bluuebunny/crossref_metadata_2025 huggingface dataset:
An integrated pipeline for NGS and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester,1857) Loss, 1899 (Digenea: Fasciolidae)
Authors: Biswal Devendra Kumar , Ghatani Sudeep , Shylla Jollin A , Sahu Ranjana , Mullapudi Nandita , Bhattacharya Alok , Tandon Veena
Published: January 2018

Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create a NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest trematode mitochondrial genome sequenced to date. The noncoding control regions are separated into two parts by the tRNA-Gly gene and donot contain either tandem repeats or secondary structures, which are typical for trematode control regions. The gene content and arrangement are identical to that of F. hepatica. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The mtDNA for the intestinal fluke is reported herein for the first time by our group that would help invesigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data. More so, it would serve as a resource for comparative mitochondrial genomics and systematic studies of trematode parasites.
Effectiveness of telenutrition in a women's weight loss program
Authors: Kuzmar Isaac E , Cortés-Castell Ernesto , Rizo Mercedes
Published: January 2018

Objective: To evaluate the effectiveness of telenutrition versus traditional nutritional consultation for obese patients. Methods: A comparative clinical study was conducted among 233 (including 20 dropouts and 60 failures) obese or overweight women who consulted a nutrition clinic in Barranquilla (Colombia) for nutritional assessment by telenutrition or traditional attention that includes a weekly follow-up consultation over 16 weeks, food consumption patterns, Body Mass Index (BMI, kg/m2) register, waist and hip circumference register. Treatment response and difference between telenutrition and traditional consultation were made according to BMI, waist, hip and initial-waist/height ratio. Data´s nonparametric statistical comparison was made. Results: In 68 (29.2%) women who chose traditional attention, 9 (37.5%) dropped out, 24 (40%) failed and 35 (23.5%) were successful, showing 1.4%(1.0 SD) BMI loss, 5.8% (3.4 SD) in waist circumference, 4.5% (2.8 SD) in hip circumference and 0.04% (0.02 SD) in iwaist/height ratio. In 165 (70.8%) women who chose telenutrition, 15 (62.5%) dropped out, 36 (60%) failed and 114 (76.5%) were successful, showing 1.1% (1.0 SD) BMI loss, 5.0% (3.2 SD) in waist circumference, 3.5% (3.1 SD) in hip circumference and 0.03% (0.02 SD) in iwaist/height ratio. A significance level of p<0.05 is considered. Conclusion: Telenutrition has a failure or dropout risk factor about half values of traditional consultation with slightly statistically significant differences. This study concludes that telenutrition can support or sometimes replace the traditional consultation when developing weight loss programs in obese women.
Ingestion of plastics at sea: does debris size really matter?
Authors: Reisser Julia , Proietti Maira , Shaw Jeremy , Pattiaratchi Charitha B
Published: January 2018

Most of our knowledge on plastic ingestion by zooplankton comes from experiments exposing invertebrates to plastic particles smaller than their feeding apparatus. By examining millimetre-sized marine plastics using a scanning electron microscope, we putatively identified some surface textures as feeding marks produced by invertebrates grazing upon the plastic biofilm. We observed sub-parallel linear scrapes with 5-14 μm spacing, which is similar to typical distances between teeth of the mandibular gnathobases of copepods. We also observed peculiar rounded marks close to an unidentified marine worm. Small portions of the plastic particles were apparently removed, and perhaps ingested, during these putative grazing activities. Thus, we suggest that (1) plastic biofouling induces plastic ingestion, and (2) plastic pieces must not necessarily be smaller than the organism for a feeding interaction to occur. Experiments exposing invertebrates to millimeter-sized plastics may support these suggestions.
Patterns of evolution of MHC Class II genes of crows (Corvus) suggest trans-species polymorphism
Authors: Eimes John A , Townsend Andrea K , Sepil Irem , Nishiumi Isao , Satta Yoko
Published: January 2018

A distinguishing characteristic of genes that code for the major histocompatibility complex (MHC) is that alleles often share more similarity between, rather than within species. There are two likely mechanisms that can explain this pattern: convergent evolution and trans-species polymorphism (TSP), in which ancient allelic lineages are maintained by balancing selection and retained by descendant species. Distinguishing between these two mechanisms has major implications in how we view adaptation of immune genes. In this study we analyzed exon 2 of the MHC class IIB in three passerine bird species in the genus Corvus: jungle crows (Corvus macrorhynchos japonensis) American crows (C. brachyrhynchos) and carrion crows (C. corone orientalis). Carrion crows and American crows are recently diverged, but allopatric, sister species, whereas carrion crows and jungle crows are more distantly related but sympatric species, and possibly share pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to test for trans-species polymorphism and convergent evolution of the MHC IIB in crows. Phylogenetic reconstructions of MHC IIB sequences revealed several well supported interspecific clusters containing all three species, and there was no biased clustering of variants among the sympatric carrion crows and jungle crows. The topologies of phylogenetic trees constructed from putatively selected sites were remarkably different than those constructed from putatively neutral sites. In addition, trees constructed non-synonymous substitutions from a continuous fragment of exon 2 had more, and generally more inclusive, supported interspecific MHC IIB variant clusters than those constructed from the same fragment using synonymous substitutions. These phylogenetic patterns suggest that recombination, especially gene conversion, has partially erased the signal of allelic ancestry in these species. While clustering of positively selected amino acids by supertyping revealed a single supertype shared by only jungle and carrion crows, a pattern consistent with convergence, the overall phylogenetic patterns we observed suggest that TSP, rather than convergence, explains the interspecific allelic similarity of MHC IIB genes in these species of crows.
Effect of ascorbic acid on Mycobacterium tuberculosis biofilms
Authors: Dalton James P , Uy Benedict , Swift Simon , Wiles Siouxsie
Published: January 2018

Planktonic cultures of Mycobacterium tuberculosis, the bacterium responsible for the lung disease tuberculosis (TB), are highly susceptible to killing by ascorbic acid (vitamin C). As planktonically grown M. tuberculosis are unlikely to be representative of the bacterium during infection, we set out to determine if ascorbic acid was also antibacterial against M. tuberculosis growing as a biofilm. We use biofilm growth as a model for the multiple phenotypic states M. tuberculosis can exist in during an infection. In our experiments we employed bioluminescent M. tuberculosis H37Rv (BSGTB1) in which light production is a non-destructive surrogate measure of bacterial viability. Light levels were monitored before and after treatment with 1mM to 256mM ascorbic acid. After 3 weeks of treatment, biofilms were disrupted, washed and inoculated into fresh media to look for sterilisation. Our findings show that ascorbic acid concentrations of 32mM or greater reduced bioluminescence produced by M. tuberculosis BSGTB1 growing in biofilms to background levels and resulted in the death of all cells within the biofilm. This indicates that M. tuberculosis biofilms are susceptible to inhibition and killing by ascorbic acid (vitamin C) and suggests that novel antibiotics with a mode of action similar to ascorbic acid could represent a useful avenue of investigation for TB treatment.
A pilot study to evaluate the magnitude of association of patient activation in HIV-infected veterans who use electronic personal health records
Authors: Crouch Pierre-Cedric , Dawson Rose Carol PhD, RN, FAAN , Johnson Mallory I. , Janson Susan
Published: January 2018

Background: The HITECH Act signed into law in 2009 requires hospitals to provide patients with electronic access to their health information through an electronic personal health record (ePHR) in order to receive Medicare/Medicaid incentive payments. Little is known about who uses these systems or the impact these systems will have on patient outcomes in HIV care. The health care empowerment model provides rationale for the hypothesis that knowledge from an electronic personal health record can lead to greater patient empowerment resulting in improved outcomes. Objective: To determine the patient characteristics and patient activation, empowerment, satisfaction, knowledge of their CD4, Viral Loads, and antiretroviral medication, and medication adherence outcomes associated with electronic personal health record use in Veterans living with HIV at the San Francisco VA Medical Center. Participants: HIV-Infected Veterans receiving care in a low volume HIV-clinic at the San Francisco VA Medical Center, divided into two groups of users and non-users of electronic personal health records. Methods: In-person surveys were completed either online or on paper and data abstraction was completed from medical records for current anti-retroviral therapy (ART), CD4 count, and plasma HIV-1 viral load. Measures: The measures included the Patient Activation Measure, Health Care Empowerment Inventory, ART adherence, provider satisfaction, current CD4 count, current plasma viral load, knowledge of current ART, knowledge of CD4 counts, and knowledge of viral load. Results: In all, 40 participants were recruited. The use of electronic personal health records was associated with significantly higher levels of patient activation and levels of patient satisfaction for getting timely appointments, care, and information. ePHR was also associated with greater proportions of undetectable plasma HIV-1 viral loads, of knowledge of current CD4 count, and of knowledge of current viral load. The two groups differed by race and computer access. There was no difference in the current CD4, provider satisfaction, Health Care Empowerment Inventory score, satisfaction with provider-patient communication, satisfaction with courteous and helpful staff, knowledge of ART, or ART adherence. Conclusions: The use of electronic personal health records is associated with positive clinical and behavioral characteristics. The use of these systems may play a role in improving the health of people with HIV. Larger studies are needed to further evaluate these associations.
Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii
Authors: Avarre Jean-Christophe , Guinand Bruno , Dugué Rémi , Cosson Jacky , Legendre Marc , Panfili Jacques , Durand Jean-Dominique
Published: January 2018

The black-chinned tilapia Sarotherodon melanotheron heudelotii Rüppell 1852 (Teleostei, Cichlidae) displays remarkable acclimation capacities. When exposed to drastic changes of salinity, which can be the case in its natural habitat, it develops quick physiological responses and keeps reproducing. The present study focused on the physiological impact of salinity on male reproductive capacities, using gene expression as a proxy of acclimation process. Two series of experimental fish were investigated: the first one was composed of fish maintained in freshwater for several generations and newly acclimated to salinities of 35 and 70, whereas the second one consisted of the descendants of the latter born and raised under their native salinity. Expression patterns of 43 candidate genes previously identified from the testes of wild males was investigated in the three salinities and two generations. Twenty of them showed significant expression differences between salinities, and their predicted function revealed that most of them are involved in the osmotic tolerance of sperm cells and/or in the maintenance of sperm motility. A high level of expression variation was evidenced, especially for fish maintained in freshwater. In spite of this, gene expression patterns allowed the differentiation between fish raised in freshwater and those maintained in hypersaline water, in both generations. Altogether, the results presented here suggest that this high variability of expression is likely to ensure the reproductive success of this species under varying salinities.
Taphonomic and sedimentological aspects of the "Picos II" paleontological site, municipality of Piranhas, Alagoas, Brazil
Authors: Asakura Yumi , da Silva Jorge Luiz Lopes , da Silva Ana Paula Lopes , da Silva Elaine Pollyanna Alves , Omena Érica Cavalcante
Published: January 2018

The paleontological site “Picos II”, located at Picos farm, municipality of Piranhas, is a fossiliferous deposit with lagoon geomorphological features. The material found was in excellent condition, two Pleistocene mammalian taxa were identified: Eremotherium laurillardi and Notiomastodon platensis. The taphonomic analysis indicates that the deposited material suffered short transportation, in high-energy environment, taking form as a single depositional event covering the crystalline basement level, with disarticulation in situ, which explains the high degree of conservation of the material. The sedimentological analysis corroborates the information obtained in taphonomic analysis. The well preserved material found in SP Picos II demonstrates the great potencial of the lagoon type deposits, with less steep lateral than tanks, and promotes a smoother transport and accommodation of skeletal elements.
Haplotypes of “Candidatus Liberibacter europaeus” also separate by geography and host species
Authors: Nelson Warrick R
Published: January 2018

“Candidatus Liberibacter europaeus” (Leu) is one of six currently known Liberibacter species. It is known primarily from pear and related species across Europe, and from Scotch broom and its associated psyllids in New Zealand (introduced from Britain). The psyllids were introduced to New Zealand as a biocontrol agent for broom and it is thought the bacterium may have been introduced as an endosymbiont of the psyllids. No symptoms in apple or pear trees have been reported, but mild symptoms can occur in broom. 16S and 16S–23S intergenic spacer region DNA sequences of this species are available from GenBank. Analysis of these sequences and associated ecological descriptions indicates the occurrence of two haplotypes, LeuA and LeuB, defined not only genetically but also by geographic range as well as by plant/psyllid host species composition. Liberibacter species are new to science and haplotype identifications enable historical accounts of relationships and spread to be generated.
Infantile colic treatment: new prospects
Authors: Savino Francesco , De Marco Angela , Ceratto Simone
Published: January 2018

Infantile colic is a common disturbance occurring in the first three months of life. It is a benign condition and one of the main causes of pediatric consultation in the early part of life because of its great impact on family life. Some pediatricians are prone to undervalue this issue and there is no consensus concerning management and treatment. In literature are growing evidences about the effectiveness of dietary, pharmacological, complementary and behavioral therapies as options for the management of infantile colic. Dietary approach is based on the avoidance of cow’s milk proteins in breast-feeding mothers and bottle-fed infants. Currently pharmacological agents over the counter or by prescription are not recommended because of reported side effects. There is limited evidence supporting the use of complementary and alternative treatments (herbal supplements, manipulative approach and acupuncture) or behavioral modification interventions. Recent studies have partially clarified the pathogenesis of this disturb and so new treatments, such as probiotics, have been proposed. Further investigations are needed in order to provide evidence-based guidelines.
Does polyandry really pay off?: The effects of multiple mating and number of fathers on morphological traits and survival in clutches of nesting green turtles at Tortuguero
Authors: Alfaro-Núñez Alonzo , Jensen Michael P. MPJ , Abreu-Grobois F. Alberto
Published: January 2018

Despite the long debate of whether or not multiple mating benefits the offspring, studies still show contradicting results. Multiple mating takes time and energy. Thus, if females fertilize their eggs with a single mating, why to mate more than once? We investigated and inferred paternal identity and number of sires in 12 clutches (240 hatchlings) of green turtles (Chelonia mydas) nests at Tortuguero, Costa Rica. Paternal alleles were inferred through comparison of maternal and hatchling genotypes, and indicated multiple paternity in at least 11 of the clutches (92%). The inferred average number of fathers was three (ranging from 1 to 5). Moreover, regression analyses were used to investigate for correlation of inferred clutch paternity with morphological traits of hatchlings fitness (emergence success, length, weight and crawling speed); and size of the mother; and an environmental variable (incubation temperature). We suggest and propose two different comparative approaches for evaluating morphological traits and clutch paternity, in order to infer greater offspring survival. First, clutches coded by the exact number of fathers and second by the exact paternal contribution (fathers who gives greater proportion of the offspring per nest). We found significant differences (P < 0.05) in clutches coded by the exact number of fathers for all morphological traits. A general tendency of higher values in offspring sired by two to three fathers was observed for the length and weight traits. However, emergence success and crawling speed showed different trends which unable us to reach any further conclusion. The second approach analysing the paternal contribution showed no significant difference (P > 0.05) for any of the traits. We conclude that multiple paternity does not provide any extra benefit in the morphological fitness traits or the survival of the offspring, when analysed following the proposed comparative statistical methods.
Multi-scale environmental filters and niche partitioning govern the distributions of riparian vegetation guilds
Authors: Hough-Snee Nate W , Laub Brian , Merritt David M. , Long A. Lexine , Nackley Lloyd L. , Roper Brett B. , Wheaton Joseph M
Published: January 2018

Across landscapes, riparian plant communities assemble under varying levels of disturbance, environmental stress, and resource availability, leading to the development of distinct riparian life-history guilds. Identifying the environmental filters that exert selective pressures and favor specific vegetation guilds within riverscapes is a critical step in setting baseline expectations for how riparia may respond to the environmental conditions anticipated under future global change scenarios. In this study, we ask (1) what functional riparian plant guilds exist across two major North American river basins? (2) What environmental filters shape riparian guild distributions? (3) Does resource partitioning between guilds influence guild distributions and co-occurrence? We identified riparian plant guilds, examining relationships between regional climate and watershed hydrogeomorphic characteristics, stream channel form, and co-occurring riparian guilds. Woody species composition was measured at 703 streams and each species’ traits were extracted from a database in five functional areas: life form, persistence and growth, reproduction, and resource use. We clustered species into guilds by morphological characteristics and attributes related to environmental tolerances, modeling guild distributions as a product of environmental filters (stressors and resources) and guild co-existence. We identified five guilds, i) a tall, deeply rooted, long-lived, evergreen tree guild, ii) a xeric disturbance tolerant shrub guild, iii) a hydrophytic, thicket-forming shrub guild, iv) a low-statured, shade-tolerant, understory shrub guild and v) a flood tolerant, mesoriparian shrub guild. Guilds were most strongly discriminated by one another species’ rooting depth, canopy height and potential to resprout and grow following biomass-removing disturbance. Hydro-climatic variables including precipitation, watershed area, water table depth, and channel form attributes reflective of hydrologic regime were predictors of guilds whose life history strategies had affinity or aversion to flooding, drought, and fluvial disturbance. Biotic interactions excluded guilds with divergent life history strategies and/or allowed for the co-occurrence of guilds that partition resources differently in the same environment. We conclude that riparian guilding provides a useful framework for assessing how disturbance and bioclimatic gradients shape riparian functional plant diversity. Multiple processes should be considered when the riparian response guilds framework is to be used as a land-use decision-support tool framework
Ecological correlates to cranial morphology in Leporids (Mammalia, Lagomorpha)
Authors: Kraatz Brian P , Bumacod Nicholas , Sherratt Emma , Wedel Mathew J
Published: January 2018

The mammalian order Lagomorpha has been the subject of many morphometric studies aimed at understanding the relationship between form and function as it relates to locomotion, primarily in postcranial morphology. The leporid cranial skeleton, however, may also reveal information about their ecology, particularly locomotion and vision. Here we investigate the relationship between cranial shape and the degree of facial tilt with locomotion (cursoriality, saltation, and burrowing) within crown leporids. Our results suggest that facial tilt is more pronounced in cursors and saltators compared to generalists. However cranial shape does not differ significantly among these locomotor groups, nor does it differ significantly between species that burrow and those that do not.
GROM-RD: Resolving genomic biases to improve read depth detection of copy number variants
Authors: Smith Sean D , Kawash Joseph K , Grigoriev Andrey
Published: January 2018

Amplifications or deletions of genome segments, known as copy number variants (CNVs), have been associated with many diseases. Read depth analysis of next-generation sequencing (NGS) is an essential method of detecting CNVs. However, genome read coverage is frequently distorted by various biases of NGS platforms, which reduce predictive capabilities of existing approaches. Additionally, the use of read depth tools has been somewhat hindered by imprecise breakpoint identification. We developed GROM-RD, an algorithm that analyzes multiple biases in read coverage to detect CNVs in NGS data. We found non-uniform variance across distinct GC regions after using existing GC bias correction methods and developed a novel approach to normalize such variance. Although complex and repetitive genome segments complicate CNV detection, GROM-RD adjusts for repeat bias and uses a two-pipeline masking approach to detect CNVs in complex and repetitive segments while improving sensitivity in less complicated regions. To overcome a typical weakness of RD methods, GROM-RD employs a CNV search using size-varying overlapping windows to improve breakpoint resolution. We compared our method to two widely used programs based on read depth methods, CNVnator and RDXplorer, and observed improved CNV detection and breakpoint accuracy for GROM-RD. GROM-RD is available at http://grigoriev.rutgers.edu/software/
DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit
Authors: Vlachakis Dimitrios , Fakourelis Paraskevas , Makris Christos , Kossida Sophia
Published: January 2018

During the past years pharmacophore modeling has become one of the key components in computer-aided drug design and generally in modern drug discovery. DrugOn is a fully interactive pipeline designed to exploit the advantages of modern programming and overcome the command line barrier with two friendly environments for the user (either novice or experienced in the field of Computer Aided Drug Design) to perform pharmacophore modeling through an efficient combination of the PharmACOphore, Gromacs, Ligbuilder and PDB2PQR suites. Our platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process. For the pharmacophore modeling we are focusing on either the characteristics of the receptor or the full molecular system, including a set of selected ligands. DrugOn can be freely downloaded from our dedicated server system at www.bioacademy.gr/bioinformatics/drugon/
Synthetic sugar for sustainable power!
Authors: Moustafa Khaled
Published: January 2018

Natural photosynthesis allows biological systems to remarkably combine carbon dioxide and water molecules under sunlight to produce energy in the form of stored sugars. The stored sugar is then used by plants and animals to exert vital biological functions. If scientists can find the right protocol and materials to mimic this natural system to produce fermentable sugars, it could be the McCoy sustainable energy source for the future. The objective here is not to recall the photosynthesis mechanism, but to provide a future brief vision for a conceptual application of photosynthesis to produce bioethanol from organic synthetized sugar rather than from plants, which should be saved for human and animal feeding.
HIV and AIDS related knowledge and attitudes towards learners infected with HIV: Survey among high school learners in Gauteng and North West provinces in South Africa
Authors: Madiba Sphiwe , Mokgatle Mathildah M
Published: January 2018

The success of the proposed HIV testing and counselling (HTC) initiative among learners at high school in South Africa depends on their acceptability of the service, which may be influenced by their HIV/AIDSknowledge, perceptions, and attitudes. The study assessed high school learners’ HIV knowledge and attitudes towards learners infected with HIV. The survey was part of formative evaluation with grade 10-12 learners in order to assess the acceptability of HTC at schools. The study consisted of 17 high schools in two provinces in South Africa. T- tests were used to compare the differences in the mean HIV knowledge scores. Logistic regressions were performed to establish relationships between demographic variables, attitudes, and HIV knowledge scores. The sample consisted of 2970 learners aged 14-27years, 1810 (61%) had had sex, and 1494 (50.3%) had tested for HIV in the past year. The majority had high knowledge scores: 87% on HIV-related knowledge, 98.6% on the modes of transmission, and 73% on prevention. Overall, HIV knowledge was high, with a total mean score of 20.5 out of 26 points. There were significant differences in the HIV knowledge total mean scores; females had higher scores (M= 20.6, SD=2.3) than males (M=20.3, SD=2.4), and the younger age group (M= 20.5, SD=2.4) had higher scores than the older age group (M=20.1, SD=2.1). A quarter (25.4%) exhibited negative attitudes, 13.9% felt that HIV-positive learners should be isolated, and 75% would not date HIV-positive learners. Attitudes were associated with gender (OR=0.48, CI: 0.41-0.57), grades (OR=3.24, CI: 2.36-4.44), and total HIV knowledge scores (OR=2.21, CI: 1.43-3.43). Despite substantial HIV knowledge, there were knowledge gaps and misconceptions, which resulted in negative attitudes towards the disease. Appropriate sexual health education and HIV prevention interventions in school are crucial in correcting the knowledge gaps as well as reducing stigma and discrimination to assist learners to be accepting of HIV-positive persons.
Achieving human and machine accessibility of cited data in scholarly publications
Authors: Starr Joan , Castro Eleni , Crosas Mercè , Dumontier Michel , Downs Robert R. , Duerr Ruth , Haak Laurel , Haendel Melissa , Herman Ivan , Hodson Simon , Hourclé Joe , Kratz John Ernest , Lin Jennifer , Nielsen Lars Holm , Nurnberger Amy , Proell Stefan , Rauber Andreas , Sacchi Simone , Smith Arthur P. , Taylor Michael , Clark Tim
Published: January 2018

This short article provides operational guidance on implementing scholarly data citation and data deposition, in conformance with the Joint Declaration of Data Citation Principles (JDDCP, http://force11.org/datacitation) to help achieve widespread, uniform human and machine accessibility of deposited data. The JDDCP is the outcome of a cross-domain effort to establish core principles around cited data in scholarly publications. It deals with important issues in identification, deposition, description, accessibility, persistence, and evidential status of cited data. Eighty-five scholarly, governmental, and funding institutions have now endorsed the JDDCP. The purpose of this article is to provide the necessary guidance for JDDCP-endorsing organizations to implement these principles and to achieve their widespread adoption.
Multimodal Imaging Brain Connectivity Analysis toolbox (MIBCA)
Authors: Santos Ribeiro Andre , Miguel Lacerda Luis , Ferreira Hugo A.
Published: January 2018

Aim: In recent years, connectivity studies using neuroimaging data have increased the understanding of the organization of large-scale structural and functional brain networks. However, data analysis is time consuming as rigorous procedures must be assured, from structuring data and pre-processing to modality specific data procedures. Until now, no single toolbox was able to perform such investigations on truly multimodal image data from beginning to end, including the combination of different connectivity analyses. Thus, we have developed the Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox with the goal of diminishing time waste in data processing and to allow an innovative and comprehensive approach to brain connectivity. Materials and Methods: The MIBCA toolbox is a fully automated all-in-one connectivity toolbox that offers pre-processing, connectivity and graph theoretical analyses of multimodal image data such as diffusion-weighted imaging, functional magnetic resonance imaging (fMRI) and positron emission tomography (PET). It was developed in MATLAB environment and pipelines well-known neuroimaging softwares such as Freesurfer, SPM, FSL, and Diffusion Toolkit. It further implements routines for the construction of structural, functional and effective or combined connectivity matrices, as well as, routines for the extraction and calculation of imaging and graph-theory metrics, the latter using also functions from the the Brain Connectivity Toolbox. Finally, the toolbox performs group statistical analysis and enables data visualization in the form of matrices, 3D brain graphs and connectograms. In this paper the MIBCA toolbox is presented by illustrating its capabilities using multimodal image data from a group of 35 healthy subjects (19-73 years old) with volumetric T1-weighted, diffusion tensor imaging, and resting state fMRI data, and 10 subjets with 18F-Altanserin PET data also. Results: It was observed both a high inter-hemispheric symmetry and an intra-hemispheric modularity associated with structural data, whilst functional data presented lower inter-hemispheric symmetry and a high inter-hemispheric modularity. Furthermore, when testing for differences between two subgroups (<40 and >40 years old adults) we observed a significant reduction in the volume and thickness, and an increase in the mean diffusivity of most of the subcortical/cortical regions. Conclusion: While bridging the gap between the high numbers of packages and tools widely available for the neuroimaging community in one toolbox, MIBCA also offers different possibilities for combining, analysing and visualising data in novel ways, enabling a better understanding of the human brain.
Association of academic stressors with sleep disturbances in medical students: is psychological stress a mediator?
Authors: Waqas Ahmed , Khan Spogmai , Sharif Waqar muhammad , khalid Uzma , Ali Asad
Published: January 2018

Introduction: Medicine is one of the most stressful fields of education because of its highly demanding professional and academic requirements. Psychological stress, anxiety, depression and sleep disturbances are highly prevalent in medical students. Methods: This cross-sectional study was undertaken at CMH Lahore Medical College and Institute of Dentistry in Lahore, Pakistan, and was approved by the CMH LMC Research Ethics Committee. Students enrolled in all yearly courses for the MBBS degree were included. The questionnaire consisted of four sections: 1) demographics 2) a table listing 34 potential stressors, 3) the 14-item Perceived Stress Scale (PSS-14), and 4) the Pittsburgh Quality of Sleep Index (PSQI). Data were analyzed in SPSS v. 20. Logistic regression was run to identify associations between group of stressors, gender, year of study, student’s background, stress and quality of sleep. Results: Total response rate was 93.9% (263/280 respondents returned the questionnaire). The mean PSS-14 score was 30.04 (6.97). Logistic regression analysis showed that cases of high-level stress were associated with year of study and academic-related stressors only. Univariate analysis identified 157 cases with high stress levels (59.7%). The mean PSQI score was 8.09 (3.12). According to PSQI score, 203/263 respondents (77.02%) were poor sleepers. Logistic regression showed that mean PSS-14 score was a significant predictor of PSQI score (OR 1.99, P<0.05). Conclusion: We found a very high prevalence of academic stress and poor sleep quality among medical students. Many medical students reported using sedatives more than once a week. Academic stressors contributed significantly to stress and sleep disorders in medical students.
Prospecting Russula senecis: A delicacy among the tribes of West Bengal
Authors: Khatua Somanjana , Dutta Arun Kumar , Acharya Krishnendu
Published: January 2018

Russula senecis, a worldwide distributed mushroom, is exclusively popular among the tribal communities of West Bengal for food purposes. The present study focuses on its reliable taxonomic identification through macro-, micro-morphological features and DNA barcoding, confirmation of its systematic placement by phylogenetic analyses, myco-chemicals and functional activities. For the first time, complete Internal Transcribed Spacer region of R. senecis has been sequenced and its taxonomic position within subsection Foetentinae under series Ingratae of the subgen. Ingratula is confirmed through phylogenetic analysis. For exploration of its medicinal properties, dried basidiocarps were subjected for preparation of a heat stable phenol rich extract (RusePre) using water and ethanol as solvent system. The antioxidant activity was evaluated through hydroxyl radical scavenging (EC50 5 µg/ml), chelating ability of ferrous ion (EC50 0.158 mg/ml), DPPH radical scavenging (EC50 1.34 mg/ml), reducing power (EC50 2.495 mg/ml) and total antioxidant activity methods (13.44 µg ascorbic acid equivalent/mg of extract). RusePre exhibited antimicrobial potentiality against Listeria monocytogenes, Bacillus subtilis, Pseudomonas aeruginosa and Staphylococcus aureus. Furthermore, different parameters were tested to investigate its chemical composition which revealed the presence of appreciable quantity of phenolic compounds along with carotenoids and ascorbic acid. HPLC-UV fingerprint indicated probable existence of at least 13 phenolics of which 10 were identified (pyrogallol> kaempferol> quercetin> chlorogenic acid> ferulic acid, cinnamic acid> vanillic acid> salicylic acid> p-coumaric acid> gallic acid). Result from the present work suggests that the fraction, RusePre, may open novel prospect as a functional ingredient in antioxidant supplements and in drugs to treat infectious disease.
Are depredation rates by reef sharks influenced by fisher behaviour?
Authors: Schifiliti Magen , McLean Dianne L , Langlois Tim J , Birt Matthew J , Barnes Peter , Kempster Ryan
Published: January 2018

Shark depredation (damage to gear and loss of bait or hooked fish by a non-target species) is a common global occurrence. Depredation events by sharks can have negative impacts for the fishers, fishery targeted species and the sharks. It is, therefore important to better understand if learning behaviour of sharks can influence rates of depredation. Recreational fishers within the World Heritage Ningaloo Reef have reported increased rates of depredation by sharks over the last 5 years. This study aimed to determine if sharks are capable of learning to associate intensive recreational fishing activities with a food reward. We also aimed to test if sharks in areas frequently fished were more habituated to recreational fishing activities than those sharks within a no-take marine sanctuary. To simulate fishing activities baited underwater video systems were deployed in the morning (A.M.), midday, and afternoon (P.M.) for six consecutive days in Fished and Unfished sites. A significant decrease in time of arrival and time to first feed of sharks was seen across days at the Fished sites. The Unfished sites had very low numbers of sharks observed (n=3) and therefore was not statistically analysed. The relative abundance of sharks did not significantly increase across days, however there was a negative correlation between lemon sharks (Negaprion sp.) and whalers (Carcharhinus sp.). Our study suggests sharks are capable of being classically conditioned to recreational fishing activities and depredation rates are influenced by fisher behaviour. We have highlighted possible mitigation strategies designed to un-condition sharks to recreational fishing, including modifying fishing practices, use of deterrents based on the sensitivity of shark senses and management strategies. The best approach is likely to be enabling fishers to become more knowledgeable of how and why shark depredation events happen and take appropriate steps to avoid them.
Describing the population structure of Rhincodon typus occurring in the waters of Oslob– Cebu, Philippines– between March 2012 and June 2013, during the provisioning interaction hours.
Authors: Araujo Gonzalo , Ponzo Alessandro , Geary Daniel , Craven Samantha , Snow Sally J , Lucey Anna R
Published: January 2018

Background: Prior to this study, the aggregation of whale sharks in the waters of Oslob had never been described. Provisioning (Orams, 2002) activities started in late 2011, and systematic data collection in March 2012, attracting over 100,000 tourists in the first year, and is currently the most reliable aggregation of R. typus in the Philippines. Methods: Daily in-­‐water photographic identification was used as a non-­‐invasive means to describe the population throughout the study period. A total of 135 sharks were identified, and IDs were independently matched by three researchers to minimize error. Photogrammetry (Rohner, 2011) was adopted to complement population description. Results: Daily sightings ranged from 2 to 23 different animals in the interaction area (mean=11.14). A total of 109 males, 15 females and 11 R. typus of undetermined sex were described. The size was estimated for 73.3% of the population, with an average of 5.36m ±1.3m. Photogrammetry posed a mean of 5.63m ±0.59m on 14 sharks, 6.75% >than researchers’ estimates. Resighting (>1d) was observed in 66.7% of the population. Five individuals were present for >300d (n=443) in the interaction area, with a maximum of 420d. Nine individuals were successfully matched across regional hotspots including Donsol and Southern Leyte. Conclusion: Despite the presence of animals in Oslob year round and the influence of the provisioning, there appears to be a seasonal influx of animals, with a maximum of 46 different animals present in the month of June 2012 and again in May 2013, contrasting with a monthly average of 28.9. It appears these waters are important to the species and it’s paramount to fully investigate the impact of the provisioning on the population of R. typus in the Philippines.
Impacts of sea level rise and climate change on coastal plant species in the central California coast
Authors: Garner Kendra , Chang Michelle , Fulda Matthew , Berlin Jon , Freed Rachel , Soo-Hoo Melissa M. , Revell David , Ikegami Makihiko , Flint Lorraine , Flint Alan , Kendall Bruce E.
Published: January 2018

Local increases in sea level caused by global climate change pose a significant threat to the persistence of many coastal plant species through exacerbating inundation, flooding, and erosion. In addition to sea level rise (SLR), climate changes in the form of air temperature and precipitation regimes will also alter habitats of coastal plant species. Although numerous studies have analyzed the effect of climate change on future habitats through species distribution models (SDMs), none have incorporated the threat of exposure to SLR. We developed a model that quantified the effect of both SLR and climate change on habitat for 88 rare coastal plant species in San Luis Obispo, Santa Barbara, and Ventura Counties, California, USA. Our SLR model projects that by the year 2100, 60 of the 88 species will be threatened by SLR. We found that the probability of being threatened by SLR strongly correlates with a species’ area, elevation, and distance from the coast, and that ten species could lose their entire current habitat in the study region. We modeled the habitat suitability of these 10 species under future climate using a species distribution model (SDM). Our SDM projects that 4 of the 10 species will lose all suitable current habitats in the region as a result of climate change. While SLR accounts for up to 9.2 km2 loss in habitat, climate change accounts for habitat suitability changes ranging from a loss of 1439 km2 for one species to a gain of 9795 km2 for another species. For three species, SLR is projected to reduce future suitable area by as much as 28% of total area. This suggests that while SLR poses a higher risk, climate changes in precipitation and air temperature represents a lesser known but potentially larger risk and a small cumulative effect from both.
Demographic rates of northern royal albatross at Taiaroa Head, New Zealand
Authors: Richard Yvan , Perriman Lyndon , Lalas Chris , Abraham Edward R.
Published: January 2018

Demographic rates, such as annual survival rate, are generally difficult to estimate for long-lived seabirds, because of the length of time required for this kind of study and the remoteness of colonies. However, a small colony of northern royal albatross (Diomedea sanfordi) established itself on the mainland of New Zealand at Taiaroa Head, making possible regular banding and monitoring of its individuals since the first chick fledged, in 1938. Data on the presence/absence of birds, as well as on breeding outcomes, were available for the period from 1989–90 to 2011–12, and included 2128 annual resightings of 355 banded individuals of known age. The main goal of the present study was to estimate the annual survival rate of juveniles, pre-breeders, and adults at Taiaroa Head. These rates were estimated simultaneously in a single Bayesian multi-state capture-recapture model. Several models were fitted to the data, with different levels of complexity. From the most parsimonious model, the overall annual adult survival rate was estimated as 0.950 (95% c.i.: 0.941–0.959). In this model, adult survival declined with age, from 0.976 (95% c.i.: 0.963–0.988) at 6 years, the minimum age at first breeding, to 0.915 (95% c.i.: 0.879–0.946) at 40 years. Mean annual survival of pre-breeders was 0.966 (95% c.i.: 0.950–0.980), and 0.933 (95% c.i.: 0.908–0.966) for juveniles. There was no discernible difference in survival between males and females, and there was no apparent trend in survival over time. Estimates of other demographic rates were also obtained during the estimation process. The mean age at first return of juveniles to the colony was estimated as 4.8 years (95% c.i.: 4.6–5.1), and the mean age at first breeding as 8.9 years (95% c.i.: 8.5–9.3). Because all the birds of the colony were banded, it was possible to estimate the total population size. The number of northern royal albatross present annually at the Taiaroa Head colony has doubled since 1989–90, and the current total population size was estimated to be over 200 individuals. The ratio of the total population size to the number of annual breeding pairs varied from 5 to 12 among years, with an overall mean of 7.65 (95% c.i.: 7.56–7.78), and this high variability highlights the need for a sufficient number of surveys of seabird breeding populations before reliable conclusions on population trends can be made. Although long-term data allowed estimates of demographic rates of northern royal albatross at Taiaroa Head, the location of the colony and the ongoing management by staff mean that the population dynamics may differ from those of the main population on the Chatham Islands.