell lines, are grown under controlled conditions outside of their natural environment. This system is very useful for different applications, for example to study physiological phenomena, or for the production of some useful molecules, or for testing the toxicity of some compounds. The life of the cells in culture is conditioned by many elements. Apart from physical factors such as pH and temperature, the growth of a cell culture is conditioned by its density: cells compete for the nutrients and growth factors available and die when they are exhausted. Moreover, dead cells release in the medium some toxic factors that, in their turn, can lead the surrounding cells to death. Additionally, the presence of exogenous toxic factors in the medium can induce cell death We present a cellular automata developed in order to reproduce the growth of a cell culture of a particular human cell line, Caco-2, derived from human colorectal adenocarcinoma cells. The cellular automata has been developed in order to reproduce the phenotype of Caco-2 cells, their cell cycle with all phases, and the influence of 4-nonylphenol (4-NP), an environmental pollutant, on this model system.

Methods: The cellular automata developed is a grid whose dimensions reproduce a cell counting Burker chamber. Two matrices have been used to take into account, respectively, the global duration of the cellular growth and the phase of the cell cycle for each cell. Two vectors are also introduced to take into account the length of each phase and their variability range. A shuffling algorithm is used to distribute the starting cells on the chamber, then the algorithm starts by assigning a variable lag phase before reproducing the start of the cell cycle with the entering of the cells in G1 phase. All the following phases of the cell cycle are characterized by a fixed length (in minutes) + 10% variability. The cell death is described by a logarithmic function that is influenced by different factors: culture density, cellular senescence, presence of dead cells in the environment of each cell, introduction of a toxic substance. The application was developed in a stand-alone manner and has been written in Java using the OpenGL library integrated in Java.

Results The application is made by an intuitive GUI to set several parameters useful for the simulation (see Figure, panel A). In order to highlight the different cell cycle phases, different colors were attributed to each phase. The cellular automata is evolving in the space and in the time reproducing the four steps of the cell cycle (G1, S, G2, M). The evolution of the simulated cell growth reproduces the phenomena present in a real Caco-2 cell culture. (Abstract truncated at 3,000 characters - the full version is available in the pdf file)
Inferring microevolution from museum collections and resampling: lessons learned from Cepaea
Authors: Ożgo Małgorzata , Liew Thor-Seng , Webster Nicole B , Schilthuizen Menno
Published: January 2018

Studies documenting Human-Induced Rapid Evolutionary Change (HIREC) routinely compare contemporary allele or morph frequency distributions with historical baselines. All too often, this involves the re-sampling of a population that was sampled at a single time point in the past. However, year-to-year fluctuations in magnitude and direction of evolutionary response may make such studies prone to erroneous conclusions, where long-term evolutionary trends are inferred from what in fact are short-term fluctuations. Here, we explore this problem by re-sampling three Dutch populations of the land snail Cepaea nemoralis, whose shell colour polymorphism is known to be under thermal and predatory selection. Each of these three populations was originally sampled in at least two different years in the past. We show that conclusions on evolutionary change are strongly dependent on which of the historical sample dates is used for comparison with the contemporary sample. Our study highlights the fact that year-to-year variation in allele frequencies may often be so strong that a simple two-point comparison is unreliable to detect long-term evolutionary trends.
Using touchscreens to explore the welfare and cognition of zoo-housed primates
Authors: Egelkamp Crystal L , Hopper Lydia M , Cronin Katherine A , Jacobson Sarah L , Ross Stephen R
Published: January 2018

Annually, over 180 million people visit zoos accredited by the Association of Zoos and Aquariums (AZA), giving them the chance to see a variety of primate species and to learn about their behavior and ecology. In the past decade, some zoos have also become increasingly involved in conducting high-quality cognitive research that not only contributes to the academic literature, but also increases our knowledge of captive primate care. Using technology such as touchscreen computers, scientists are able to explore a range of primate cognitive abilities through different types of computer tasks. In 2004, Lincoln Park Zoo scientists began a comparative touchscreen research program with resident Western-lowland gorillas (Gorilla gorilla gorilla) and chimpanzees (Pan troglodytes). In 2015, this research program was expanded to include Japanese macaques (Macaca fuscata). This applied and comparative research is exploring several facets of primate cognition: serial learning, prosociality, affective states, and individual preferences. The purpose of this research is threefold: to learn more about primates’ cognitive abilities; to develop new ways to assess and positively impact primate welfare; and to facilitate public engagement with science. Both the macaque and ape facilities at Lincoln Park Zoo were designed specifically to accommodate touchscreen research that could be conducted in view of zoo guests while the primates remain in their social group during voluntary testing sessions. The cognitive research demonstrations are interpreted by zoo educators every weekday, where guests can observe the primates working on the touchscreens, and ask questions about the research. This zoo-based cognitive research program offers benefits to scientists, zoo visitors as well as to the animals themselves, as the research strives to improve the care and management of program participants.
Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank
Authors: Brown Tanya , Otero Christopher , Grajales Alejandro , Rodriguez Estefania , Rodriguez-Lanetty Mauricio
Published: January 2018

Examination of host-microbe interactions in basal metazoans, such as cnidarians is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1-V4 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. These results contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. Instead, our findings suggest that environmental settings, not host specificity seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.
Landsat Satellite Observations and Crowd-Sourced Data Provide Near Real-Time Monitoring of Chimpanzee Habitat
Authors: Pintea Lilian , Jantz Samuel Martin , Nackoney Janet Ruth , Hansen Matthew C
Published: January 2018

The endangered chimpanzee (Pan troglodytes) is threatened by habitat loss from resource extraction and land conversion, as well as illegal bushmeat hunting and disease. It has been estimated that more than 70% of chimpanzee's tropical forest habitats in Africa are now threatened by human-induced land use change. Recent developments in remote sensing and cloud computing enable the use of satellite observations to provide a synoptic view of chimpanzee habitats at finer spatial and temporal resolutions that are locally relevant and consistent across the entire species’ range. We present a practical Decision Support System to be used by the Jane Goodall Institute and partners to annually monitor and forecast chimpanzee habitat health in Africa. The system integrates Earth observations from 30-meter resolution Landsat data with a species-specific habitat model and a model forecasting future land use change, enhanced by crowd-sourced field data collected by local communities and rangers using the Open Data Kit app and Android mobile smartphones and tablets. Current habitat health status of the chimpanzee in Africa between 2000 and 2014 and future habitat health until 2030 will be presented and discussed. While coarser-scale and static chimpanzee habitat models have been previously developed, this project is the first to develop a dynamic monitoring system updated annually via Earth observations data that will systematically monitor threats and changes in habitat over time.
The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets
Authors: Li Zi , He Wenqi , Lan Yungang , Zhao Kui , Lv Xiaoling , Lu Huijun , Ding Ning , Zhang Jing , Shi Junchao , Shan Changjian , Gao Feng
Published: January 2018

An acute outbreak of porcine hemagglutinating encephalomyelitis virus (PHEV) infection in piglets, characterized with neurological symptoms, vomiting, diarrhea, and wasting, occurred in China. Coronavirus-like particles were observed in the homogenized tissue suspensions of the brain of dead piglets by electron microscopy, and a wild PHEV strain was isolated, characterized, and designated as PHEV-CC14. Histopathologic examinations of the dead piglets showed characteristics of non-suppurative encephalitis, and some neurons in the cerebral cortex were degenerated and necrotic, and neuronophagia. Similarly, mice inoculated with PHEV-CC14 were found to have central nervous system (CNS) dysfunction, with symptoms of depression, arched waists, standing and vellicating front claws. Furthmore, PHEV-positive labeling of neurons in cortices of dead piglets and infected mice supported the viral infections of the nervous system. Then, the major structural genes of PHEV-CC14 were sequenced and phylogenetically analyzed, and the strain shared 95%-99.2% nt identity with the other PHEV strains available in GenBank. Phylogenetic analysis clearly proved that the wild strain clustered into a subclass with a HEV-JT06 strain. These findings suggested that the virus had a strong tropism for CNS, in this way, inducing nonsuppurative encephalitis as the cause of death in piglets. Simultaneously, the predicted risk of widespread transmission showed a certain variation among the PHEV strains currently circulating around the world. Above all, the information presented in this study can not only provide good reference for the experimental diagnosis of PHEV infection for pig breeding, but also promote its new effective vaccine development.
Fear of predators as an ecosystem service
Authors: Zanette Liana Y , Clinchy Michael
Published: January 2018

The fear that predators instill in prey induces short-term anti-predator behaviours across every animal taxa that are beneficial in avoiding immediate death, but carry costs; one of the most well-established being that scared prey eat less. These findings, that animals stop eating to avoid being eaten under perceived predation risk, are not controversial. What is controversial is whether such fear effects can be long-term and powerful enough to affect wildlife prey populations and generate trophic cascades. For example, some have suggested that the restoration of wolves to Yellowstone National Park also restored the fear of predators, reducing elk foraging and in turn the pregnancy rate, contributing to rapidly declining elk numbers. Other Yellowstone researchers have suggested that the restoration of fear has generated a trophic cascade whereby scared elk eat less, increasing the food that elk eat. The prospect that fear can help restore populations and ecosystems has critical management implications, but to implement a management plan fear effects must be quantified. Indeed, the enormous amount of often acrimonious debate centred on whether fear can affect populations and ecosystems lingers in both the scientific and public policy domains because studies have largely been based on natural experiments. Manipulations that establish whether fear effects actually do exist for wildlife can help resolve management debates, and are critical for conservation and management on a global scale because the status of large carnivores world-wide is quite dismal with 77 % of species in decline. Public policy would also benefit because if restoring large carnivores also restores fear such that degraded ecosystems can become healthy again, then this has real implications for human lives and livelihoods. We present research from our lab and others, in which perceived predation risk has been experimentally manipulated in free-living wildlife. The results to date definitively demonstrate that fear effects do exist. Fear alters prey foraging behaviour, and fearful prey in turn produce 50 % fewer offspring; fear permanently impairs the reproduction of surviving offspring; and restoring the fear of large carnivores generates cascading effects down at least four tiers in the food chain. Given the enormous effects that fear has in nature, we elaborate on how manipulating fear using sound can be a particularly useful management tool for diagnosing and treating environmental ills. We describe a new system we have designed (Automated Behavioural Response systems-ABRs) that allows any researcher working on any wildlife species to conduct manipulations that quantify fear effects. We conclude that fear has its uses. Fear is good for the environment and as such, management may sometimes need to inject fear artificially for short-term goals (e.g. crop protection) but in many cases, the best and cheapest long-term solution might be to restore native predators where lost.
Exploration of immunoglobulin transcriptomes from mice immunized with three-finger toxins and phospholipases A2 from the Central American coral snake, Micrurus nigrocinctus
Authors: Laustsen Andreas H , Engmark Mikael , Clouser Christopher , Timberlake Sonia , Vigneault Francois , Gutiérrez José María , Lomonte Bruno
Published: January 2018

Snakebite envenomings represent a neglected public health issue in many parts of the rural tropical world. Animal-derived antivenoms have existed for more than a hundred years and are effective in neutralizing snake venom toxins when timely administered. However, the low immunogenicity of many small but potent snake venom toxins represents a challenge for obtaining a balanced immune response against the medically relevant components of the venom. Here, we employ next generation sequencing of the immunoglobulin (Ig) transcriptome of mice immunized with a three-finger toxin and a phospholipase A2 from the venom of the Central American coral snake, Micrurus nigrocinctus. Results showed that only low frequencies of mRNA encoding IgG isotypes, the most relevant isotype for therapeutic purposes, were present in splenocytes of mice immunized with 6 doses of the toxins over 90 days. Furthermore, analysis of Ig heavy chain transcripts showed that no particular combination of variable (V) and joining (J) gene segments had been selected in the immunization process, as would be expected after a strong humoral immune response to a single antigen. Combined with the titration of toxin-specific antibodies in the sera of immunized mice, these data support the low immunogenicity of three-finger toxins and phospholipases A2 found in elapid snake venoms, and highlight the need for future studies analyzing the complexity of antibody responses to toxins at the molecular level.
White discoloration on leaves and flower-like outgrowth on stem: A new species or hormonal disequilibrium?
Authors: Ng Wenfa
Published: January 2018

Strange patterns of white discoloration on leaves as well as unusual outgrowth that resembles arrested generation of new branches on stem were observed on a plant in Singapore. The white discoloration patterns were random in size and shape but radiated from the veins of the leaf, with a higher concentration in the center and no discoloration in the outer regions. Possible explanations for the coloration pattern on the leaves include: (i) a new species, and more serious (ii) a plant disease of a hormonal nature or mediated by microbe pathogenesis or both. Observations of the plant stem revealed that the length of the stem is of regular segments, with each section punctuated by a ring-like structure. However, an evident flower-like (or, from a different perspective, rose-like) outgrowth in the middle of one section suggested that it is a sprout point for the development of a new branch. But the development was halted in unexplained ways, leaving behind an arrested ring. Though the above may be part of normal development, it could also be signs that the plant is under significant environment stress such as high temperature or manifesting the effects of uptake of toxins, which impacts on equilibrium of hormones in the plant. Most puzzling, the outgrowth that likely will form the basis of a new branch appeared in a lower segment of the stem without branches – which pointed tantalizingly to a hormonal disequilibrium cause. Collectively, the plant mentioned above was likely to be in distress in two scenarios. Specifically, (i) as a new plant species with a different leaf coloration pattern (white round patches on green background) but suffering from a hormonal disease manifesting as outgrowth in the stem, or (ii) a leaf discoloration pattern due to microbe infestation of the xylem in the leaf that led to reduced chlorophyll production in areas of microbe growth together with a systemic hormonal disequilibrium that result, through unknown mechanisms, in flower-like outgrowth in areas of stems not associated with sprouting of branches. Written as a rapid communication to inform the scientific community of a possible new plant species or an early indication of a plant disease likely to be hormonal disequilibrium that impacts on development of a mature plant, interested researchers may explore further the initial observations reported in this short note.
Estimation of bovine pelvic limb inertial properties using an elliptical model
Authors: Paolucci Leopoldo Augusto , Gomides Luciana de Melo M , Las Casas Estevam B. , Faleiros Rafael Resende , de Andrade André Gustavo Pereira , Paz Cahuê Francisco Rosa , Fedotova Veronika , Menzel Hans
Published: January 2018

Development of new techniques and appropriate equipment for treatment of long bone fractures in bovines has been an objective of recent veterinary research. Accurate estimates of body segment inertial parameters (BSIP) are essential for determination of forces acting on limbs and play an important role in an appropriate prosthesis development. The aim of the present study is to examine the mass distribution properties and to suggest a geometric model of bovine right pelvic limb based on these mass distribution properties. Four Holstein breed male calves were filmed by one high-speed camera while walking on a force plate. The animals and two cadaveric specimens were examined in axial computer tomography scanner and the images were exported in DICOM (Digital Imaging and Communication in Medicine) format into a set of software and a computational model was obtained. This model provided information for geometric model construction. Measures of segmental mass, positions of segmental center of mass (CoM) and longitudinal moment of inertia (MoI) of segments of the right pelvic limb were estimated based on the proposed model. These estimates were compared with measurements obtained from a computational model and showed consistent accuracy. This study not only presents a technique that may be applied to other body segments and to different species, but also provides insight into bovine musculoskeletal system necessary to improve the models for dynamic analysis of movement and our understanding of bovine gait.
The pollination potential of Apis cerana Feb., Apis mellifera L. (Hymenoptera; Apidae) on yield of apricot (Prunus armeniaca)
Authors: Gurmani Hafiz Tahir Waqas , Jaleel Waqar , Saeed Shafqat , Gurmani Aisha Riaz , Saeed Qamar , Naqqash Muhammad Nadir , Ghouri Fozia , Munawar Muhammad Siddique , Sial Muhammad Umair , Rahman Saqib , Aine Qurat Ul
Published: January 2018

There are various methods of pollination, such as wind and insects, in apricot. However, wind is not considered as an effective pollinating agent for apricot because of sticky pollens, and apricot needs insects to carry pollens from stamens to the stigma of another plant. Honeybees are significant floral visitors among other pollinators for the pollination of apricot. The efficacy of pollination by two honey bee species, Apis cerana and Apis mellifera, in apricot under controlled condition was examined in the present study. One hive of each honey bee species was kept in orchard and their effect on the yield of apricot fruit setting was measured. The number of honey bees of these two species and other pollinators foraging on the open branches were also observed regularly during three different timings (i.e. 9.00am, 12.00pm, and 3.00pm) a day. Apis cerana population showed that it was directly proportional to the emergence of flowers and similar phenomenon was observed at the shedding of flowers. Significantly higher fruit yield (81%) in open-pollinated branches than closed-branches (19%) was recorded. Moreover, fruit size and quality was better in open-pollinated branches than closed-branches (covered with muslin cloth). We concluded that A. cerana was more active than A. mellifera during flowering and shedding in apricot. This study will help to manipulate the timings of insecticide spray in apricot orchard because the populations of honey bees and other pollinators will not be affected if spray done in the late evening (18.00pm to 19.00pm).
Reconstructing evolutionary timescales using phylogenomics
Authors: Tong K. Jun , Lo Nathan , Ho Simon Y W
Published: January 2018

Reconstructing the timescale of the Tree of Life is one of the principal aims of evolutionary biology. This has been greatly aided by the development of the molecular clock, which enables evolutionary timescales to be estimated from genetic data. In recent years, high-throughput sequencing technology has led to an increase in the feasibility and availability of genome-scale data sets. These represent a rich source of biological information, but they also bring a set of analytical challenges. In this review, we provide an overview of phylogenomic dating and describe the challenges associated with analysing genome-scale data. We also report on recent phylogenomic estimates of the evolutionary timescales of mammals, birds, and insects.
Nonlinear temperature effects on multifractal complexity of metabolic rate of mice
Authors: Labra Fabio A , Bogdanovich Jose M , Bozinovic Francisco
Published: January 2018

Complex physiological dynamics have been argued to be a signature of healthy physiological function. Here we test whether the complexity of metabolic rate fluctuations in small endotherms decreases with lower environmental temperatures. To do so we examine the multifractal temporal scaling properties of the rate of change in oxygen consumption r(VO2), in the laboratory mouse Mus musculus, assessing their long range correlation properties across 7 different environmental temperatures, ranging from 0°C to 30°C. To do so, we applied multifractal detrended fluctuation analysis (MF-DFA), finding that r(VO2) fluctuations show two scaling regimes. For small time scales below the crossover time (approximately 102 seconds), either monofractal or weak multifractal dynamics are observed depending on whether Ta<15°C or Ta > 15°C respectively. For larger time scales, r(VO2) fluctuations are characterized by an asymptotic scaling exponent that indicates multifractal anti-persistent or uncorrelated dynamics. For both scaling regimes, a generalization of the multiplicative cascade model provides very good fits for the Renyi exponents τ(q), showing that the infinite number of exponents h(q) can be described by only two independent parameters, a and b. We also show that the long-range correlation structure of r(VO2) time series differs from randomly shuffled series, and may not be explained as an artifact of stochastic sampling of a linear frequency spectrum. These results show that metabolic rate dynamics in a well studied micro-endotherm are consistent with a highly non-linear feedback control system.
GreenScaler: Automatically training software energy model with big data
Authors: Chowdhury Shaiful Alam , Gil Stephanie , Romansky Stephen , Hindle Abram
Published: January 2018

Software energy consumption is a performance related non-functional requirement that complicates building software on mobile devices today. Energy hogging applications are a liability to both the end-user and software developer. Measuring software energy consumption is non-trivial, requiring both equipment and expertise, yet many researchers have found that software energy consumption can be modelled. Prior works have hinted that with more energy measurement data one can make more accurate energy models but this data was expensive to extract because it required energy measurement of running test cases (rare) or time consuming manually written tests. We address these concerns by automatically generating test cases to drive applications undergoing energy measurement. Automatic test generation allows a model to be continuously improved in a model building process whereby applications are extracted, tests are generated, energy is measured and combined with instrumentation to train a grander big-data model of software energy consumption. This continuous process has allowed the authors to generate and extract measurements from hundreds of applications in order to build accurate energy models capable of predicting the energy consumption of applications without end-user energy measurement. We clearly show that models built from more applications reduce energy modelling error.
Did I make a mistake? Finding the impact of code change on energy regression
Authors: Chowdhury Shaiful Alam , Gil Stephanie , Romansky Stephen , Hindle Abram
Published: January 2018

Software energy consumption is a performance related non-functional requirement that complicates building software on mobile devices today. Energy hogging applications are a liability to both the end-user and software developer. Measuring software energy consumption is non-trivial, requiring both equipment and expertise, yet many researchers have found that software energy consumption can be modelled. Prior works have hinted that with more energy measurement data one can make more accurate energy models but this data was expensive to extract because it required energy measurement of running test cases (rare) or time consuming manually written tests. We address these concerns by automatically generating test cases to drive applications undergoing energy measurement. Automatic test generation allows a model to be continuously improved in a model building process whereby applications are extracted, tests are generated, energy is measured and combined with instrumentation to train a grander big-data model of software energy consumption. This continuous process has allowed the authors to generate and extract measurements from hundreds of applications in order to build accurate energy models capable of predicting the energy consumption of applications without end-user energy measurement. We clearly show that models built from more applications reduce energy modelling error.
The genetic and morphological evolution of fish through Cytochrome C Oxidase Subunit 1 (COX1)
Authors: Marzouk Sammer
Published: January 2018

Cytochrome C Oxidase Subunit 1 (COX1) is a protein that helps to catalyze the reduction of water into oxygen in Eukaryotes. Through the analyzation of COX1 from online public genetic databases in 16 species of fish, an evolutionary phylogeny of fish was derived from the data. This paper considered three hypotheses: Axolotl (Ambystoma mexicanum) and Tiktaalik (Tiktaalik roseae) share a common ancestor was determined; that A.gueldenstaedtii and P.spathula both share a common ancestor; and that P.marinus and S.acanthias are the outliers of the phylogeny. The evolutionary phylogeny used the percent ID between the two species of fish. From these differences, analysis is done to 2016. the data and the data is used to make phylogenies based on the morphological and genetic evolution of these fish. From the data derived from the phylogenies, the results demonstrates the claims that Axolotl (Ambystoma mexicanum) and Tiktaalik (Tiktaalik roseae) share a common ancestor was determined, A.gueldenstaedtii and P.spathula both share a common ancestor, and P.marinus and S.acanthias are the outliers of the phylogeny. The data gathered can be used to connect tetrapods to fish, and contribute to the theory that tetrapods came from fish. The information presented in this paper can be used to make a complete phylogeny of all organisms in the biosphere.
10 simple rules for designing and analyzing field experiments in ecology
Authors: Nazal Basma
Published: January 2018

A set of 10 fundamental rules to successfully design, execute, and analyze biological field experiments. This list tackles the main components of an experiment beginning with the hypothesis and predictions, to the design and execution, as well as statistical analysis and interpretation of data in order for researchers to create the best experimental design for their project. Although this paper is aimed at field experiments in ecology, many of the rules are applicable to other streams of biology.
Intraspecific variation in the diet of the Mexican garter snake Thamnophis eques
Authors: Manjarrez Javier , Pacheco-Tinoco Martha , Venegas-Barrera Crystian S
Published: January 2018

The Mexican Garter Snake (Thamnophis eques) is a terrestrial-aquatic generalist because it feeds on both aquatic and terrestrial prey. We describe size-related variation and slight sexual variation in the diet of Thamnophis eques through analysis of 262 samples of identifiable stomach contents in snakes from 23 locations on the Mexican Plateau. The Mexican Garter Snakes we studied ate prey items mostly fish, followed in lesser amounts, respectively, by leeches, earthworms, frogs, and tadpoles. Correspondence analysis suggested that the frequency of consumption of various prey items differed between the categories of age and sex of snakes, and the general pattern was a reduction of prey item diversity with size of snake. Snake length was correlated positively with mass of ingested prey. Large snakes consumed large prey and continued to consume smaller prey. In general, no differences were found between the prey taxa of male and female snakes, although males ate two times more tadpoles than females. Males and females did not differ in the mass of leeches, earthworms, fishes, frogs and tadpoles that they ate, and males and females that ate each prey taxon were similar in length. We discuss proximate and functional determinants of diet and suggest that the observed intraspecific variation in Mexican Garter Snakes could be explored by temporal variation in prey availability, proportions of snake size classes and possible sexual dimorphism in head traits and prey dimensions to assess the role of intersexual resource competition.
Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi
Authors: Ishengoma Edson , Agaba Morris , Cavener Douglas R
Published: January 2018

Background. The capacity of species to respond and perceive visual signal is integral to their evolutionary success. Giraffe is closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with most of them. To what extent giraffe unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood.

Methods. The recent availability of giraffe and okapi genome provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site test of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and their corresponding orthologous sequences from other mammals obtained from public gene banks.

Results. Signatures of selection was identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW in giraffe. Significant selection divergence was identified in SAG while positive selection was detected in LUM when okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants.

Discussion. By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and okapi vision adaptation. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and okapi habitat. Moreover, requirement for long distance vision associated with predation likely played an important role in the adaptive pressure on giraffe vision genes.
Microbes and cancer: Coming a full circle
Authors: Srihari Sriganesh , Srihari Sulakshana
Published: January 2018

Microbes, particularly viruses, have had a chequered history in cancer research. Considered in the 1960s and 1970s as the main cause of cancers, a decade later microbes were set aside as inconsequential to the field. However, with confirmed links established between microbial infections and certain cancers in the last several years – e.g. human papillomavirus infection and cervical cancer, and Helicobacter pylori infection and gastric cancer – the field has slowly started to take notice of microbes again. Today, we know that about 15% of all cancer cases reported worldwide is due to microbes. Moreover, latest research findings suggest that viruses can be engineered to selectively target and kill cancer cells. A healthy microbiome in the human gut is also thought to aid responses to certain cancer therapies. Therefore, microbes appear to be back in the game now. Here we present a short perspective of the ‘full circle’ that microbes have come and their relevance to cancer research.
Atropos: specific, sensitive, and speedy trimming of sequencing reads
Authors: Didion John P , Martin Marcel , Collins Francis S
Published: January 2018

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves a four-fold increase in trimming accuracy and a decrease in execution time of ~50% (using 16 parallel execution threads). Furthermore, Atropos maintains high accuracy even when trimming simulated data with a high rate of error. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of most current-generation sequencing data sets.

Atropos is open source and free software written in Python and available at https://github.com/jdidion/atropos.
Atropos: specific, sensitive, and speedy trimming of sequencing reads
Authors: Didion John P , Martin Marcel , Collins Francis S
Published: January 2018

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Availability. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.