bluuebunny/crossref_metadata_2025 huggingface dataset:
Urimem, a membrane that can store urinary proteins simply and economically, makes the large-scale storage of clinical samples possible
Authors: Jia Lulu , Liu Xuejiao , Liu Liu , Li Mingxi , Gao Youhe
Published: January 2018

Biological samples from patients are invaluable for both medical research and medical practice. Ideally, the samples should be preserved for the same period of time as the duration of their corresponding medical records. Urine is a body fluid that can be non-invasively acquired, and it contains important biological information about the patient. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. In other words, urine is likely to be a better biomarker source than blood. Here, we propose a method to adsorb urinary proteins onto a polyvinylidene fluoride (PVDF) membrane called Urimem. The method is very simple and inexpensive and requires minimal sample handling. It does not use organic solvents, and it is environmentally friendly. The proteins on the membrane are dried and stored in vacuum bag, which keeps the protein pattern faithfully preserved. The membrane may even permit storage at room temperature for weeks. The quantity of eluted proteins from the membrane is sufficient for biomarker validation experiments. Using this simple and inexpensive urinary protein preservation method, it is possible to begin preserving urine samples from all consenting patients. Thus, medical research especially biomarker research can be conducted more economically, ultimately benefiting the patients who provided the samples. This sample storage approach can facilitate the biomarker research and potentially change the landscape of medical research and medical practice.
ELM: Enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset
Authors: Ueno Keisuke , Ishii Akihiro , Ito Kimihito
Published: January 2018

Emerging viral diseases, most of which are caused by the transmission of viruses from animals to humans, pose a threat to public health. Discovering pathogenic viruses through surveillance is the key to preparedness for this potential threat. Next generation sequencing (NGS) helps us to identify viruses without the design of a specific PCR primer. The major task in NGS data analysis is taxonomic identification for vast numbers of sequences. However, taxonomic identification via a BLAST search against all the known sequences is a computational bottleneck. Here we propose an enhanced lowest-common-ancestor based method (ELM) to effectively identify viruses from massive sequence data. To reduce the computational cost, ELM uses a customized database composed only of viral sequences for the BLAST search. At the same time, ELM adopts a novel criterion to suppress the rise in false positive assignments caused by the small database. As a result, identification by ELM is more than 1,000 times faster than the conventional methods without loss of accuracy. We anticipate that ELM will contribute to direct diagnosis of viral infections. The web server and the customized viral database are freely available at http://bioinformatics.czc.hokudai.ac.jp/ELM/.
Orexin A exerts more thermogenic than orexinergic functions
Authors: Messina Giovanni , Chieffi Sergio , Monda Marcellino
Published: January 2018

In this article we focus on the role of orexin A in the thermoregulatory functions and its link to food intake. This peptide is named orexin A to emphasize the increase in food intake due to this peptide. The influence of eating behavior could be only secondary to change in the thermoregulatory set-point to reach a determined core temperature. Our viewpoint is compared with vision of other authors, finding possible concordance and disagreement. Activity of the sympathetic nerves system, brown adipose tissue and central body temperatures, heart rate and food intake were monitored to measure the modifications induced by an intracerebroventricular injection of orexin A on the thermoregulation and eating behavior in various experimental conditions.
Coalescent: an Open-Science framework for Importance Sampling in Coalescent theory
Authors: Tewari Susanta , Spouge John L
Published: January 2018

Importance sampling is widely used in coalescent theory to compute data likelihood. Efficient importance sampling requires a trial distribution close to the target distribution of the genealogies conditioned on the data. Moreover, an efficient proposal requires intuition about how the data influence the target distribution. Different proposals might work under similar conditions, and sometimes the corresponding concepts overlap extensively. Currently, there is no framework available for coalescent theory that evaluates proposals in an integrated manner. Typically, problems are not modeled, optimization is performed vigorously on limited datasets, user interaction requires thorough knowledge, and programs are not aligned with the current demands of open science. We have designed a general framework (http://coalescent.sourceforge.net) for importance sampling, to compute data likelihood under the infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. The framework computes the data likelihood and provides maximum likelihood estimates of the mutation parameter. Well-known benchmarks in the coalescent literature validate the framework’s accuracy. We evaluate several proposals in the coalescent literature, to discover that the order of efficiency among three standard proposals changes when running time is considered along with the effective sample size. The framework provides an intuitive user interface with minimal clutter. For speed, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework accessible to a large community.
How to turn USA science degrees into science careers
Authors: Stelling Allison
Published: January 2018

This essay discusses the current situation in USA Science, Technology, Engineering, and Math (STEM) higher education. Possible solutions to the current "skills gap" facing an entire generation of young Americans are considered. It is put forth that an "Industry PhD" may be helpful for guiding the next generation of scientists into stable careers in the sciences. Discovery science, wherein one discovers natural laws of the universe, requires a different toolkit than one needs for doing applied science. This is the proposed "Academic PhD" track. Applied science is usually focused around a three to five year targeted plan, with a directly patentable application as the "end product". Discovery science usually takes longer, and is by its very nature uncertain. However, one must discover natural laws before one can apply and patent them. Both "Academic PhD" and "Industry PhD" tracks are required for healthy economic growth in industrial nations.
Brazil 2014 Butterfly Effect: the 2014 World Cup creates the potential for a malaria outbreak in sub–Saharan Africa
Authors: Faust Christina L , Dobson Andrew P
Published: January 2018

The 2014 World Cup Brazil will create excitement around the globe, but viewership in Africa should be especially high after South Africa 2010 and the growing popularity of football. The time difference and scheduling of matches, however, means that 86% of live matches will be shown during active Anopheles feeding times, increasing risk for malaria for millions of Africans. The aim of this commentary is to draw attention to this potential outbreak and to suggest efforts to mitigate outbreaks.
Detailed comparison of two popular variant calling packages for exome and targeted exon studies
Authors: Warden Charles D , Adamson Aaron W , Neuhausen Susan L , Wu Xiwei
Published: January 2018

The Genome Analysis Toolkit (GATK) is commonly used for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but an equally comprehensive comparison for VarScan not yet been performed. More specifically, we compared four lists of variants called by GATK (using the UnifiedGenotyper and the HaplotypeCaller algorithms, with and without filtering low quality variants) and three lists of variants called using VarScan (with varying sets of parameters). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. We found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a high quality gene list, with high concordance (>97%) when compared to high quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84-88% of the high-quality GATK SNPs in the exome datasets. We also assessed the impact of pre-processing (e.g., indel realignment and quality score base recalibration using GATK). In most cases, these pre-processing steps had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. More broadly, we believe the metrics used for comparison in this study can be useful in assessing the quality of variant calls in the context of a specific experimental design. As an example, a limited number of variant calling comparisons are also performed on two additional variant callers.
Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells
Authors: Mournetas Virginie , Nunes Quentin M. , Murray Patricia A. , Sanderson Christopher M. , Fernig David G.
Published: January 2018

Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.
Child, parent, and healthcare professionals’ perspectives on HIV infection status disclosure to children
Authors: Gachanja Grace , Burkholder Gary J , Ferraro Aimee
Published: January 2018

Background. HIV disclosure is a challenging process for parents and healthcare professionals. The majority of HIV-infected persons live in Sub-Saharan Africa where HIV disclosure guidelines for a parent's and a child's illness are nonexistent. While there are two theoretical models of HIV disclosure, their utility in explaining disclosure in African cultures is largely unknown.

Methods. This qualitative phenomenological study was conducted in Kenya to describe the lived experiences of HIV-positive parents and their children during the disclosure process. Thirty four participants consisting of 16 HIV-positive parents, 7 HIV-positive children, 5 HIV-negative children, and 6 healthcare professionals were engaged in in-depth, semistructured interviews. Interview data were analyzed using the modified Van Kaam method.

Results. HIV disclosure is a complex process involving factors such as a parent's and child's state of health, ART consumption, stigma/discrimination, and sexuality concerns. Parents take years to prepare for and perform disclosure of theirs and/or their children's illnesses to their infected and noninfected children. They perform disclosure when they feel ready in stages, based on the birth order of their children, the perception of “the right time,” the child's understanding and maturity level, and whose illness(es) they intend to disclose at the time of disclosure.

Conclusion. HIV disclosure is challenging and each disclosure session performed is planned and geared to the particular child receiving disclosure. Parents and healthcare professionals are challenged by disclosure and can benefit from creation of HIV disclosure guidelines accompanied by culturally sensitive manuals and training programs aimed at parents and healthcare professionals to ease the process of disclosure.
Study on antibacterial activity of Calotropis procera
Authors: Muzammal Muhammad
Published: January 2018

Comparative study of plant extracts crude and aqueous, methanolic and ethanolic with antibiotics, provide evidence that calotropis procera extracts has the similar antibacterial activity as these antibiotics against test pathogens i.e. Salmonella typhi and E.coli. The analysis of antimicrobial activity of aqueous, methanolic and ethanolic extract of leaves and flower of Calotropis procera was carried out in disc method and also determined MIC value at 600nm through optical density using spectrophotometer. The zone of inhibition produced by extracts was examined and compares it with zone produced by antibiotics. The effect exhibited by ethanolic extract of leaves and flower was significantly greater than the aqueous and methanolic extract of leaves and flower. Crude extracts i.e. latex, leaves, fruit and flower crude extracts. Among them, flower crude extracts shows similar zone of inhibition to test anitibiotics.while in MIC value, we made different concentration of extracts and antibiotics.i.e for crude we made 25%, 50%.75% and 100% concentration of crude juice and for the aqueous, methanolic and ethanolic we made 0.5mg/mL,1mg/mL,2mg/mL,3mg/mL,4mg/mL, 5mg/mL and 6mg/mL in Dimethyl salfoxide, and same antibiotics concentration. Aqueous leaves extracts show MIC at 0.5mg/ml against E.coli while against Salmonella it shows MIC at 1mg/ml... We also determine phytochemical analysis for presences of different compounds in crude extracts. The obtained results provide a support for the use of Calotropis procera, in traditional medicine and suggest its further advance investigation.
Resolving antagonistic interactions among clinical isolates of Acinetobacter baumannii with phylogenetic analysis
Authors: Heitkamp Rae , Sahl Jason , Summers Amy , Roth Amanda L. , Kirkup Benjamin C
Published: January 2018

Acinetobacter baumannii is a nosocomial species frequently isolated from the traumatic wounds of injured military personnel and increasingly detected in civilian healthcare facilities. Many clinical isolates of A. baumannii are drug resistant, so new treatments are needed for infections. Recently, the ability of strains of conspecific bacteria to inhibit the growth of other strains has been observed in increasing numbers of species. We previously reported on intraspecific semisolid-phase growth inhibition (antagonism) among 94 clinical isolates of A. baumannii. These antagonistic interactions may be the result of genetically-encoded molecules, so more closely related isolates would be expected to produce similar patterns of interactions caused by identically active gene products. However, the phylogeny of clinical A. baumannii below the species level has not been established for this set of isolates.In this study, we used Phylomark to identify three genetic loci that recapitulated a whole-genome phylogeny of published A. baumannii genomes and we created a parsimony-based phylogeny from the 1.2 kilobase concatenated sequences. One clade appeared to exhibit the highest incidence of antagonistic interactions against all other isolates screened, except for itself and one relatively distant clade. This clade's nearest neighbor was susceptible to the most consistent antagonistic activity by the first clade; both of these clades appear to belong to MLST ST1 with reference strain AYE. Other isolates with high rates of antagonistic activity fall outside of ST1. Future studies aim to elucidate the genetic basis of the antagonism phenotype in clinical Acinetobacter, particularly in the most antagonistic isolates. The next step will be to mine these interactions to identify expressed antimicrobial molecules with potential for drug therapy.
Medicines, shaken and stirred: a critical review on the ecotoxicology of pharmaceutical mixtures
Authors: Backhaus Thomas
Published: January 2018

Analytical monitoring surveys routinely confirm that organisms in the environment are exposed to complex multi-component pharmaceutical mixtures. We are hence tasked with the challenge to take this into consideration when investigating the ecotoxicology of pharmaceuticals. This review first provides a brief overview of the fundamental approaches for mixture toxicity assessment, which is then followed by a critical review on the empirical evidence that is currently at hand on the ecotoxicology of pharmaceutical mixtures. It is concluded that, while the classical concepts of Concentration Addition and Independent Action (Response Addition) provide a robust scientific footing, several knowledge gaps remain. This includes in particular the need for more and better empirical data on the effects of pharmaceutical mixtures on soil organisms as well as marine flora and fauna, and exploring the quantitative consequences of toxicokinetic, toxicodynamic and ecological interactions. Increased focus should be put on investigating the ecotoxicology of pharmaceutical mixtures in environmentally realistic settings.
Patient beliefs and attitudes towards the acceptability of receiving alcohol use enquiry from general practitioners: a literature review
Authors: Leong Louis , Tam Chun Wah Michael
Published: January 2018

Background: Routine use of alcohol screening questionnaires is recommended in primary care, but patient beliefs and attitudes towards the acceptability of receiving alcohol enquiry from general practitioners (GPs) are unclear.

Methods: We searched medical databases to identify published empirical research on patient beliefs, attitudes and experiences towards receiving alcohol discussions from GPs. Coherent themes were synthesised from the results of the included studies using a realist perspective. Seventeen studies were included in the review – the majority were quantitative surveys from the UK, Nordic countries, North America and Australia.

Results and Discussion: GPs are seen to be legitimate providers of lifestyle advice, but patients may not find alcohol enquiry acceptable in a specific consultation. Alcohol discussions are less acceptable than those on other health promotion topics. The context of the consultation, such as the reason for presenting and the patient-doctor relationship, has an important influence on the situational acceptability of alcohol enquiry.

Conclusion: Although GP involvement in health promotion is perceived as legitimate, alcohol enquiry in consultations can be fraught and unwelcome. Contextual factors pertaining to the consultation appear to be important but these have not been well explored in the literature. Conclusions from this review should be restricted to societies with “Temperance” drinking cultures.
Limits of uncertainty about estimates of probability of ecological events
Authors: Keil Petr
Published: January 2018

Probability (\(P\)) of binomial event is a commonly estimated quantity in ecology. Recently, interest has moved to estimation and communication of the associated uncertainty about the estimates of \(P\). Here I use the principle of maximum entropy to introduce truncated exponential probability density function \(f(P)\) on a closed interval [0,1] that gives expectation of the uncertainty, given that the only information we have is a single-number estimate \(P_{single}\), which I assume to represent mean \(\mu\) of an unknown probability density distribution of \(P\). This expectation puts an upper bound on the maximum uncertainty about \(P\). I also present the associated cumulative distribution function, quantile function, and random number generator. I demonstrate the MaxEnt \(f(P)\) on a species distribution model predicting probability of a species' occurrence on a geographic map. The MaxEnt \(f(P)\) presented here can be used to make conservative probabilistic statements about probability statements, and it can be used as an alternative to beta distribution, and as the least informative prior distribution of \(P\) in Bayesian modelling.
A surge of p-values between 0.041 and 0.049 in recent decades (but negative results are increasing rapidly too)
Authors: de Winter Joost , Dodou Dimitra
Published: January 2018

It is known that statistically significant (positive) results are more likely to be published than non-significant (negative) results. However, it has been unclear whether any increasing prevalence of positive results is stronger in the “softer” disciplines (social sciences) than in the “harder” disciplines (physical sciences), and whether the prevalence of negative results is decreasing over time. Using Scopus, we searched the abstracts of papers published between 1990 and 2013, and measured longitudinal trends of multiple expressions of positive versus negative results, including p-values between 0.041 and 0.049 versus p-values between 0.051 and 0.059, textual reporting of “significant difference” versus “no significant difference”, and the reporting of p < 0.05 versus p > 0.05. We found no support for a “hierarchy of sciences” with physical sciences at the top and social sciences at the bottom. However, we found large differences in reporting practices between disciplines, with p-values between 0.041 and 0.049 over 1990–2013 being 65.7 times more prevalent in the biological sciences than in the physical sciences. p-values near the significance threshold of 0.05 on either side have both increased but with those p-values between 0.041 and 0.049 having increased to a greater extent (2013-to-1990 ratio of the percentage of papers = 10.3) than those between 0.051 and 0.059 (ratio = 3.6). Contradictorily, p < 0.05 has increased more slowly than p > 0.05 (ratios = 1.4 and 4.8, respectively), while the use of “significant difference” has shown only a modest increase compared to “no significant difference” (ratios = 1.5 and 1.1, respectively). We also compared reporting of significance in the United States, Asia, and Europe and found that the results are too inconsistent to draw conclusions on cross-cultural differences in significance reporting. We argue that the observed longitudinal trends are caused by negative factors, such as an increase of questionable research practices, but also by positive factors, such as an increase of quantitative research and structured reporting.
A suffrutescent Helianthus from Los Angeles County, California
Authors: Baznekian Aleksi
Published: January 2018

A suffrutescent individual, belonging to the genus Helianthus, and bearing resemblance to H. annuus, has been observed in Los Angeles County, California. This individual was observed to woody proximally; not a character of the herbaceous annual sunflower, H. annuus. Photographs of this woody individual and a general herbaceous representative H. annuus are presented in this article. Dr. David J. Keil, an Asteraceae (sunflower family) taxonomist, suggests that a new shrubby species of Helianthus may be present in California, and thus, this suffrutescent individual may be a representative of that woody species. It may also be a woody variety of H. annuus.
Combining Physical and Virtual Contexts through Augmented Reality: Design and Evaluation of a prototype using drug box as marker for antibiotics’ training
Authors: Nifakos Sokratis , Tomson Tanja , Zary Nabil
Published: January 2018

Introduction: Antimicrobial resistance is a global health issue. Studies have shown that improved antibiotic prescription education among healthcare professionals reduces mistakes during the antibiotic prescription process. The aim of this study was to investigate novel educational approaches that through the use of Augmented Reality technology could make use of the real physical context and thereby enrich the educational process of antibiotics prescription. The objective is to investigate which type of information related to antibiotics could be used in an augmented reality application for antibiotics education. Methods: This study followed the Design Based Research Methodology composed of the following main steps: problem analysis, investigation of information that should be visualized for the training session and finally the involvement of the end users the development and evaluation processes of the prototype. Results: Two of the most important aspects in antibiotics’ prescription processes, to represent in an augmented reality application, are the antibiotic guidelines and the side effects. Moreover, this study showed how this information could be visualized from a mobile device using an Augmented Reality scanner and antibiotic drug boxes as markers. Discussion: In this study we investigated the usage of objects from a real physical context such as drug boxes and how they could be used as educational resources. The logical next steps are to examine how this approach of combining physical and virtual contexts through Augmented Reality applications could contribute to the improvement of competencies among healthcare professionals and its impact on the decrease of antibiotics resistance.
Visual Analytics in healthcare education: Exploring novel ways to analyze and represent big data in undergraduate medical education
Authors: Vaitsis Christos , Nilsson Gunnar , Zary Nabil
Published: January 2018

Big data in undergraduate medical education that consist the medical curriculum are beyond human abilities to be perceived and analyzed. The medical curriculum is the main tool used by teachers and directors to plan, design and deliver teaching activities, assessment methods and student evaluation in medical education in a continuous effort to improve it. It remains unexploited mainly for medical education improvement purposes. The emerging research field of Visual Analytics has the advantage to combine data analysis and manipulation techniques, information and knowledge representation, and human cognitive strength to perceive and recognize visual patterns. Nevertheless, there is lack of findings reporting use and benefits of Visual Analytics in medical education.

We analyzed data from the medical curriculum of an undergraduate medical program concerning teaching activities, assessment methods and results and learning outcomes in order to explore Visual Analytics as a tool for finding ways of representing big data from undergraduate medical education for improvement purposes. We used Cytoscape to build networks of the identified aspects and visualize them.

The analysis and visualization of the identified aspects resulted in building an abstract model of the examined data from the curriculum presented in three different variants; (i) learning outcomes and teaching methods, (ii) examination and learning outcomes and (iii) teaching methods, learning outcomes, examination results and gap analysis

This study identified aspects of medical curriculum. The implementation of VA revealed three novel ways of representing big data from undergraduate medical education. It seems to be a useful tool to explore such data and may have future implications on healthcare education. It also opens a new direction in medical informatics research.
A genetic manipulation of motor neuron excitability does not alter locomotor output in Drosophila larvae
Authors: McKiernan Erin C.
Published: January 2018

Are motor neurons just passive relayers of the signals they receive? Or, do motor neurons shape the signals before passing them on to the muscles, thereby influencing the timing of motor behavior? Few direct tests of the role of motor neuron intrinsic properties in shaping motor behavior have been carried out, and many questions remain about the role of specific ion channel genes in motor neuron function. In this study, two potassium channel transgenes were expressed in Drosophila larval motor neurons to increase their excitability. Mosaic animals were created in which some identified motor neurons expressed the transgenes while others did not. Motor output underlying crawling was compared in muscles innervated by control and experimental neurons in the same animals. No effect of the transgenic manipulation on motor output was seen. Possible explanations for these results are discussed, and future experiments are outlined that could shed light on how the larval nervous system produces normal motor output in the face of altered motor neuron excitability.
Mapping of dextral : sinistral proportions in the chirally dimorphic land snail Amphidromus inversus
Authors: Schilthuizen Menno , Looijestijn Sylvia , Chua Sek Chuan , Aguirre Gutiérrez Jesús , Castillo Cajas Ruth F.
Published: January 2018

One of the very few snail taxa that display genetic antisymmetry (that is, roughly equal mixes of genetically determined clockwise [D] and anticlockwise [S] coiled individuals within a single population) are the circa 35 species of the tropical tree snail subgenus Amphidromus. Previous work has shown that this may be due to a particular type of sexual selection, in which sperm transfer is improved in copulations between the two mirror-image morphs. However, it is not yet clear why so often significant deviations from 50:50 proportions are found. Modelling studies show that population structure will affect the degree by which the dimorphism is skewed towards the morph associated with the recessive allele. In this study, we mapped the proportions of sinistrals (PropS) in 56 demes in A. inversus on the Malaysian island of Kapas. We also mapped population density, predation rates, and several measures of vegetation structure. Our results show that PropS amounts on average to 0.65, but across the island it varies from 0.30 to 0.85. Density and overall predation are inversely correlated. A general linear model selection procedure results in the proportion of sinistrals to be positively correlated with density and predation on dextrals. We find no overwhelming evidence for a role for drift in explaining the deviations from equal S:D proportions, but we do argue that further study of crab-snail interactions may be warranted.
Removal of corallivorous snails as a proactive conservation tool
Authors: Williams Dana E , Miller Margaret W , Bright Allan J , Cameron Caitlin M
Published: January 2018

Corallivorous snail feeding is a common source of tissue loss for the threatened coral Acropora palmata, accounting for roughly one-quarter of tissue loss in monitored study plots over seven years. However, corallivory by Coralliophila abbreviata is one of the few major sources of partial mortality (contrasting with threats such as bleaching, disease, or storm disturbances) that may be locally managed. We conducted a field experiment to explore the effectiveness and feasibility of snail removal. Long-term monitoring plots on six reefs in the upper Florida Keys were assigned to one of three removal treatments: 1) removal from A. palmata only, 2) removal from all host coral species, or 3) no-removal controls. During the initial removal in June 2011, 639 snails were removed from twelve 150 m2 plots. Snails were removed two additional times during a seven month “removal phase”, then counted at five surveys over the next 19 months to track recolonization. At the conclusion, snails were collected, measured, and sexed. Before-After-Control-Impact analysis revealed that both snail abundance and feeding scar prevalence were reduced in removal treatments compared to the control, but there was no difference between removal treatments. Recolonization by snails to baseline abundance is estimated to be 4.3 years and did not differ between removal treatments. Recolonization rate was significantly correlated with baseline snail abundance. Maximum snail size decreased from 47.0 mm to 34.6 mm in the removal treatments. The effort required to remove snails from A. palmata was 30 diver minutes per 150 m2 plot, compared with 51 minutes to remove snails from all host corals. Since there was no additional benefit observed with removing snails from all host species, removals can be more efficiently focused on only A. palmata colonies, and in areas where C. abbreviata abundance is high, to effectively conserve A. palmata in targeted areas.
Using Encyclopedia of Life’s TraitBank to identify plant traits associated with vulnerability
Authors: Caldwell Iain R. , Hart Edmund M.
Published: January 2018

Certain biological traits seem to predispose some species to greater extinction risk than others and, when vulnerability information is limited, could be used as proxies to identify understudied species likely in need of protection. In the past, identifying broadly applicable traits associated with extinction risk has been hampered by the difficulty of collecting information for a broad range of species (both geographically and taxonomically), with most comparative analyses focusing on regional and/or taxon specific patterns. However, efforts to collect and compile existing trait information from regional and taxon specific datasets into a single repository are making it possible to analyze patterns between traits and vulnerability on ever broader scales. We compared trait information from one such repository, the Encyclopedia of Life (EOL) TraitBank, to information on threat status from the International Union for the Conservation of Nature (IUCN) Red List to determine whether such consolidated data can help either clarify previously identified associations or identify new associations between plant traits and threat risk. Using generalized linear mixed effects models (GLMM’s) we found five plant traits that could be used to predict whether a species is threatened or not: ‘plant growth form’, ‘life cycle habit’, ‘low temperature tolerance’, ‘soil depth’ and ‘foliage porosity in winter’. Threatened plant species tend to be trees rather than shrubs or grasses, live for more than one season (i.e. perennials), be less tolerant of cold temperatures, require deep soil for good growth, and have less dense foliage in the winter. Both ‘plant growth form’ and ‘life cycle habit’ have been identified as correlates of vulnerability in past studies and both are relatively easy to use as diagnostic characters, which is ideal for identifying understudied species of potential conservation concern. However, how these two traits relate to vulnerability seems context dependent, with opposite relationships in past regional or taxon specific studies. Unfortunately we could not identify further traits that could add explanatory power to those relationships with the existing data on EOL’s TraitBank but the repository is still growing and the inclusion of additional traits and/or species from other datasets could clarify these relationships further.
Arterial spin labeling versus BOLD in pharmacological fMRI
Authors: Stewart Stephanie , Koller Jonathan , Campbell Meghan , Black Kevin
Published: January 2018

A carefully controlled study allowed us to compare the sensitivity of ASL (arterial spin labeling) and BOLD (blood oxygen level dependent) fMRI for detecting the effects of the adenosine A2a antagonist tozadenant in Parkinson disease . Only ASL detected the direct effect of tozadenant. BOLD was more sensitive to a cognitive task, which (unlike most drugs) allows on-off comparisons over short periods of time. Neither ASL nor BOLD could detect a cognitive-pharmacological interaction. These results are consistent with the known relative advantages of each fMRI method, and suggest that for drug development, directly imaging pharmacodynamic effects with ASL may have advantages over cognitive-pharmacological interaction BOLD, which has hitherto been the more common approach to pharmacological fMRI.
Synthesis and anti-tubercular activity of 3-substituted benzothiophene-1,1-dioxides
Authors: Chandrasekera N. Susantha , Bailey Mai A , Files Megan , Alling Torey , Florio Stephanie K , Ollinger Juliane , Odingo Joshua , Parish Tanya
Published: January 2018

We demonstrated that the 3-substituted benzothiophene-1,1-dioxide class of compounds are effective inhibitors of Mycobacterium tuberculosis growth under aerobic conditions. We examined substitution at the C-3 position of the benzothiophene-1,1-dioxide series systematically to delineate structure-activity relationships influencing potency and cytotoxicity. Compounds were tested for inhibitory activity against virulent M. tuberculosis and eukaryotic cells. The tetrazole substituent was most potent, with a minimum inhibitory concentration (MIC) of 2.6 µM. However, cytotoxicity was noted with even more potency (Vero cell TC50 = 0.1 µM). Oxadiazoles had good anti-tubercular activity (MICs of 3–8 µM), but imidazoles, thiadiazoles and thiazoles had little activity. Cytotoxicity did not track with anti-tubercular activity, suggesting different targets or mode of action between bacterial and eukaryotic cells. However, we were unable to derive analogs without cytotoxicity; all compounds synthesized were cytotoxic (TC50 of 0.1–5 µM). We conclude that cytotoxicity is a liability in this series precluding it from further development. However, the series has potent anti-tubercular activity and future efforts towards identifying the mode of action could result in the identification of novel drug targets.
The integrated model of consciousness
Authors: Smith Graeme E
Published: January 2018

Consciousness is simple by definition, and complex by extension. For the first time we may have a look into some of the complexities of Human Consciousness, and how they may have accreted to core consciousness over millenia. From a Core Consciousness that can be traced to the Optical Tectum in early pre-amphibious ancestors, or even earlier in the evolutionary record, to an advanced model that includes at least 6 different sub-models, and grew from an early model of consciousness, we will see the accretion of layers of consciousness upon the basic core consciousness despite setbacks and variations in the evolution of the brain. Similar to some theories that make the mistake of Scala Naturae this theory shows a scale of elaboration that is not meant to reflect the pattern of evolution, merely a list of elaborations that has become standard within the human brain. It is not meant to be exhaustive, merely indicative of the complexity of consciousness as experienced by human beings. That the stages in development of the human brain make a track through time, is not meant to mean that in fact this track was as straight forward or simple as the model might suggest.
A note of caution: the threshold of toxicological concern (TTC) is unsuited as a decision rule for deciding whether mixture risk assessment is necessary
Authors: Backhaus Thomas
Published: January 2018

The threshold of toxicological concern has been suggested as a decision rule on whether a mixture risk assessment is required. According to the recent opinion on mixture toxicity, published by the EU scientific committees, mixture effects are not to be expected, if the mixture components do not share the same mode or mechanism of action and are present at or below their individual TTCs. This, however, ignores the statistical error propagation that is encountered when handling multi-component chemical mixtures, which results in a huge probability that one or more mixture components are de facto more toxic than estimated by the corresponding TTC. It is hence argued that the TTC is a valuable tool to bridge data gaps in case experimental toxicity data are missing, but it is unsuited without further refinement as a decision criterion on whether a mixture assessment is needed in a given exposure scenario.
The Kern Fever in the Emergency Department Study (Kern FEDS): Clinical appearance, serious bacterial illness, and the meaning of uncertainty.
Authors: Walsh Paul , Capote Allan , Garcha Davinder , Nguyen Vu , Sanchez Yvette , Mendoza Nanse , Thabit Christina , Aguilar Valerie , Pusavat James
Published: January 2018

Background: Emergency department (ED) fever management algorithms require the clinician to categorize febrile children as ‘ill’ or ‘not ill’ appearing when determining the risk for serious bacterial illness (SBI). This study describes a natural experiment where an ED pediatric chart allowed clinicians a third option, ‘unsure’. Hypotheses: We hypothesized (1) that chart prompts would improve documentation of clinical appearance, and (2) that exam findings and prevalence of serious bacterial illness in infants categorized as ‘unsure’ would be intermediate between those who were ill and not ill appearing. Design: We conducted a retrospective study of 3005 ED patients aged 0-24 months who had microbiology testing for fever in the ED between 1/1/2006 and 11/30/2009. We modeled overall appearance as the dependent and individual physical findings as the independent variables with ordinal logistic regression to help establish the validity of clinical appearance as a concept. We then compared the prevalence of the components of SBI, bacterial meningitis, pneumonia, urinary tract infection (UTI) and positive blood cultures, between the categorizations, not ill appearing, unsure and ill appearing. Results: Clinical appearance was documented in 60/583 (10.3%) whose encounter was recorded on the template without prompts versus 2036/2420 (84%) with prompts (p<0.001). Age odds ratio (OR) 1.04 (95% CI 1.01, 1.07) weight (quintile) OR 0.81 (95% CI 0.70, 0.95), dehydration OR 9.68 (95% CI 7.17, 13.01), tachycardia OR 1.31 (95% CI 1.04, 1.68), tachypnea OR 2.44 (95% CI 1.61, 3.68), prior antipyretics OR 0.65 (95% CI 0.52, 0.83) and prior antibiotics OR 2.56 (95%CI 1.71, 3.82) were associated with appearance. There was an ordinal relationship between appearance and the prevalence of bacterial meningitis and pneumonia for the categories ill appearing, unsure, and not ill appearing. The prevalence of positive blood cultures among children categorized as ‘not ill appearing' and 'unsure' was similar. Urinary tract infection (UTI) prevalence was similar regardless of appearance. Conclusion: Charting prompts increased documentation of clinical appearance. There was an ordinal relationship between the prevalence of meningitis, and pneumonia, across the categories 'ill appearing', 'unsure' and 'not ill appearing'. This was not the case for blood cultures or UTI.
Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: Analysis with multiple merger coalescent models
Authors: Árnason Einar , Halldórsdóttir Katrín
Published: January 2018

A high-fecundity organisms, such as Atlantic cod, can withstand substantial natural selection and can at any time simultaneously replace alleles at a number of loci due to their excess reproductive capacity. High-fecundity organisms may reproduce by sweepstakes leading to highly skewed heavy-tailed offspring distribution. Under such reproduction the Kingman coalescent of binary mergers breaks down and models of multiple merger coalescent are more appropriate. Here we study nucleotide variation at the Ckma (Creatine Kinase Muscle type A) gene in Atlantic cod. The gene shows extreme differentiation between the North (Canada, Greenland, Iceland, Norway, Barents Sea) and the South (Faroe Islands, North-, Baltic-, Celtic-, and Irish Seas) with a between regions FST > 0.8 whereas neutral loci show no differentiation. This is evidence for natural selection. The protein sequence is conserved by purifying selection whereas silent and non-coding sites show extreme differentiation. Relative to outgroup the site-frequency spectrum has three modes, a mode at singleton sites and two high frequency modes at opposite frequencies representing divergent branches of the gene genealogy that is evidence for balancing selection. Analysis with multiple-merger coalescent models can account for the high frequency of singleton sites and indicate reproductive sweepstakes. Coalescent time scales with population size and with the inverse of variance in offspring number. Parameter estimates using multiple-merger coalescent models show fast time-scales. Time-scales of mitochondrial DNA are about square root of the effective population size and time-scales of nuclear genes are much faster.
Quantitative measurement of odor detection thresholds using an air dilution olfactometer, and association with genetic variants in a sample of diverse ancestry
Authors: Cook Gillian R , Krithika S. , Edwards Melissa , Kavanagh Paula , Parra Esteban J
Published: January 2018

Genetic association studies require a quantitative and reliable method for odor threshold assessment in order to examine the contribution of genetic variants to complex olfactory phenotypes. Our main goal was to assess the feasibility of a portable Scentroid air dilution olfactometer for use in such studies. Using the Scentroid SM110C and the SK5 n-butanol Sensitivity Kit (IDES Canada Inc.), n-butanol odor thresholds were determined for 182 individuals of diverse ancestry (mean age: 20.4 ± 2.5 years; n = 128 female; n = 54 male). Threshold scores from repeat participants were used to calculate a test-retest reliability coefficient, which was statistically significant (r = 0.754, p < 0.001, n = 29), indicating that the Scentroid provides reliable estimates of odor thresholds. In addition, we performed a preliminary genetic analysis evaluating the potential association of n-butanol odor thresholds to six single-nucleotide polymorphisms (SNPs) putatively involved in general olfactory sensitivity (GOS). The results of multiple linear regression analysis revealed no significant association between the SNPs tested and threshold scores. However, our sample size was relatively small, and our study was only powered to identify genetic markers with strong effects on olfactory sensitivity. Overall, we find that the Scentroid provides reliable quantitative measures of odor detection threshold and is well suited for genetic studies of olfactory sensitivity.
A new potentially promising concept in diagnosis of occult infection with help of PET-CT
Authors: Sarsenov Dauren , Ergün Eser Lay
Published: January 2018

In the light of recent advances in radionuclide diagnostics of occult infectious states, it is clearly seen that positron emission tomography will have a part in routine work-up especially for critically ill patients in near future. For the purpose of further development of a specific agent that might be capable of detecting a living microorganism in occult focus inside the host organism, we come with a concept of probably a new radiopharmaceutical agent besides well-known fluorinated glucose, labelled leucocytes and gallium based radiopharmaceuticals. The aim of this opinion letter is to propose a specific agent for almost all bacteria and fungi genera not depending on host’s metabolism, thus letting differentiation of infection foci from host’s tissue. The discussion of this letter is mainly on the background of developing a compound for folate biosynthesis in bacteria and fungi which is a specific way of metabolization by the mentioned species which is provided by microbiological studies.