bluuebunny/crossref_metadata_2025 huggingface dataset:
The interplay between habitat structure and chemical contaminants on biotic responses of benthic organisms
Authors: Mayer Pinto Mariana , Matias Miguel G , Coleman Ross A
Published: January 2018

Habitat structure influences the diversity and distribution of organisms, potentially affecting their response to disturbances by either affecting their ‘susceptibility’ or through the provision of resources that can mitigate impacts of disturbances. Chemical disturbances due to contamination are associated with decreases in diversity and functioning of systems and are also likely to increase due to coastal urbanisation. Understanding how habitat structure interacts with contaminants is essential to predict and therefore manage such effects, minimising their consequences to marine systems. Here, we manipulated two structurally different habitats and exposed them to different types of contaminants. Effects of contamination and habitat structure interacted, affecting species richness. More complex experimental habitats were colonized by a greater diversity of organisms than the less complex habitats. These differences disappeared, however, when habitats were exposed to contaminants, suggesting that contaminants can override effects of habitats structure at small spatial scales. These results provide insight into the complex ways that habitat structure and contamination interact and the need to incorporate evidence of biotic responses from individual disturbances to multiple stressors. Such effects need to be taken into account when designing and planning management and conservation strategies to natural systems.
True´s beaked whale (Mesoplodon mirus) in Macaronesia
Authors: Aguilar de Soto Natacha , Martín Vidal , Silva Monica , Edler Roland , Reyes Cristel , Carrillo Manuel , Schiavi Agustina , Morales Talia , García-Ovide Belen , Sanchez-Mora Anna , Garcia-Tavero Nerea , Steiner Lisa , Scheer Michael , Gockel Roland , Walker Dylan , Villa Enrico , Szlama Petra , Carroll Emma
Published: January 2018

The True´s beaked whale (Mesoplodon mirus, True 1913) is a poorly studied member of the speciose Ziphiidae family. Its distribution in the North Hemisphere is thought to be restricted to the temperate or warm temperate waters of the North Atlantic, while a small number of stranding records from the Southern Hemisphere suggest a wider distribution, extending from the Atlantic coast of Brazil to South Africa, Australia and the Tasman Sea coast of New Zealand. Here we i) report the first molecular confirmation of the occurrence of True´s beaked whales around the Azores and Canary Islands (Macaronesian ecoregion), the species’ southern limit in the northeast Atlantic; ii) describe a new colouration for this species; and iii) contribute to the sparse worldwide database of live sightings, including the first underwater video, of this species. In November 2012, a 390 cm male True’s beaked whale stranded in El Hierro, Canary Islands. In July 2004, a subadult male True’s beaked whale was found floating dead near Faial, Azores. Species identification was confirmed in both cases using mitochondrial DNA control region and cytochrome b gene markers. The whale that stranded in the Canary Islands had a clearly delimited white area on its head, extending posteriorly from the tip of the beak to cover the blowhole dorsally and the gular grooves ventrally. This colouration contrasts with previous descriptions for the species and it may be rare, but it demonstrates that True´s beaked whales show variable colourations in the North Atlantic. This is confirmed by sightings data. Given the presence of this species around the Azores and the Canary Islands, it would be expected that True´s beaked whales also occur in the area between these archipelagos, including the islands of Madeira.
Has human culture "shaped" the shape bias: Comparisons with other apes
Authors: Vonk Jennifer M
Published: January 2018

Children show a bias toward information about shape when categorizing unfamiliar objects or learning new labels for objects. We presented two adult zoo-housed chimpanzees (Pan troglodytes) and 3- to 5-year old children with a relational matching task in which samples and comparison stimuli matched on either shape or color. Whereas children at all ages performed above chance on the task, chimpanzees performed at close to chance levels overall. However, closer examination of their performance revealed that, whereas children performed better on shape (86%) versus color trials (78.5%), chimpanzees showed the opposite pattern, performing at chance on shape trials (49%) and above chance on color trials (72%). I propose that the shape bias arises because of cultural effects, whereas color may be a more salient natural cue that differentiates, for instance, between ripe and non-ripe fruit. Interestingly, earlier work with orangutans and one gorilla, however, showed that the apes initially performed best on shape trials, but learned quickly to match more effectively by color. In a second order relational task, preferences were less clear. Further work is needed to determine the evolutionary history of the shape bias in human children.
Examination of antimicrobial activity of selected non-antibiotic products
Authors: Kruszewska Hanna , Zaręba Tomasz , Mrówka Agnieszka , Tyski Stefan S
Published: January 2018

A variety of pharmaceutical preparations, which are applied in the management of non-infectious diseases, have shown in vitro some antimicrobial activity. These drugs are called “non-antibiotics”. So far, a lot of attention has been focused on phenothiazines, thioxanthenes and other agents with affinities to cellular transport systems or agents showing other inhibition mechanism. Several authors confirmed that some non-antibiotics are “helper compounds”, which enhance the in vitro activity of certain antibiotics against specific bacteria (ex. omeprazole and nizatidine enhance the effect of metronidazole on Helicobacter pylori). The aim of this study was to detect and characterise the antimicrobial activity of non-antibiotic drugs, selected from the pharmaceutical products analysed during the state control performed in National Medicines Institute in Warsaw. Over 100 pharmaceutical preparations were randomly chosen from different groups of drugs. The surveillance study was performed on standard ATCC microbial strains used for drug control: Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Candida albicans and Aspergillus brasiliensis. It was shown that the drugs listed below inhibited growth of at least one of the examined strains: Cyclaid 100 mg cap. (ciclosporine), Heminevrin 300 mg cap. (clomethiazole edisylate), Hydroxycarbamid Teva 500 mg caps. (hydroxycarbamide), Ibandronat Apotex 150 mg tab., Ossica 150 mg tab. (ibandronic acid), Lazivir 150 mg + 300 mg tab. (lamivudyne, zydovudine), No-Spa Max 80 mg tab. (drotaverine HCl) and Rupafin 10 mg tab. (rupatadine). The MIC values of active substances of above drugs were evaluated. The broad spectrum of activity was found in case of clomethiazole which inhibited growth of all tested strains ( MIC: 1.6 – 3.2 mg/ml ). All tested bacterial strains were inhibited by hydroxycarbamide (MIC: 0.8 - 1.6 mg/ml). The high activity against Gram-positive strains was found for drotaverine and rupatadine (MIC: 0.4 mg/ml). Mould strain A. brasiliensis was inhibited by ibandronic acid (MIC 3.2 mg/ml), clomethiazole (MIC 1.6 mg/ml) and cyclosporine (MIC 0.8 mg/ml). Moreover ibandronic acid was active against P. aeruginosa in relatively low concentration (MIC: 0.2 mg/ml). In case of antiviral tablets Lazivir (two active substance: lamivudine and zidovudine) only zidovudine inhibited growth of E. coli in very low concentration 0.00125 mg/ml whereas lamivudine to concentration 1.6 mg/ml did not show any inhibition towards tested strains. The antimicrobial activity of the drugs emphasize a necessity of neutralization of their activity during microbial purity assays of pharmaceutical products.
Population structure, migratory behavior and spawning habitat of East Atlantic and Mediterranean bluefin tuna revealed by a multi-annual electronic tagging program
Authors: Quílez-Badia Gemma , Ospina-Alvarez Andres , Sainz Trápaga Susana , Di Natale Antonio , Abid Noureddine , Rodríguez López Naima A , Tudela Sergi
Published: January 2018

During 2008-2014, 101 pop-up satellite and 31 internal archival electronic tags were deployed in bluefin tuna (12 to 250 kg in weight) in the Western and Central Mediterranean and in the Atlantic coast of Morocco. Time at liberty spanned from 18 to 391 days. In the Western and Central Mediterranean, two behavioral patterns / contingents (highly migratory and resident) were observed to co-occur. Imprinting of early Atlantic migrants is hypothesized to explain the existence of the two contingents. None of the “resident” individuals left the Mediterranean during the whole tracking period. None of the tuna present in the Mediterranean at some point crossed over to the Eastern Mediterranean. The occurrence of potential Mediterranean spawners in North Atlantic waters beyond the 45oW was also observed.
Sex differences in object manipulation in wild immature chimpanzees and bonobos: Preparation for tool use?
Authors: Koops Kathelijne , Furuichi Takeshi , Hashimoto Chie , van Schaik Carel P.
Published: January 2018

Sex differences in immatures predict behavioral differences in adulthood in many mammal species. Because most studies have focused on sex differences in social interactions, little is known about possible sex differences in ‘preparation’ for adult life with regards to tool use skills. We investigated sex and age differences in object manipulation in immature apes. Chimpanzees (Pan troglodytes) use a variety of tools across numerous contexts, whereas bonobos (Pan paniscus) use few tools and none in foraging. In both species, a female bias in adult tool use has been reported. We studied object manipulation in immature chimpanzees at Kalinzu (Uganda) and bonobos at Wamba (Democratic Republic of Congo). We confirmed that chimpanzees showed higher rates and more diverse types of object manipulation than bonobos. Against expectation, male chimpanzees showed higher object manipulation rates than females, whereas in bonobos no sex difference was found. However, object manipulation by male chimpanzees was play-domi nated, whereas manipulation types of female chimpanzees were more diverse. Manipulation by young immatures (<3 years old) of both species was similarly dominated by play, but only in chimpanzees did it become more diverse with age. In chimpanzees, object types became more tool-like (i.e. sticks) with age, further suggesting preparation for tool use in adulthood (i.e. ant-dipping). The male bias in object manipulation in immature chimpanzees, along with the late onset of tool-like object manipulation, indicates that not all (early) object manipulation in immatures prepares for subsistence tool use. Object play may also function in motor skill practice for male-specific behaviors like dominance displays.
Detection of phase transitions in the studies of active substances and solid dosage forms
Authors: Łaszcz Marta , Trzcińska Kinga , Witkowska Anna
Published: January 2018

Polymorphism is the ability of a compound in the solid state to exist in different crystalline forms. Molecules, having the same chemical composition, exhibit different spatial arrangements and/or exist in different configurations and conformations. In pseudopolymorphs (solvates) molecules of solvents are incorporated into the crystal lattice. Contrary to the crystalline forms of polymorphs, amorphous forms are characterized by the lack of long-range molecule arrangements. The spatial arrangement of molecules in an active substance determines its physical properties and influences the bioavailability and stability of a drug product. The most frequent phase transitions that can be present in an active substance include: polymorphic transition, hydration, dehydration, amorphisation and crystallization. The knowledge about the phase transitions which can arise during the active substance manufacturing, formulation process and stability studies is very important. Phase transitions may lead to the formation of an undesirable phase of the active substance with different properties than its desirable form. Studies of phase transitions in an active substance contained in a solid dosage form are very complicated, because there are many additional factors to consider, including a small concentration of the active substance, the presence of crystalline and amorphous placebo constituents, as well as the interactions between the active substance and the excipients. There are a number of methods used to characterize crystalline and amorphous forms of the active substance. A definitive evidence of polymorphism or pseudopolymorphism is the demonstration of a nonequivalent structure by single crystal X-ray diffraction. X-ray powder diffraction (XRPD) and variable temperature X-ray powder diffraction (VT-XRPD) can also be used to provide an unequivocal proof of polymorphism and pseudopolymorphism. Other methods, including e.g. differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) as well as Raman (RS) and infrared spectroscopes (IR), help to further characterize the crystalline and amorphous forms. In this presentation, a few examples of phase transition studies in the active substances and solid dosage forms will be discussed: structural and physicochemical studies of olopatadine hydrochloride conformational polymorphs, phase transitions of dutasteride performed by the VT-XRPD method, erlotynib polymorphism studies performed by means of RS and the evaluation of analytical methods for the detection of phase transitions in tablets containing aripiprazole and imatinib.
Faunal communities are invariant to fragmentation in experimental seagrass landscapes
Authors: Lefcheck Jonathan S , Marion Scott R , Lombana Alfonso V , Orth Robert J
Published: January 2018

Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4-400 m2 in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused mesopredators and epifaunal communities using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the number of patches and the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at more realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities.
The FDA adaptive trial design guidance in a nutshell - A review in Q&A format for decision makers
Authors: Gottlieb Klaus
Published: January 2018

The FDA adaptive trial design guidance (1) is a thoughtful but lengthy document that explains on 50 pages wide-ranging and important topics “such as ... what aspects of adaptive design trials (i.e., clinical, statistical, regulatory) call for special consideration, ... when to interact with FDA while planning and conducting adaptive design studies, ... what information to include in the adaptive design for FDA review, and ... issues to consider in the evaluation of a completed adaptive design study.” [20-24]. The advice in the guidance is often misinterpreted, misquoted or ignored. This is unfortunate because an appropriate use of adaptive designs could increase the chances of success in drug development programs. Decision makers rely on the advice of regulatory affairs professionals and statisticians to interpret the guidance. Unfortunately, many clinical trial statisticians and regulatory professionals only have a rudimentary understanding of the guidance, presumably because the document is somewhat inscrutable for both audiences, too ‘regulatory’ for statisticians, too ‘statistical’ for regulatory people. This digest was therefore written with three goals in mind: 1) Make the content of the guidance more accessible through a question & answer format, 2) shorten the content from 50 to 10 pages by excerpting the most important dictums, and 3) keep fidelity to the original guidance by frequent use of direct quotes with reference to the respective lines in the original FDA guidance where the quote can be found in square brackets.
Dramatyping: A generic algorithm for detecting reasonable temporal correlations between drug administration and lab value alterations
Authors: Newe Axel
Published: January 2018

According to the World Health Organization, one of the criteria for the standardized assessment of case causality in adverse drug reactions is the temporal relationship between the intake of a drug and the occurrence of a reaction or a laboratory test abnormality. This article presents and describes an algorithm for the detection of a reasonable temporal correlation between the administration of a drug and the alteration of a laboratory value course. The algorithm is designed to process normalized lab values and is therefore universally applicable. It has a sensitivity of 0.932 for the detection of lab value courses that show changes in temporal correlation with the administration of a drug and it has a specificity of 0.967 for the detection of lab value courses that show no changes. Therefore the algorithm is appropriate to screen the data of electronic health records and to support human experts in revealing adverse drug reactions. A reference implementation in Python programming language is available.
Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects
Authors: Elbrecht Vasco , Taberlet Pierre , Dejean Tony , Valentini Alice , Usseglio-polatera Philippe , Beisel Jean-nicolas , Coissac Eric , Boyer Frederic , Leese Florian
Published: January 2018

Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. In comparison to COI, the 16S marker amplified more insect species and amplified more equally, probably due to decreased primer bias. Rough estimation of biomass might thus be less biased with 16S than with COI. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of species will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey in a context where it is possible to build a local reference database, the 16S marker could be more appropriate.
Rushing Roulette – how do learners perform routine tasks under time pressure?
Authors: Topps David , Popovic Ana , Horne Teejay , Rawling Jean M , Topps Maureen
Published: January 2018

Introduction: Remediating, or preferably, predicting which residents will have difficulty before they need remediating, is a challenging task. Most of us perform better when pumped for an exam. But how do we respond when under routine pressures? Do weaker learners adapt differently, despite coaching? Methods: Using an adaptation of virtual patient software, we explored how learners cope with handling repetitive yet time-sensitive routine tasks. We emulated the performance of routine tasks within a virtual electronic medical record (EMR) environment, tracking individual learner activity and decision pathways, time to act (with and without enforced pressure from programmed time-outs) and their adaptation trajectories over time with coaching. Learners were assessed using Situational Judgement and modified Script Concordance Testing, with reproducible and granular time constraints introduced into the clinical reasoning process. Results: Our case designs introduce a number of competing elements: time pressures, competing priorities and instructions, resource availability and unpredictable outcomes. Learner behaviour is assessed using a variety of metrics including time-stamped decision points, decision pathways and internal counter scores. Clinical reasoning pathways, as compared to a reference peer panel, are in turn compared with and without the time pressures. Conclusions: Predictive analytics have made great promises in diagnosing problems for learners in difficulty but are complex and expensive to deploy widely. Our simpler, rapidly reproducible approach may provide a more practical solution.
Occurrence of twin embryos in the eastern bluebird
Authors: Bailey Robyn L. , Clark Gerald E.
Published: January 2018

We report the first record of presumed twinning in eastern bluebird (Sialia sialis) and provide a review of previously reported twinning events in wild birds. A nest containing twin eastern bluebird nestlings was monitored in 2013 in central Pennsylvania and reported to the Cornell Lab of Ornithology’s NestWatch program, a national program where volunteers submit data on wild nesting birds. A presumed double-yolked egg of a free-living eastern bluebird pair hatched successfully, and twin nestlings lived for 11 days in a nest box shared by three siblings. Due to the rarity of twinning in wild birds, engaging the public to monitor large numbers of nests is the most likely approach to documenting twinning in wild populations, and citizen science provides the infrastructure for individuals to share observations.
Eight open questions in the computational modeling of higher sensory cortex
Authors: Yamins Daniel LK , DiCarlo James J
Published: January 2018

Propelled by recent advances in biologically-inspired computer vision and artificial intelligence, the past five years have seen significant progress in using deep neural networks to model response patterns of neurons in higher visual cortical areas. In this paper, we briefly review this progress and then discuss eight key “open questions” that we believe will drive research in computational models of sensory systems over the next five years, both in visual cortex and beyond. Throughout, our focus is on challenges that will require both cutting-edge algorithmic developments as well as next-generation neuroscience and cognitive science experiments.
Evaluating the assessment metrics of the Integrated Cognitive Simulator’s laparoscopic appendicectomy module
Authors: Mordaunt Dylan A , Windsor John A , Loveday Benjamin
Published: January 2018

Background: Simtics Integrated Cognitive Simulator (ICS) is a software learning environment, previously demonstrated to be of use to surgical trainees in learning the cognitive aspects of procedural skills. It also includes a Test-Mode, which has not previously been assessed for its ability to discriminate between experienced and non-experienced operators. Methods: 10 experienced and 10 non-experienced participants performed a laparoscopic appendicectomy using the ICS laparoscopic appendicectomy (LA) module. Total score, total time, and four further metrics (incorrect hand, incorrect instrument, incorrect location, time > 15s per step) were recorded for each individual, across the four sections and nine steps of the simulation. Results: Median total score was greater amongst surgically experienced participants than surgically inexperienced participants (26.5 %, p = 0.023). Instrument use was a significant discriminator between these groups in 2 of 4 of the ICS LA sections.
First documented record of the Belted Kingfisher Megaceryle alcyon (Linnaeus, 1758) in mainland Ecuador
Authors: Cisneros-Heredia Diego F
Published: January 2018

I present the first documented record of the Belted Kingfisher Megaceryle alcyon in mainland Ecuador. A young male M. alcyon was observed and photographed on the surroundings of Puerto López, province of Manabí, Ecuador in September 2005. A very rare vagrant in mainland Ecuador, M. alcyon was previously known from a single sighting in December 1995. In the absence of strong evidence for the occurrence of M. alcyon in mainland Ecuador, it remains classified as a hypothetical species in all country’s ornithological reference, pending corroborating evidence, which is now provided.
Synthesis and physicochemical characterization of the impurities and the key intermediate of pemetrexed disodium, an anticancer drug
Authors: Michalak Olga , Gruza Mariusz , Łaszcz Marta , Trzcińska Kinga , Witkowska Anna , Bujak Iwona , Cmoch Piotr
Published: January 2018

Pemetrexed is an antifolate antineoplastic agent that acts by inhibiting the formation of precursor purine and pyrimidine nucleotides. Pemetrexed prevents the formation of DNA and RNA, which are required for the growth and survival of both normal and cancer cells. A pharmaceutical product containing pemetrexed disodium as the active ingredient is used for the treatment of malignant pleural mesothelioma (MPM) and metastatic non-small cell lung cancer (NSCLC). The European Medicine Agency and the U.S. Food and Drug Administration require complete physicochemical characteristic not only for an active pharmaceutical ingredient, but also for its key synthetic intermediates and the impurities formed during synthesis drug products. Therefore the development of the synthesis methods for impurities and new crystalline forms of pemetrexed diacid – a key intermediate of pemetrexed disodium was described. Physicochemical characterizations of impurities and pemetrexed diacid were performed by means of thermal analysis, spectroscopic methods and powder diffraction. Structures elucidation on the basis of two-dimensional NMR experiments were discussed in details. Additionally, in this work, the crystal structure of pemetreksed diacid form C will be presented, together with its spectroscopic and thermal characteristics. The identification of these impurities and the intermediate is essential for the quality control during the production of the pemetrexed disodium salt.
A framework for smartphone-enabled, patient-generated health data analysis
Authors: Gollamudi Shreya S , Topol Eric J , Wineinger Nathan E
Published: January 2018

Background: Digital medicine and smartphone-enabled health technologies provide a novel source of human health and human biology data. However, in part due to its intricacies, few methods have been established to analyze and interpret data in this domain. We previously conducted a six-month interventional trial examining the efficacy of a comprehensive smartphone-based health monitoring program for individuals with chronic disease. This included 38 individuals with hypertension who recorded 6,290 blood pressure readings over the trial. Methods: In the present study we provide a hypothesis testing framework for unstructured time series data, typical of patient-generated mobile device data. We used a mixed model approach for unequally spaced repeated measures using autoregressive and generalized autoregressive models, and applied this to the blood pressure data generated in this trial. Results: We were able to detect, roughly, a 2 mmHg decrease in both systolic and diastolic blood pressure over the course of the trial despite considerable intra- and inter-individual variation. Furthermore, by supplementing this finding by using a sequential analysis approach, we observed this result over three months prior to the official study end – highlighting the effectiveness of leveraging the digital nature of this data source to form timely conclusions. Conclusions: Health data generated through the use of smartphones and other mobile devices allow individuals the opportunity to make informed health decisions, and provide researchers the opportunity to address innovative health and biology questions. The hypothesis testing framework we present can be applied in future studies utilizing digital medicine technology or implemented in the technology itself to support the quantified self. The study was registered at clinicaltrials.gov (NCT01975428).
Lateral presentation alters overall viewing strategy
Authors: Luke Christopher J , Pollux Petra M J
Published: January 2018

Eye tracking has been used during face categorisation and identification tasks to identify perceptually salient facial features and infer underlying cognitive processes. However, viewing patterns are influenced by a variety of gaze biases, drawing fixations to the centre of a screen and horizontally to the left side of face images (left-gaze bias). In order to investigate potential interactions between gaze biases uniquely associated with facial expression processing, and those associated with screen location, face stimuli were presented in three possible screen positions to the left, right and centre. Comparisons of fixations between screen locations highlight a significant impact of the screen centre bias, pulling fixations towards the centre of the screen and modifying gaze biases generally observed during facial categorisation tasks. A left horizontal bias for fixations was found to be independent of screen position but interacting with screen centre bias, drawing fixations to the left hemi-face rather than just to the left of the screen. Implications for eye tracking studies utilising centrally presented faces are discussed.
An explicit-solvent conformation search method using open software
Authors: Gaalswyk Kari , Rowley Christopher N
Published: January 2018

Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify the most probable conformations from the simulated trajectory. This work-flow was tested on drug molecules a-amanitin and cabergoline to illustrate its capabilities and effectiveness. The preferred conformations of these molecules in gas phase, implicit solvent, and explicit solvent are significantly different.
BioAssay templates for the semantic web
Authors: Clark Alex M , Litterman Nadia K , Kranz Janice E , Gund Peter , Gregory Kellan , Bunin Barry A
Published: January 2018

Annotation of bioassay protocols using semantic web vocabulary is a way to make experiment descriptions machine-readable. Protocols are communicated using concise scientific English, which precludes most kinds of analysis by software algorithms. Given the availability of a sufficiently expressive ontology, some or all of the pertinent information can be captured by asserting a series of facts, expressed as semantic web triples (subject, predicate, object). With appropriate annotation, assays can be searched, clustered, tagged and evaluated in a multitude of ways, analogous to other segments of drug discovery informatics. The BioAssay Ontology (BAO) has been previously designed for this express purpose, and provides a layered hierarchy of meaningful terms which can be linked to. Currently the biggest challenge is the issue of content creation: scientists cannot be expected to use the BAO effectively without having access to software tools that make it straightforward to use the vocabulary in a canonical way. We have sought to remove this barrier by: (1) defining a bioassay template data model; (2) creating a software tool for experts to create or modify templates to suit their needs; and (3) designing a common assay template (CAT) to leverage the most value from the BAO terms. The CAT was carefully assembled by biologists in order to find a balance between the maximum amount of information captured vs. low degrees of freedom in order to keep the user experience as simple as possible. The data format that we use for describing templates and corresponding annotations is the native format of the semantic web (RDF triples), and we demonstrate some of the ways that generated content can be meaningfully queried using the SPARQL language. We have made all of these materials available as open source (http://github.com/cdd/bioassay-template), in order to encourage community input and use within diverse projects, including but not limited to our own commercial electronic lab notebook products.
Can a low carrying capacity and a highly stochastic environment induce a predator pit in elk populations?
Authors: Horne Jon , Bergen Scott , Hurley Mark
Published: January 2018

Due to concern over declining elk populations and the unknown effects of wolf predation, Idaho Department of Fish and Game initiated a survival study of elk in north-central Idaho. A total of 82 adult and 80 calves (~6 months old) were captured and fitted with GPS radio-collars from the winter of 2009 – winter 2014. Adult survival rates averaged 86% (range 76% - 97%). Calf survival rates averaged 44% but varied dramatically from year to year. We used a stochastic model of elk-wolf dynamics to investigate the implications of a highly stochastic growth rates indicative of the observed survival rates. In particular, we were interested in the interaction between elk density-dependent growth, carrying capacity and the amount of stochasticity in predation rates. We found that when predation rates were highly stochastic and carrying capacities were low, populations behave as if they were in a predator pit but if carrying capacity was high or stochasticy low, populations grew out of the predator pit. These results suggest that in a stochastic environment, populations may actually be influenced by both bottom-up and top-down forcing simultaneously as opposed to being governed by one or the other.
NMR. Issues in configuration determination
Authors: Staszewska-Krajewska Olga
Published: January 2018

It is well known that the biological properties of compounds are directly related to the configuration of their stereogenic centers. Therefore, the determination of the compound spatial structure, including its configuration, is crucial for better understanding of the mode of action of bioactive compounds and the design of new drugs. The nuclear Overhauser effect has been shown to be highly useful in NMR spectroscopy for characterizing and refining organic chemical structures. However, the results are not always conclusive. During the presentation the most common problems associated with the acquisition and interpretation of NOE data will be discussed. Other alternative measurement parameters (chemical shifts and coupling constants 3JH-H), which are usually neglected when assigning configuration, will be presented. Also RDS (residuel dipolar coupling) measurements, that are an alternative to NOE measurements, will be briefly explained. The second part of the presentation will be devoted to determining the relative configuration of β-lactams. Recently we have found that the assignment of relative configuration at the bridgehead carbon atom of bicyclic carbapenams can be easily achieved by analyzing chemical shifts of the geminal protons of the methylene group at the C-3 carbon atom. This observation can be attributed to the influence of the anisotropy of the neighboring carbonyl group and can be easily correlated with the configuration at the bridgehead carbon atom. The study showed that the proposed simple relationship can also be used for other azabicyclic compounds.
What Box: a task for assessing language lateralisation in young children
Authors: Badcock Nicholas A , Spooner Rachael , Hofmann Jessica , Flitton Atlanta J , Elliott Scott , Kurylowicz Lisa , Lavrencic Louise M , Payne Heather M , Holt Georgina K , Holden Anneka , Churches Owen F , Kohler Mark J , Keage Hannah AD
Published: January 2018

The assessment of active language lateralisation in infants and toddlers is challenging. It requires an imaging tool that is unintimidating, quick to setup, and robust to movement, in addition to an engaging and cognitively simple procedure that elicits language processing. Functional Transcranial Doppler Ultrasound (fTCD) offers a suitable technique and here we report on a suitable method to elicit active language production in young children. The 34-second ‘What Box’ trial presents an animated face ‘searching’ for an object. The face ‘finds’ a box that opens to reveal an object, which may be labelled spontaneously, in response to a “What’s this?” prompt, or in response to the object label. What Box conducted with 95 children (1 to 5 years-of-age, completing a median of 7 trials), who were left-lateralised on average. The task was validated (ρ = 0.4) against the gold standard Word Generation task in a group of older adults (n = 65, 60 to 85 years-of-age, median of 24 trials). Existing methods for assessing lateralisation of active language production have been used with 4-year-old children while passive listening has been conducted with sleeping 6-month-olds. This is the first active method to be successfully employed with infants, toddlers, and pre-schoolers, and show good correspondence to Word Generation in older adults.
Hierarchical organization of a Sardinian sand dune plant community
Authors: Cusseddu Valentina , Ceccherelli Giulia , Bertness Mark
Published: January 2018

Coastal sand dunes have attracted the attention of plant ecologists for over a century, but they have largely relied on correlations to explain dune plant community organization. We experimentally examined longstanding hypotheses that sand binding, interspecific interactions, abiotic factors and seedling recruitment are drivers of sand dune plant community structure in Sardinia, Italy. Removing foundation species from the fore, middle and back dune habitats over 3 years led to erosion and habitat loss on the fore dune and limited plant recovery that increased with dune elevation. Reciprocal species removals in all zones suggested that interspecific competition is common, but that dominance is transient, particularly due to sand burial disturbance in the middle dune. A fully factorial 2-year physical factor manipulation of water, nutrient availability and substrate stability revealed no significant proximate response to these abiotic factors in any dune zone. In the fore and middle dune, plant seeds are trapped under adult plants during seed germination, and seedling survivorship and growth generally increase with dune height in spite of increased herbivory in the back dune. Sand and seed erosion lead to limited seed recruitment on the fore dune while high summer temperatures and allelopathy lead to competitive dominance of woody plants in the back dune. Our results suggest that Sardinian sand dune plant communities are hierarchically organized, structured by sand binding foundation species on the fore dune, sand burial in the middle dune and increasingly successful seedling recruitment, growth and competitive dominance in the back dune.
Reporting quality of randomized and non-randomized controlled trial abstracts from chicken research
Authors: Sukon Peerapol , Kongpechr Saijai , Bubpahou Sakolwan , Boonpian Natchaya , Manasrisureeyun Natyaon
Published: January 2018

In publication of a controlled trial article from health science research, the abstract is an important part that readers usually read first and then decide whether to read the whole article; therefore, information provided in the abstract should be adequate. The CONSORT (consolidated standards of reporting trials) for Abstracts checklist has been developed and used as a guideline for authors to prepare their manuscripts. This checklist has also been used as a tool to evaluate published abstracts. The objectives of this study were to evaluate reporting quality of randomized controlled trial (RCT) and non-RCT abstracts from chicken research and to determine factors associated with the reporting quality. We searched PubMed for RCT and non-RCT abstracts involving chicken research published between 2006 and 2015. The included abstracts were evaluated using the modified CONSORT for Abstracts checklist. The primary outcome was a mean overall quality score (OQS), which, for each abstract, was a sum of items reported in the modified CONSORT for Abstracts checklist. In addition, some pre-specified factors were evaluated for their association with the reporting quality using simple and multiple linear regression analyses. A total of 949 abstracts (n=262 for RCT and n=687 for non-RCT abstracts) were included and evaluated. Although OQS was significantly greater in RCT than in non-RCT abstracts (mean ± SD, 6.7 ± 0.9 vs 3.3 ± 1.1; P-value<0.001), both mean scores were still less than half of the full score of 15. Only 2 items—objective and conclusions—were adequately reported (>80%) in both types of the abstracts. Items concerning trial design, participants, interventions, randomization, and number randomized were adequately reported only in the RCT abstracts. In contrast, items concerning the study as randomized in the title, clearly defined primary outcome, blinding, numbers analyzed, estimated effect size and its precision for the primary outcome, trial registration, and funding were not reported or reported less than 5% in both RCT and non-RCT abstracts. In this study, 4 factors—year of publication, number of trials reported, number of experimental groups reported, and sample size reported—were associated with OQS. That is, abstracts with higher OQS were published more recently, reported a single trial rather than multiple trials, reported number of experimental groups rather than not reported, and reported sample size rather than not reported. These factors explained about 37.5% of the variance of OQS. In conclusion, reporting quality of RCT and non-RCT abstracts from chicken research was suboptimal. Therefore, efforts especially the development of specific guidelines based on the CONSORT for Abstracts checklist should be made for reporting controlled trial abstracts from chicken research to improve the transparency, completeness, and sufficiently detailed of reporting.
Novel degradation pathway of 2-chloro-4-aminophenol in Arthrobacter sp. SPG
Authors: Arora Pankaj K , Srivastava Alok , Singh Vijay
Published: January 2018

A novel degradation pathway of 2-chloro-4-aminophenol (2C4AP) was studied in an Arthrobacter sp. SPG that utilized 2C4AP as a sole carbon and energy source. The 2C4AP degradation was initiated by a 2C4AP-deaminase that catalyzed the conversion of 2C4AP into chlorohydroquinone (CHQ) with removal of ammonium ion. In the next step, a CHQ-dehalogenase catalyzed the dehalogenation of CHQ to hydroquinone (HQ). The further degradation of HQ was proceeded with ring cleavage and the formation of γ-hydroxymuconic semialdehyde. This is the first report of degradation of 2C4AP by any bacteria.
Delivering a medical school elective with massive open online course (MOOC) technology
Authors: Robinson Robert
Published: January 2018

Introduction: The educational technology of massive open online courses (MOOCs) has been successfully applied in a wide variety of disciplines and are an intense focus of educational research at this time. Educators are now looking to MOOC technology as a means to improve professional medical education, but very little is known about how medical MOOCs compare with traditional content delivery. Methods: A retrospective analysis of the course evaluations for the Medicine as a Business elective by fourth year medical students at Southern Illinois University School of Medicine (SIU-SOM) for the 2012-2015 academic years was conducted. This course was delivered by small group discussions for 2012-2014 and delivered via MOOC technology in 2015. Learner ratings were compared between the two course delivery methods using routinely collected course evaluations. Results: Course enrollment has ranged from 6-19 students per year in the 2012-2015 academic years. Student evaluations of the course are favorable in the areas of effective teaching, accurate course objectives, meeting personal learning objectives, recommending the course to other students, and overall when rated on a 5 point Likert scale. Ratings show no statistically significant difference between the small group or MOOC format versions of the course (p = 1.00 for all comparisons). Discussion: Students found this elective to be an effective means of meeting their personal learning objectives when delivered in a small group discussion format or by using MOOC technology. The primary advantage of this new course format is flexibility of time and place for learners, allowing them to complete the course objectives when convenient for them. The course evaluations indicate this is a change that is acceptable to the target audience. Conclusions: This study shows that learner evaluations of a fourth year medical school elective course do not significantly differ when delivered in small group discussions or via MOOC technology. This suggests that MOOCs may be a reasonable format to deliver medical school courses.
Experimental evidence for concentration-dependence and intra-specific variation of movement behaviour in American lobster (Homarus americanus) larvae
Authors: Pedersen Eric J , Stanley Ryan R.E. , Snelgrove Paul V.R. , Guichard Frederic
Published: January 2018

Predicting dispersal paths of marine larvae with long pelagic durations, such as American lobster (Homarus americanus), requires understanding the cues to which larvae respond, and how that response reflects changes in larval behaviour. If larvae respond to conspecific presence by varying their movement, this behaviour can bias laboratory estimates of environmental responses. We tested whether larvae actively decreased their local intraspecific density by measuring how the vertical distribution of larvae changed under high versus low concentrations of conspecifics. We observed weak increases in vertical dispersion at higher concentrations in both newly-hatched larvae and in post-larvae, but not in intermediate larval stages. Further, we found that larvae from different mothers consistently differed in vertical distribution, which may indicate maternal effects on dispersal behavior. We also tested for differences in horizontal swimming behaviour in high and low concentrations, by fitting a novel random walk model that allowed us to model both larval interactions and persistent turning behaviours. We showed substantial reduction in diffusive behaviour under high concentration conditions resulting from more frequent turns by each larva, but no evidence for consistent avoidance of conspecifics. Our study is the first to demonstrate concentration-dependent behaviours in lobster larvae.