bluuebunny/crossref_metadata_2025 huggingface dataset:
Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method
Authors: Machado António , Castro Joana , Cereija Tatiana , Almeida Carina , Cerca Nuno
Published: January 2018

Bacterial vaginosis (BV) is one of most common vaginal infection and its diagnosis by classical methods reveals low specificity. Our goal was to compare the accuracy of BV diagnosis between the gold standard method, Nugent score, and our novel Peptide Nucleic Acid Fluorescence in situ Hybridization (PNA-FISH) methodology, which targets Lactobacillus and Gardnerella vaginalis populations. Epidemiological characteristic of the population under study (n=150) mirrored what has been described before in other major studies. Our results have shown a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI, from 92.6 to 99.4%), which attests the clinical value of this PNA-FISH approach. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization, and the criteria defined by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis.
Analysis of the self-medication pattern among Brazilian users of the public health system
Authors: Corradi Carregal Daniel , Oliveira Prata Silveira Luiza
Published: January 2018

Self-medication is a common practice not only in Brazil but also in other countries. It consists of "the selection and use of drugs by people to treat self-diagnosed diseases or symptoms and must be understood as an element of self-care". Included in this prescription generic name (or orientation) of drugs by non-qualified people, as friends, family or the pharmacy clerks, these cases are also called "illegal medical practice". The present data confirm the importance of the study of self-medication and support the hypothesis of a naive and excessive belief of our society in the power of drugs, which contributes to the growing demand for pharmaceutical products for any type of disorder, as banal and self-limited. Thus, the drug was incorporated into the dynamics of consumer society and therefore is subject to the same tensions, interests and stiff competition in any market sector, moving away from its primary aim, the prevention, diagnosis and treatment of diseases. These results reinforce the need to inform people on the proper use of medications, as well as appropriate measures to ensure the supply of products needed, effective, safe and affordable.
IslandHunter – A Java-based GI detection software
Authors: Baichoo Shakuntala , Goodur Haswanee , Ramtohul Vyasanand
Published: January 2018

Over the past decade, researchers have discovered that apart from the essential genes, bacterial genomes also contain a variable amount of accessory genes acquired by horizontal gene transfer (HGT) that are categorized as genomic islands (GIs). GIs encode adaptive traits, which might be beneficial for the species under certain growth or environmental conditions. It has always been a challenge for biologists to identify GIs within a bacterial genome as they evolve very rapidly. This paper proposes a standalone software, IslanHunter, that has been developed using Java and BioJava and can extract GI regions using GC content, codon usage bias, dinucleotide frequency bias, tetranucleotide frequency bias, k-mer signature analysis (2-mer, 3-mer, 4-mer, 5-mer, and 6-mer) and presence of mobility genes. IslandHunter provides a simple graphical user interface where disclosed GIs are displayed in a tree-view and a circular graph. Users are presented with options to save the GI regions as blocks of DNA sequences in FASTA format. They can later use these predicted GI regions for further analysis. IslandHunter can take as input, files in GenBank, EMBL or FASTA formats. IslandHunter provides flexible display options and save options. The software has been evaluated against exiting tools with good performance. It is available for evaluation at https://github.com/ShakunBaichoo/IslandHunter .
The degree of change of collembolan community structure related to anthropic soil disturbance
Authors: Sandler Rosana V , Falco Liliana B , Di Ciocco César A , Castro-Huerta Ricardo , Coviella Carlos E
Published: January 2018

Edaphic fauna play a crucial role in soil processes such as organic matter incorporation and cycling, nutrient content, soil structure, and stability. Collembolans in particular, play a very significant role in nutrient cycling and soil structure. The structure and functioning of the soil fauna can in turn be affected by soil use, leading to changes in soil characteristics and its sustainability. Therefore, the responses of soil fauna to different soil management practices, can be used as ecological indicators. Three different soil uses were researched: agricultural fields (AG) with 50 years of continuous farming, pastures entering the agricultural cycle (CG), and naturalized grasslands (NG). For each soil use, three fields were selected. Each sampling consisted of three soil samples per replicate. Collembolans were extracted from the samples and identified to family level. Five families were found: Hypogastruridae, Onychiuridae, Isotomidae, Entomobryidae, and Katiannidae. Soils were also characterized by means of physical and chemical analyses. The index of degree of change of diversity, was calculated. The results show that the biological index of degree of change can detect soil use effects on the collembolan community. Somewhat surprisingly the index showed that the diversity of collembolans is higher in the high anthropic impact site AG, followed by CG and being lower in lower impact sites, NG. The results also show that collembolan families respond differently to soil use. The families Hypogastruridae, Onychiuridae, and Isotomidae presented differences between systems. Therefore collembolan community structure can be a useful tool to assess agricultural practices´ impacts on soil.
Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium
Authors: Perrineau Marie-Mathilde , Price Dana C , Mohr Georg , Bhattacharya Debashish
Published: January 2018

Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strains of the unicellular red alga Porphyridium purpureum that surprisingly contain 42 group II introns in their plastid genomes. We focused on a subset of these introns that encode mobility-conferring intron-encoded proteins (IEPs) and found them to be distributed among the strains in a lineage-specific manner. The reverse transcriptase and maturase domains were present in all lineages but the DNA endonuclease domain was deleted in vertically inherited introns, demonstrating a key step in the loss of mobility. P. purpureum plastid intron RNAs had a classic group IIB secondary structure despite variability in the DIII and DVI domains. We report for the first time the presence of twintrons (introns-within-introns, derived from the same mobile element) in Rhodophyta. The P. purpureum IEPs and their mobile introns provide a valuable model for the study of mobile retroelements in eukaryotes and offer promise for biotechnological applications.
Prolactin and fMRI response to SKF38393 in the baboon
Authors: Miller Brad D. , Marks Lauren A. , Koller Jonathan , Newman Blake J. , Bretthorst G. Larry , Black Kevin J
Published: January 2018

Background: This study’s goal was to provide dose-response data for a dopamine agonist in the baboon using standard methods (replicate measurements at each dose, across a range of doses), as a standard against which to subsequently validate a novel pharmacological MRI (phMRI) method. Dependent variables were functional MRI (fMRI) data from brain regions selected a priori, and systemic prolactin release. Necessary first steps included estimating the magnitude and time course of prolactin response to anesthesia alone and to various doses of agonist. These first steps (“time course studies”) were performed with three agonists, and the results were used to select promising agonists and to guide design details for the single-dose studies needed to generate dose-response curves.

Methods: We studied 6 male baboons (Papio anubis) under low-dose isoflurane anesthesia after i.m. ketamine. Time course studies charted the changes in plasma prolactin levels over time after anesthesia alone or after an intravenous (i.v.) dose of the dopamine D1-like agonists SKF82958 and SKF38393 or the D2-like agonist pramipexole. In the single-dose dopamine agonist studies, one dose of SKF38393 (ranging from 0.0928 – 9.28 mg/kg, N=5 animals) or pramipexole (0.00928 – 0.2 mg/kg, N=1) was given i.v. during a 40-minute blood oxygen level dependent (BOLD) fMRI session, to determine BOLD and plasma prolactin responses to different drug concentrations. BOLD response was quantified as the area under the time-signal curve for the first 15 minutes after the start of the drug infusion, compared to the linearly predicted signal from the baseline data before drug. The ED50(estimated dose that produces 50% of the maximal possible response to drug) for SKF38393 was calculated for the serum prolactin response and for phMRI responses in hypothalamus, pituitary, striatum and midbrain.

Results: Prolactin rose 2.4- to 12-fold with anesthesia alone, peaking around 50-90 minutes after ketamine administration and gradually tapering off but still remaining higher than baseline on isoflurane 3-5 hours after ketamine. Baseline prolactin level increased with age. SKF82958 0.1mg/kg i.v. produced no noticeable change in plasma prolactin concentration. SKF38393 produced a substantial increase in prolactin release that peaked at around 20-30 minutes and declined to pre-drug levels in about an hour. Pramipexole quickly reduced prolactin levels below baseline, reaching a nadir 2-3 hours after infusion. SKF38393 produced clear, dose-responsive BOLD signal changes, and across the four regions, ED50 was estimated at 1.6-7.7mg/kg.

Conclusions: In the baboon, the dopamine D1receptor agonist SKF38393 produces clear plasma prolactin and phMRI dose-response curves. Variability in age and a modest sample size limit the precision of the conclusions.
Neutering of cats and dogs in Ireland; pet owner self-reported perceptions of enabling and disabling factors in the decision to neuter
Authors: Downes Martin J , Downes Marie T , Devitt Catherine , More Simon J
Published: January 2018

Background: Failure among pet owners to neuter their pets results in increased straying and overpopulation problems. Variations in neutering levels can be explained by cultural differences, differences in economic status in rural and urban locations, and owner perceptions about their pet. There are also differences between male and female pet owners. There is no research pertaining to Irish pet owner attitudes towards neutering their pets. This paper identified the perceptions of Irish cat and dog owners that influenced their decisions on pet neutering. Results: Focus groups were conducted with 43 pet (cats and dogs) owners. Two major categories relating to the decision to neuter were identified: (1) enabling perceptions in the decision to neuter (subcategories were: controlling unwanted pet behaviour; positive perceptions regarding pet health and welfare outcomes; perceived owner responsibility; pet function; and the influence of veterinary advice), and (2) disabling perceptions in the decision to neuter (subcategories were: perceived financial cost of neutering; perceived adequacy of existing controls; and negative perceptions regarding pet health and welfare outcomes). Conclusions: Pet owner sense of responsibility and control are two central issues. Understanding how pet owners feel about topics such as pet neutering, can help improve initiatives aimed at emphasising the responsibility of population control of cats and dogs.
Capsules of the diatom Achnanthidium minutissimum arise from fibrillar precursors and foster attachment of bacteria
Authors: Leinweber Katrin , Kroth Peter G
Published: January 2018

Achnanthidium minutissimum is a benthic diatom that may form biofilms on submerged, aquatic surfaces. Within these biofilms, A. minutissimum cells produce extracellular structures which facilitate substrate adhesion, such as stalks and capsules. Both consist of extracellular polymeric substance (EPS), but the microstructure and development stages of the capsules are so far unknown, despite a number of hypotheses about their function, inlcuding attachment and protection. We coupled scanning electron microscopy (SEM) to bright-field microscopy (BFM) and found that A. minutissimum capsules mostly possess an unstructured surface. However, capsule material that was mechanically stressed by being stretched between or around cells displayed fibrillar substructures. Fibrils were also found on the frustules of non-encapsulated cells, implicating that A. minutissimum capsules may develop from fibrillar precursors. Energy-dispersive X-ray (EDX) spectroscopy revealed that the capsule material contains little to no silicon, suggesting that the capsule does not arise from the cell wall. We furthermore show that bacteria attach preferentially to capsules, instead of non-encapsulated A. minutissimum cells, which supports the idea that capsules mediate diatom-bacteria interactions.
A metabolomic approach to health assessment in the whale shark, Rhincodon typus
Authors: Dove Alistair D , Leisen Johannes , Zhou Manshui , Byrne Jonathan , Webb Harry , Gelbaum Les , Viant Mark , Kubanek Julia , Fernandez Facundo
Published: January 2018

Background. No studies have evaluated the biochemistry of whale sharks. The illness of two animals in the collection at Georgia Aquarium provided an opportunity to evaluate the blood chemistry of healthy and unhealthy animals in a search for biomarkers of health in this species. Methods. In the absence of existing data on whale shark biochemistry, we used a discovery based approach called metabolomics, wherein the compounds (and sometimes their concentrations) in a fluid sample can be determined using proton NMR spectroscopy and mass spectrometry. Samples from both healthy and unhealthy whale sharks were compared by both methods. NMR data were analysed by principal components analysis whereas the MS data were evaluated for presence/absence frequency for each analyte Results. PCA of proton NMR data could clearly discriminant between samples from healthy and unhealthy whale sharks. Analysis of PC loadings identified a shift region that was driving this discrimination and subsequent experiments determined that this region consisted of homarine, or n-methyl picolinic acid. Mass spectrometric data revealed 26 compounds that varied meaningfully, implying that they may be biomarkers of health in this species. A set of keto-acids was more frequently encountered in unhealthy animals, which was consistent with their primary clinical presentation (inappetance) Conclusion. Metabolomic approaches proved a powerful way to explore biochemistry of whale sharks, discriminating healthy from unhealthy and offering a selection of potential biomarker compounds for use in future studies of this species. The obvious next step is to attempt to obtain samples from field populations so that
Health care workers’ perspectives about disclosure to HIV-infected children; Cross-sectional survey of health facilities in Gauteng and Mpumalanga provinces, South Africa
Authors: Madiba Sphiwe , Mokgatle Mathildah
Published: January 2018

The perspectives and practices of health care workers (HCWs) regarding disclosure to HIV-infected children have not been adequately investigated ten years after the roll-out of pediatrics antiretroviral therapy (ART). The aim of the study was to examine the opinions of HCWs about disclosure to HIV-infected children and determine their role in disclosure to children accessing ART in centers in South Africa. This was a cross-sectional survey using a semi-structured questionnaire among HCWs in ART centers at three hospitals and 48 primary health facilities in two provinces in South Africa. Of the 206 HCWs, 140 (68.2%) were nurses, 44 (21.5%) were lay counsellors, and 4 (2%) were doctors. The majority (n=183, 89.3%) felt that disclosure benefits children and they should be told about their HIV status. Over half (n=93, 51.4%) recommended 11-18 years as the appropriate age to disclose. Half (n= 99, 48.5%) said that caregivers should take the lead to disclose, 87 (42.7%) said that disclosure is a shared responsibility of caregivers and HCWs, and 18 (8.8%) said HCWs should lead disclosure. HCWs perceived their role as that of preparing the caregiver for disclosure and the child to understand the disease. However, the lack of guidelines and training on disclosure counselling for children affects their ability to fully participate in disclosure to children. There is a need to adopt t he World Health Organizations’ disclosure guidelines for children and adapt them to the local cultural and community contexts and train HCWs to guide, support, and assist caregivers in their disclosure to HIV-infected children.
Amino-acid site variability among natural and designed proteins
Authors: Jackson Eleisha L. , Ollikainen Noah , Covert III Arthur W. , Kortemme Tanja , Wilke Claus O.
Published: January 2018

Computational protein design attempts to create protein sequences that fold stably into pre-specified structures. Here we compare alignments of designed proteins to alignments of natural proteins and assess how closely designed sequences recapitulate patterns of sequence variation found in natural protein sequences. We design proteins using RosettaDesign, and we evaluate both fixed-backbone designs and variable-backbone designs with different amounts of backbone flexibility. We find that proteins designed with a fixed backbone tend to underestimate the amount of site variability observed in natural proteins while proteins designed with an intermediate amount of backbone flexibility result in more realistic site variability. Further, the correlation between solvent exposure and site variability in designed proteins is lower than that in natural proteins. This finding suggests that site variability is too uniform across different solvent exposure states (i.e., buried residues are too variable or exposed residues too conserved). When comparing the amino acid frequencies in the designed proteins with those in natural proteins we find that in the designed proteins hydrophobic residues are underrepresented in the core. From these results we conclude that intermediate backbone flexibility during design results in more accurate protein design and that either scoring functions or backbone sampling methods require further improvement to accurately replicate structural constraints on site variability.
Fighting a moving target: Leapfrogging to new information systems for malaria vector monitoring and control
Authors: Braganca Mauro , de Sousa Bruno , Charlwood Jacques Derek
Published: January 2018

In order to adapt control efforts to the moving target of malaria, new ways of rapidly processing and using data are required to produce usable information. Portable electronic devices with software applications, collectively known as mHealth, are increasingly used to assist health services and manage patient information. Here we describe the development of an mHealth system, using mobile phones, for data collection and analysis in resource-constrained environments. The system overcomes many of the difficulties presented by other mHealth systems. An asynchronous, Internet connection-independent data collection system, similar to web-based architecture, is proposed. Reporting and advanced statistical and epidemiological analysis, with external data integration, such as environmental datasets, is demonstrated by a pilot assessment of the system in Mozambique. We argue that this technology can provide the entomological and epidemiological information needed for sensible decision-making processes and the development of public health policies regarding malaria control.
High prevalence of asymptomatic carrier state with 2009 pandemic influenza virus in a remote rural South Indian community in the year 2012
Authors: Kumar Anita A , Palamaner Subash Shantha Ghanshyam , Sethi Mansha , Khanna Rohit C
Published: January 2018

Introduction:

There is scarcity of global data with regards to rates of asymptomatic carrier state due to 2009 pandemic H1N1 influenza virus. It will be interesting to study asymptomatic carrier state in the year 2012 when the global pandemic has been controlled. In this study we have attempted to evaluate the rates of asymptomatic carrier state due to this virus in a remote rural community from South India.

Methods:

380 consecutive, asymptomatic, community living adults without history of respiratory illness in the last 30 days were studied. Demographic and clinical profile was noted. Throat swab was obtained and tested by RT-PCR (reverse transcriptase polymerase chain reaction) for swine influenza A (HINI) as per CDC (Centers for Disease Control) protocol. Participants who were positive in this test were followed weekly by clinical evaluation for a period of 4 weeks to look for onset of respiratory symptoms.

Results:

Mean age was 42.58 yrs. Males formed 48.3% of the cohort. Mean body mass index was 23.62 kg/m2. 16.3% and 10.5% were diagnosed to have diabetes mellitus and hypertension respectively. None of the study participants had received seasonal influenza vaccine or pandemic H1N1 influenza vaccine. RT-PCR identified asymptomatic infection in 41 participants (10.8%). In uni-variate and multi-variate logistic regression analysis there were no significant associations between having asymptomatic carrier state, diabetes diagnosis, gender, age, BMI, hemoglobin A1C%. On follow-up none of the 41 positive participants developed respiratory symptoms.

Conclusion:

High prevalence of asymptomatic carrier state after 2009 H1N1 influenza virus pandemic was found in our study in the year 2012. The significance of asymptomatic infection remains unclear.
An integrated model of brain structure and function
Authors: Beaumont Nick J
Published: January 2018

The fluid in the extracellular space around the neurons and glial cells is enclosed within the brain, kept separate from the circulation and the rest of the body-fluid. This brain interstitial fluid forms a distinct compartment; a sponge-like “inverse cell” that surrounds all the cells. During neuronal resting and action potentials, sodium and potassium ions shuttle into, and out of, this “Reciprocal Domain” within the brain. This localised flux of ions is the counterpart to all the neuronal electrochemical activity (having the same intensity and duration, at the same sites in the brain), so a complementary version of all that potential information is integrated into this space within the brain. This flux of cations in the Reciprocal Domain may indirectly influence neuronal activity in the brain, creating immensely complex feedback. This Reciprocal Domain is unified throughout the brain, and exists continuously throughout life. This model identifies which species have such Reciprocal Domains, and how many times similar systems evolved. This account of the Reciprocal Domain of the brain may have clinical implications; it could be vulnerable to disruption by chemical insult, traumatic injury or pathology. These are key characteristics of our core selves; this encourages the idea that this Reciprocal Domain makes a crucial contribution to the brain. This hypothesis is explored and developed here.
A longitudinal study of potential mediators of the relationship between inattention and academic achievement in a community sample of elementary school children
Authors: Gray Sarah , Tannock Rosemary
Published: January 2018

Introduction: Behavioral attention, working memory (WM), and academic achievement share significant variance, but the direction of relationships across development are unknown. The aim of the present study was to determine whether WM mediates the pathway between inattentive behaviour and subsequent academic outcomes. Methods: 204 students from grades 1-4 (50% female) were recruited from elementary schools. Participants received assessments of WM and achievement at baseline and one year later. Teachers completed the SWAN behaviour rating scale both years. Mediation analysis with PROCESS (Hayes, 2013) was used to determine mediation pathways. Results: Inattention indirectly and directly influenced math addition, subtraction and calculation scores through its effect on visual-spatial WM. Children who displayed better attention had higher WM scores, and children with higher WM scores had stronger scores on math outcomes. Bias-corrected bootstrap confidence intervals for the indirect effects were entirely below zero for three out of four math outcomes. WM did not mediate the direct relationship between inattention and math and reading fluency scores. Discussion: Findings identify inattention and WM as longitudinal predictors for math addition, subtraction and calculation outcomes one year later, with visual-spatial WM as significant mediator. Results highlight the close relationship between inattention and WM and their importance in the development of math skills.
Evidence for protection of targeted reef fish on the largest marine reserve in the Caribbean
Authors: Pina-Amargós Fabián , González-Sansón Gaspar , Martín-Blanco Félix , Valdivia Abel
Published: January 2018

Effective marine reserves can restore fish abundance and diversity in areas impacted by overfishing, but the outcomes of some reserves in developing countries where resources for enforcement are limited have seldom been evaluated. Here we assess whether the establishment of the largest marine reserve in the Caribbean has had a positive effect on the abundance of commercially valuable reef fish species in relation to neighboring unprotected areas. We surveyed 25 sites including two reef habitats (reef crest and reef slope) inside and outside the marine reserve Gardens of the Queen in Cuba over a 1.5-year period. Densities of the most targeted reef fish species were significantly higher inside than outside the reserve in both habitats. This trend was mostly consistent over time. Supporting evidence from previously published studies in the area indicates that habitat complexity, benthic communities, and the intensity of fishing pressure were similar inside and outside the reserve before reserve establishment. Additionally, reported differential fish behavior towards divers inside and outside the reserve and relative low poaching inside the reserve supported our results. Therefore, the differences observed during the study in the density of targeted reef fish among non-reserve and reserve sites have likely resulted from protection.
Selaginella and the satyr: Euptychia westwoodi larval performance on an ancient plant lineage
Authors: Hamm Christopher
Published: January 2018

Members of the plant genus Selaginella are often considered living fossils, as extant taxa are virtually indistinguishable from 300 Ma fossils. In contrast, the brush-footed butterflies are a relatively recent radiation, having diversified primarily within the last 60 Ma. Satyrs are among the most derived of these butterflies, likely radiated ~35 Ma and are known primarily for their high diversity and propensity to feed on grasses and sedges. In contrast to its close relatives, the Neotropical satyr genus Euptychia also feeds on Selaginella, which is thought to be nutrient poor. Using no choice feeding experiments, I compared growth rates Costa Rican E. westwoodi that were offered two species of Selaginella, to those that were offered Lasiascis rusifolia, a grass commonly fed upon by close relatives. I discovered E. westwoodi larvae fed on two species of Selaginella and there was no difference in mass gained between the two species. However, larvae refused to feed on L. ruscifolia and lost mass over the course of the trial and expired unless they were transferred to Selaginella. To the best of my knowledge, these are the first data to report larval performance of the butterfly genus Euptychia or any Selaginella feeding insect. . Though far from conclusive, these results support the proposition that Euptychia have lost the ability to feed on other host plants and are now specialized on grasses.
Quantization of mental stress using various physiological markers
Authors: Apoorvagiri FNU , Nagananda Mandya Sannegowda
Published: January 2018

The aim of this study is to quantize mental stress by integrating different physiological markers like reaction time, photoplethysmograph (PPG), heart rate variability (HRV) and subjective markers like questionnaire. The study included 10 subjects of age between 22 and 26 years. Study materials include the results of PSS questionnaire, simple reaction time, PPG data, HRV data during a stress inducing stroop test. The study suggests that mental stress can be quantized when stress is induced acquisitively and more accurate quantification of stress can be achieved by integrating many physiological parameters.
The selenium content of SEPP1 versus selenium requirements in vertebrates
Authors: Penglase Sam , Hamre Kristin , Ellingsen Ståle
Published: January 2018

Selenoprotein P (SEPP1) distributes selenium (Se) throughout the body via the circulatory system. The Se content of SEPP1 varies from 7 to 18 Se atoms depending on the species, but the reason for this variation remains unclear. Herein we provide evidence that vertebrate SEPP1 Sec content correlates positively with Se requirements (R2=0.88). As the Se content of full length SEPP1 is genetically determined, this presents a unique case where a nutrient requirement can be predicted based on genomic sequence information.
Causal relationship between occupational dysfunction and depression in healthcare workers: A study using structural equation model
Authors: Teraoka Mutsumi , Kyougoku Makoto
Published: January 2018

Purpose: The purpose of this study is to identify the impacts of occupational dysfunction on depression in healthcare workers (nurses, physical therapists, and occupational therapists) in hospitals.

Methods: Healthcare workers responded to a questionnaire based on the Classification and Assessment of Occupational Dysfunction (CAOD) and Center for Epidemiologic Studies Depression Scale (CES-D). CAOD and CES-D were examined using the following methods: descriptive statistics, exploratory factor analysis (EFA), confirmatory factor analysis (CFA), and a causal sequence model.

Results: CFA of CAOD had 16 items and 5 factors (CFI=0.958, TLI=0.946, RMSEA＝0.092). CFA of CES-D had 20 items and 4 factors (CFI=0.950, TLI=0.942, RMSEA=0.060). The results suggest that occupational dysfunction had positive causal effects on depression (CFI=0.926, TLI=0.920, RMSEA=0.059).

Conclusion: This model refers to the relationship between depression and occupational dysfunction. Therefore, assessment and intervention on classification of occupational dysfunction for healthcare workers would be beneficial in the prevention of depression.
Is there a field proxy for brain size in great-tailed grackles (Quiscalus mexicanus)?
Authors: Logan Corina J , Palmstrom Christin
Published: January 2018

There is an increasing need to validate and collect data approximating brain size on individuals in the field to understand what evolutionary factors drive brain size variation within and across species. We investigated whether we could accurately estimate endocranial volume (a proxy for brain size) as measured by computerized tomography (CT) scans, using external skull measurements and/or by filling skulls with beads and pouring them out into a graduated cylinder for male and female great-tailed grackles. We found that while females had much stronger correlations than males, estimations of endocranial volume from external skull measurements or beads did not correlate with CT volumes at a standard that surpassed our strict criteria. We found no accuracy in the ability of external skull measures to predict CT volumes because prediction intervals from data points overlapped extensively. We conclude that we are unable to detect individual differences in endocranial volume using external skull measurements. These results emphasize the importance of validating and explicitly quantifying the predictive accuracy of brain size proxies for each species, and each sex, under consideration.
Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit
Authors: Scharm Martin , Waltemath Dagmar
Published: January 2018

The COMBINE archive is a digital container format for files related to a virtual experiment in computational biology. It eases the management of numerous files related to a simulation study, fosters collaboration, and ultimately enables the exchange of reproducible research results. The CombineArchive Toolkit is a software for creating, exploring, modifying, and sharing COMBINE archives. Open model repositories such as BioModels Database are a valuable resource of models and associated simulation descriptions. However, so far no tool exists to export COMBINE archives for a given simulation study from such databases. Here we demonstrate how the CombineArchiveToolkit can be used to extract reproducible simulation studies from model repositories. We use the example of Masymos, a graph database with a sophisticated link concept to connect model-related files on the storage layer.
Investigation of the interplay between SKP2, CDT1 and Geminin in cancer cells
Authors: Ballabeni Andrea , Zamponi Raffaella
Published: January 2018

Geminin has a dual role in the regulation of DNA replication: it inhibits replication factor CDT1 activity during the G2 phase of the cell cycle and promotes its accumulation at the G2/M transition. In this way Geminin prevents DNA re-replication during G2 phase and ensures that DNA replication is efficiently executed in the next S phase. CDT1 was shown to associate with SKP2, the substrate recognition factor of the SCF ubiquitin ligase complex. We investigated the interplay between these three proteins in cancer cell lines. We show that Geminin, CDT1 and SKP2 could possibly form a complex and propose the putative regions of CDT1 and Geminin involved in the binding. We also show that, despite the physical interaction, SKP2 depletion does not substantially affect CDT1 and Geminin protein levels. Moreover, we show that while Geminin and CDT1 levels fluctuate, SKP2 levels, differently than in normal cells, are almost steady during the cell cycle of the tested cancer cells.
Bird migratory flyways influence the phylogeography of the invasive brine shrimp Artemia franciscana in its native American range
Authors: Muñoz Joaquín , Amat Francisco , Green Andy J , Figuerola Jordi , Gómez Africa
Published: January 2018

Since Darwin’s time, waterbirds have been considered an important vector for the dispersal of continental aquatic invertebrates. Bird movements have facilitated the worldwide invasion of the American brine shrimp Artemia franciscana, transporting cysts (diapausing eggs), and favouring rapid range expansions from introduction sites. Here we address the impact of bird migratory flyways on the population genetic structure and phylogeography of A. franciscana in its native range in the Americas. We examined the sequence variation for two mitochondrial gene fragments (COI and 16S for a subset of the data) in a large set of population samples representing the entire native range of A. franciscana. Furthermore, we performed Mantel tests and redundancy analyses (RDA) to test the role of flyways, geography and human introductions on the phylogeography and population genetic structure at a continental scale. A. franciscanamitochondrial DNA was very diverse, with two main clades, largely corresponding to Pacific and Atlantic populations, mirroring American bird flyways. There was a high degree of regional endemism, with populations subdivided into at least 12 divergent, geographically restricted and largely allopatric mitochondrial lineages, and high levels of population structure ( Φ ST of 0.92), indicating low ongoing gene flow. We found evidence of human-mediated introductions in nine out of 39 populations analysed. Once these populations were removed, Mantel tests revealed a strong association between genetic variation and geographic distance (i.e., isolation-by-distance pattern). RDA showed that shared bird flyways explained around 20% of the variance in genetic distance between populations and this was highly significant, once geographic distance was controlled for. The variance explained increased to 30% when the factor human introduction was included in the model. Our findings suggest that bird-mediated transport of brine shrimp propagules does not result in substantial ongoing gene flow; instead, it had a significant historical role on the current species phylogeography, facilitating the colonisation of new aquatic environments as they become available along their main migratory flyways.
Of mice, macaques and men: scaling of virus dynamics and immune responses
Authors: Althaus Christian L
Published: January 2018

In this Opinion piece, I argue that the dynamics of viruses and the cellular immune response depend on the body size of the host. I use allometric scaling theory to interpret observed quantitative differences in the infection dynamics of lymphocytic choriomeningitis virus (LCMV) in mice (Mus musculus), simian immunodeficiency virus (SIV) in rhesus macaques (Macaca mulatta) and human immunodeficiency virus (HIV) in humans. There are indications that viral replication and the proliferation of CD8+ T cell responses are slower in larger animals. Whether this influences the ability of the cellular immune responses to eradicate viruses during the acute phase of an infection remains unclear, however.
Disease threat does not predict attractiveness preference in a United Kingdom dataset: a replication attempt and commentary on White et al., Psych Sci 2013
Authors: Nilsonne Gustav , Renberg Adam , Tamm Sandra , Lekander Mats
Published: January 2018

Background: A study by White et al. found that population disease burden predicted preference for attractive politicians in U.S. congressional elections. Aim: We aimed to replicate this finding using data from the United Kingdom. Method: We regressed rated sexiness of elected members of parliament on health metrics from their constituencies: life expectancy, infant mortality, and self-rated health. Results: None of the health metrics predicted rated sexiness of members of parliament. Conclusion: Further investigation is needed to verify whether the proposed relationship is important and whether it is moderated by other factors such as cross-cultural differences.
Reconstructing baselines for Caribbean predatory reef fishes
Authors: Valdivia Abel , Cox Courtney , Bruno John
Published: January 2018

The natural, pre-human, abundance of most large predators is unknown due to the lack of historical data and the poor understanding of the natural factors that control their populations. We assessed the relationship between the biomass of predatory reef fishes and several anthropogenic and environmental variables to (1) predict among site variability in predator abundance in response to both human impacts and natural factors, and (2) estimate historical baselines of fish predator biomass in the absence of humans. We hypothesized that predatory fish abundance declines with human influence but is also strongly associated with natural environmental variability. We assessed the biomass structure of reef fishes at 39 sites over three years across the greater Caribbean. Using generalized linear mixed effect models, we examined the relationships between the biomass of predatory reef fishes and a comprehensive set of 29 anthropogenic, physical, spatial, biotic, and management-related covariates. We used the best explanatory models to predict the biomass of fish predators in the absence of humans. Predatory reef fish biomass was higher in marine reserves but strongly negatively related to human impacts, especially coastal development. Over 50% of the variability in predator biomass, however, was also explained by non-human factors including reef complexity, ocean productivity, and prey abundance. Comparing site-specific predicted values to field observations suggests predatory reef fish biomass has declined by 80-95% in most sites, even within most marine reserves. Bottom-up forces are critical (yet often overlooked) drivers of reef fish communities across gradients of human exploitation. This suggests that we could underestimate historical biomass at sites that provide ideal conditions for predators or greatly overestimate that of seemingly predator-depleted sites that may have never supported large predator populations due to suboptimal environmental conditions. We highlight areas that are natural “hot spots” of predator biomass that can be targeted for strategic protection and restoration.
An genetic algorithm approach for profiling computational performance measures
Authors: Sant Ana Lima Matheus
Published: January 2018

This paper present a Genetic Algorithm(GA) approach for clustering data metric of computational performance measures collected from vmstat and sar tools. The proposed work models the genes, chromosomes, species and environment based on the dataset and presents an algorithm to analyze patterns and classify the records. The proposed method submits the performance information to an N-Dimensional Histogram in order to obtain the distribution of data that is used as input to the cluster initialization. The individual from each species undergoes successive crossover, mutation and selection operations to improve and evolve the initial population to a given environment state. The fitness-function is determined by the N-Dimensional Euclidean distance. The selection method is based on the Roulette-Wheel Selection, Elitist Selection and Truncation Selection. The results presented were obtained from seven test scenarios.
Catch, bycatch and discards of the Galapagos Marine Reserve small-scale handline fishery
Authors: Zimmerhackel Johanna S , Schuhbauer Anna C , Usseglio Paolo , Heel Lena C , Salinas-de-León Pelayo
Published: January 2018

Fisheries bycatch is one of the most significant marine conservation issues as valuable fish are wasted and protected species harmed with potential negative ecological and socio-economic consequences. Even though there are indications that the small-scale handline fishery of the Galapagos Marine Reserve has a low selectivity, information on its bycatch never has been published. We therefore assessed the bycatch of the Galapagos handline fishery by estimating the bycatch ratio, determining species compositions of landings and bycatch, and identifying fishers’ reasons for discarding certain individuals using onboard monitoring and interview data. Moreover, we used interview surveys to reveal historical trends in the bycatch ratio. The estimated bycatch ratio of 0.40 confirmed a low selectivity of this fishery. Characterisation of the catch resulted in a total of 19 target species which were dominated by groupers, and 53 non-target species, with grunts and groupers being most prominent. Most individuals were not landed for economic motivations, either because species (77.4%) or sizes (17.7%) are not marketable and to a lesser extent for regulatory reasons (5.9%). However, sharks were after grunts with 69% the second most often mentioned bycatch taxa during interview surveys. We found that small sized individuals of some of the most exploited species suffer high bycatch mortality because they are used as bait. Moreover, over half of interviewees perceived a historical decrease in bycatch ratios that was explained by a diversification of the catch composition due to the reduction in abundance of the traditionally most important target species. As some target species show signs of overfishing and to date there are no specific regulations for the finfish fishery in place, we recommend the investigation of different gear settings such as the use of different hooks and bait species. Furthermore, we suggest the integration of faster growing species to the local market as well as spatio-temporal closures, and minimum and maximum catch sizes for overexploited species in order to improve the selectivity and sustainability of the Galapagos handline fishery.
Effects of mapping algorithms on gene selection for RNA-Seq analysis: pulmonary response to acute neonatal hyperoxia
Authors: Chu Chin-Yi , Bhattacharya Soumyaroop , Zhou Zhongyang , Yee Min , Lopez Ashley , Lunger Valerie A , Buczynski Bradley , Oreilly Michael , Mariani Thomas
Published: January 2018

Background: A major goal of RNA-Seq data analysis is to reconstruct the full set of gene transcripts expressed in a biological sample in order to quantify their expression levels. The process typically involves multiple steps including mapping short sequence reads to a reference genome, and estimating expression levels based on these mappings. Multiple algorithms and approaches for each processing step exist, and the impact of different methods on estimation of gene expression is not entirely clear.

Methods: We evaluated the impact of three common mapping algorithms on differential expression analysis in an RNA-Seq dataset describing the lung response to acute neonatal hyperoxia. RNA-Seq data generated using the Illumina platform were mapped and aligned using CASAVA, TopHat, and SHRiMP against the mouse genome. Significance Analysis of Microarrays and Cuffdiff were used to identify differentially expressed genes between hyperoxia-challenged and age matched control mice.

Results: 1403 genes were detected as differentially expressed by least one mapping and gene selection method. A majority of genes (>65%) were identified by all three mapping methods, regardless of the gene selection approach. Expression patterns for 52 genes were examined by quantitative polymerase chain reaction (qPCR). Importantly, we found different validation rates for genes selected by each method; 72% for CASAVA, 69% for TopHat and 63% for SHRiMP. Surprisingly, the validation rate for genes selected by all three mapping methods was no greater than the best single method.

Conclusion: The choice of mapping strategy impacts the reliability of gene selection for RNA-Seq data analysis.
Indirect effects of overfishing on Caribbean reefs: Sponges overgrow reef-building corals
Authors: Loh Tse-Lynn , McMurray Steven E , Henkel Timothy P , Vicente Jan , Pawlik Joseph R
Published: January 2018

Consumer-mediated indirect effects at the community-level are difficult to demonstrate empirically. Here, we show an explicit indirect effect of overfishing on competition between sponges and reef-building corals from surveys of 69 sites across the Caribbean. Removal of sponge-eating angelfishes and parrotfishes resulted in > 3 fold increase in overgrowth of corals by sponges, with coral-sponge contact increasing from 11.0% to 25.6%, and these sponges were mostly species palatable to sponge predators. Palatable species have faster rates of growth or reproduction than defended sponges, which instead make metabolically expensive chemical defenses. On average, overfished sites had lower macroalgal cover, contrary to prevailing assumptions about seaweed control by herbivorous fishes. Coral-sponge competition provides an additional and unambiguous justification for marine protected areas (MPAs) in the Caribbean, where the conceptual model of sponge community ecology and defense trade-offs is notable for the clarity of top-down control and indirect effects across a broad geographic region.