bluuebunny/crossref_metadata_2025 huggingface dataset:
Importance of Posidonia oceanica meadows for the distribution of the mollusc bivalve Pinna nobilis (Linnaeus, 1758) in the Capo Carbonara Marine Protected Area
Authors: Cinti Maria-Francesca , Frau Francesca , Atzori Fabrizio , Corrias Stefano
Published: January 2018

Posidonia oceanica meadows are the preferential habitat for many plant and animal protected species including the mollusc bivalve Pinna nobilis. In this study, we evaluated the importance of the substrate structure for the distribution of the species in the Capo Carbonara Marine Protected Area (Sardinia south east), recognized as a Specially Protected Area of Mediterranean Importance (SPAMI) and Site of Community Importance (SCI ITB040020) of the Natura 2000 network. For this purpose four study areas, exposed to the North West and South East of the Capo Carbonara promontory, and characterized by P. oceanica meadows on both sandy and rocky substrates, with a total area of about 20ha, have been investigated. Visual sightings were conducted in situ during the months of September and October 2013 and 2014 along linear transects at depths between 1 and 10 meters to collect information on the presence, morphometric characteristics and depth of specimens of P. nobilis. A total of 139 individuals were recorded, 126 of them were alive (90.6%) and 13 were dead (9.4%); 51 individuals (36.7%) were found on rocky substrates, with a mortality rate of 6.2%, an average height of 34.4±9.9 cm, and at an average depth of 4.7±1.7 m. On sandy substrates, the number of individuals was 88 (63.3%), with a mortality rate of 11.4% and average height of 39.65±14.3 cm, at the average depth of 5.8±2.1 m. This study confirmed the importance of P. oceanica for the distribution of P. nobilis, which showed a preference for P. oceanica meadows set on sandy substrate. Therefore, for the management purposes of the Capo Carbonara Marine Protected Area, it would be interesting to understand which are the main causes of the greater mortality registered on sandy substrate and if these causes are related to environmental (i.e. sedimentation, predation) and/or anthropogenic (i.e. anchoring, collecting) factors.
Node-Match Tool
Authors: Sharma Asankhaya
Published: January 2018

We present a tool Node-Match that can do ontology matching using node ranking over graphical representation of the ontologies. Simple ontology matching algorithms are based on lexical measures that only consider text similarity. Taking the shape and structure of the ontology into account while matching can lead to better results [1, 2, 3]. Node-Match illustrates the difference between the two approaches. It is based on S-Match [4] an open source toolkit for lightweight ontology matching and alignment. S-Match supports a rich GUI for designing lightweight ontologies and several ontology alignment algorithms. We use the Department Ontology from the running example in [1] to show the difference between difference ontology matching algorithms.
Assessing the importance of genetic and ecological factors for the occurrence of patchy flowering in Posidonia oceanica
Authors: Jahnke Marlene , Pagès Jordi F , Alcoverro Teresa , Lavery Paul S , McMahon Kathryn M , Procaccini Gabriele
Published: January 2018

The occurrence of sexual reproduction and flowering synchronization of angiosperms has been widely studied and may be induced by external or internal cues. Although factors such as predator satiation and pollination efficiency may explain why synchronization can increase individual fitness, the actual mechanisms of synchronization are obscure for the majority of plant species. In this study we aimed to assess the importance of ecological and genetic factors in shaping flowering heterogeneity of Posidonia oceanica at the small spatial scale (metres), where shoots and patches were subjected to similar levels of the major potential external drivers such as temperature and light availability. We assessed four external ecological factors (vegetative tissue production, leaf nitrogen and carbon content and herbivory) and three genetic factors (heterozygosity, relatedness and clonality). We sampled six patches with contrasting flower abundances at three different localities and analysed whether spatial heterogeneity in the abundance of flowers was due to (1) clone identity and clone synchronization, (2) variation in nutrient availability per individual, potentially caused by spatial heterogeneity in herbivory rates (or nutrient re-location via clonal integration) or (3) kin selection and sibling synchronization. Moreover, we also investigated if levels of genetic diversity, specifically observed heterozygosity as a proxy for individual fitness, differ between flowering patches and patches with low flower abundance. We show that genetic factors play a major role: Both internal relatedness and heterozygosity have a significant positive interaction with the abundance of flowers. Moreover, vegetative tissue production and the number of clones per patch were negatively correlated with the number of flowers, although at a low level of significance. Sharing of clones within localities was almost exclusively among patches with high flower abundance and patches with low flower abundance, respectively. Our results support the kin selection hypothesis and indirectly the resource-budget hypothesis, as well as an interaction between genetic factors and environmental factors as cause for the observed heterogeneous flowering patterns. Overall, the results shed new light onto the mechanisms explaining flowering synchronization in P. oceanica.
A consensual Diving-PAM protocol to monitor Posidonia oceanica photosynthesis
Authors: Gobert Sylvie , Lepoint Gilles , Silva João , Santos Rui , Lejeune Pierre , Dujardin Patrick , Delvaux Bruno , Cornelis Jean-Thomas , Richir Jonathan
Published: January 2018

The seagrass Posidonia oceanica is widely recognized as an effective bioindicator of the health status of Mediterranean coastal waters. Chlorophyll fluorescence measurements, in particular through the Pulse Amplitude Modulated (PAM) fluorometry method, are performed to study aquatic plant ecology and vitality and to assess their responses to diverse stressful factors. However, the current understanding of P. oceanica photosynthetic responses to environmental stresses does only allow scientists to use the PAM-method as a complementary tool to other more-robust monitoring techniques. Consequently, a more in-depth knowledge of the natural causes of variability of P. oceanica photosynthetic responses are a prerequisite to any surveys relying on that time and cost-effective method. In the framework of the STARECAPMED project, this work aimed to determine the influence of several environmental (depth, daytime, season) and plant-specific characteristics (leaf age, leaf part analyzed, epiphytic coverage) on the photosynthetic responses (Y, ETR, RLC) of P. oceanica. Water temperature, irradiance and several biochemical parameters of the seagrass (chl.a, chl.b, C, N, P, micronutrients such as Fe, Cu) were measured as well. The field survey was performed in a pristine meadow in the Calvi Bay, Corsica. Environmental and plant-physiological characteristics deeply influenced P. oceanica photosynthetic responses. As an example, ETR decreased with depth, contrary to Y that mostly increased. ETR was lower in the basal part of leaf blade, and the epiphytic coverage of leaf tips slightly increased their ETR compared to leaf tips cleaned of epiphytes. Depth and leaf part-related variations in RLC were also observed. Because of this natural variability, it appears essential to develop a consensual protocol of chlorophyll fluorescence measurements to publish reliable and comparable results between studies. We therefore notably suggest to perform measurements close to midday, when photosynthetic responses are the highest; at 10-15 m depth in order to avoid, among others, low depth light irradiance variability; on the middle part of the 3rd-4th external leaf, well developed, highly photosynthetic, and little epiphyted. Finally, because P. oceanica fluorescence was correlated with N, P and chl.b leaf contents, the PAM-method could afterwards be used as bioindicator technique, according to the protocol proposed.
Spatial patterns of the Zostera noltei meadows across the Atlantic coast of Morocco: is there a latitudinal gradient?
Authors: Bououarour Oussama , El Kamcha Reda , Boutahar Loubna , Tnoumi Ali , Zourarah Bendahhou , Benhoussa Abdelaziz , Bazairi Hocein
Published: January 2018

Seagrass meadows exist in most shallow, sheltered, soft-bottomed marine coastlines and estuaries throughout the world and rank among the most productive systems in the ocean. Zostera noltei Hornemann is a small seagrass largely widespread in intertidal areas of Western Europe and North-West Africa, the Mediterranean Sea and in the Black Sea.

In Morocco, intertidal Zostera noltei meadows were identified at six coastal ecosystems across c.a. 2500 km of its Atlantic coast (Tahaddart estuary, Moulay Bousselham, Sidi Moussa, Oualidia, Khnifiss lagoons and Dakhla Bay). The present work aimed at assessing the spatial and latitudinal variation of Z. noltei meadows by measuring the density of shoots, leaf biomass, root-rhizome biomass, number of leaf /shoot and the average length and width of leafs. Samples were conducted between December 2014 and January 2015, using a hand PVC corer (12.5 of diameter). When possible, a downstream and upstream comparison is performed in each site.

Density of shoots fluctuated between 1972 and 9833 shoots m-2. Leaves biomass varied between 32 and 259 gDW/m2 and root-rhizome biomass oscillated between 21 and 314 gDW/m2. Number of leaves per shoot fluctuated between 2.47 and 3.4 leaf per shoot, the leaf length between 4.9 and 30.8 cm and the leaf width 0.6 and 2 mm. These results showed, on the one hand, a clear spatial variation across a downstream-upstream gradient in each site and, on the other hand, a latitudinal pattern in the biomass and morphometry of the Z. noltei meadows across the Atlantic coast of Morocco. Significant differences were evidenced for all variables (ANOVA, p<0.05). The root-rhizome biomass and density of shoots are higher southward while the number of leaves per shoot, leaf biomass and the average length and width of the leaves are greater northward.

These results are compared with literature data from the distribution range of Z. noltei. Further analysis regarding the genetics, the associated benthic invertebrates and the sediment contamination are being performed and will increase the knowledge on such ecosystems and help in understanding their interaction with environment conditions.
Allele specific expression in worker reproduction genes in the bumblebee Bombus terrestris
Authors: Amarasinghe Harindra E , Toghill Bradley J , Nathanael Despina , Mallon Eamonn B
Published: January 2018

Methylation has previously been associated with allele specific expression in ants. Recently, we found methylation is important in worker reproduction in the bumblebee Bombus terrestris. Here we searched for allele specific expression in twelve genes associated with worker reproduction in bees. We found allele specific expression in Ecdysone 20 monooxygenase and IMP-L2-like. Although we were unable to confirm a genetic or epigenetic cause for this allele specific expression, the expression patterns of the two genes match those predicted for imprinted genes.
The tolerability of transcranial electrical stimulation used across extended periods in a naturalistic context by healthy individuals
Authors: Paneri Bhaskar , Khadka Niranjan , Patel Vaishali , Thomas Chris , Tyler William , Parra Lucas C , Bikson Marom
Published: January 2018

Transcranial electrical stimulation (tES) is one of the most widely implemented forms of non-invasive neuromodulation in basic and clinical neuroscience. Further, the use of tES by healthy populations for various purposes is growing widespread daily. The effects of tES protocols on the skin and other tissues has remained uncharacterized when used across extended periods of time by healthy individuals. Therefore, we examined the basic safety and tolerability profile of two distinct tES protocols used repeatedly across an extended period of time by healthy subjects and report our findings here for the first time. The safety and tolerability profile previously accumulated regarding extended use of tES in clinical populations is compelling and supports a low-risk or non-significant risk designation. In the present study, we tested the tolerability (safety) and compliance, compared to sham, of two common tES approaches having a current density < 2 mA/cm2; transcranial Direct Current Stimulation (tDCS) or transcranial Pulsed Current Stimulation (tPCS) used by healthy subjects three to five days (17 - 20 minutes per day) per week for up to six weeks in a naturalistic environment. In this study 100 healthy subjects were randomized to one of three treatment groups: tDCS (n = 33), tPCS (n = 30), or sham (n = 37) and blinded to the treatment condition. The tES and sham waveforms were delivered through self-adhering electrodes on the right lateral forehead and back of the neck. We conducted 1905 treatment sessions (636 sham, 623 tDCS, and 646 tPCS sessions) on study volunteers over a six-week period. There were no serious adverse events in any treatment condition. Common side effects were primarily restricted to influences upon the skin and included skin tingling, itching, and mild burning sensations. The incidence of these events in active tES treatment arms (tPCS, tDCS) was equivalent or significantly lower than their incidence in the sham treatment arm. Other adverse events had a rarity (< 5% incidence) that could not be statistically distinguished across the treatment groups. Some subjects withdrew early from the study for atypical headache (sham n = 2, tDCS n = 2, and tPCS n = 3), atypical discomfort (sham n = 0, tDCS n = 1, and tPCS n = 1), or atypical skin irritation (sham n = 2, tDCS n = 8, and tPCS n = 1). The compliance (elected sessions completed) for tPCS was significantly greater when compared to sham (p = 0.007). The present study represents the most comprehensive analysis of tES tolerability and safety in healthy subjects to date. Limited to the hardware, electrodes, and protocols tested here, we conclude that repeated use of limited output tES across extended periods, is well tolerated and poses no significant risks to healthy subjects, as previously observed in clinical studies.
Could biorational insecticides be used in the management of aflatoxigenic Aspergillus spp. and their insect vectors in stored wheat?
Authors: Khan Tiyyabah , Shahid Ahmad Ali , Khan Hafiz Azhar Ali
Published: January 2018

Insect pests in stored wheat cause significant losses and play an important role in the dispersal of viable fungal spores of various species including aflatoxin producing Aspergillus spp. The problems of insecticide resistance in stored insects and environmental hazards associated with fumigants and conventional grain protectants underscore the need to explore reduced risk insecticides to control stored insects and the ultimate effect on fungal infection inhibition. The purpose of this study was to investigate the insecticidal potential of four biorational insecticides: spinosad, thiamethoxam, imidacloprid and indoxacarb on wheat against Rhyzopertha dominica and Sitophilus oryzae and the subsequent effect of insects’ mortality on Aspergillus flavus and A. parasiticus infection in grains. Spinosad and thiamethoxam were the most effective insecticides against R. dominica compared to S. oryzae followed by imidacloprid. Spinosad applied at 0.25, 0.5 and 1ppm and thiamethoxam at 2 and 4ppm concentrations resulted in complete mortality of R. dominica and >90% infection inhibition of A. flavus and A. parasiticus. However, indoxacarb was more toxic against S. oryzae compared to R. dominica. The mortality of R. dominica was directly related to the percent infection inhibition of A. flavus and A. parasiticus in all the treatments. Whereas, mortality of S. oryzae was only related to the percent infection inhibition of A. parasiticus in all the treatments. The results show that although both spinosad and thiamethoxam can provide protection against R. dominica and fungal infections in stored grains, more potent reduced risk insecticides and/or their combinations would be needed than either of these to provide broad spectrum protection of stored grains. In conclusion, the results of the present study provide baseline data for the management of aflatoxigenic fungi by controlling stored insects using biorational insecticides .
Combining complexity measures of EEG data: multiplying measures reveal previously hidden information
Authors: Burns Thomas F
Published: January 2018

Many studies have noted significant differences among human EEG results when participants or patients are exposed to different stimuli, undertaking different tasks, or being affected by conditions such as epilepsy or Alzheimer's disease. Such studies often use only one or two measures of complexity and do not regularly justify their choice of measure beyond the fact that it has been used in previous studies. If more measures were added to such studies, however, more complete information might be found about these reported differences. Such information might be useful in confirming the existence or extent of such differences, or in understanding their physiological bases. In this study I analysed publically-available EEG data using a range of complexity measures to determine how well the measures correlated with one another. The complexity measures did not all significantly correlate, suggesting that different measures were measuring unique features of the EEG signals and thus revealing information which other measures were unable to detect. Therefore, the results from this analysis suggests that combinations of complexity measures reveal unique information which is in addition to the information captured by other measures of complexity in EEG data. For this reason, researchers using individual complexity measures for EEG data should consider using combinations of measures to more completely account for any differences they observe and to ensure the robustness of any relationships identified.
Kernel probability estimation for binomial and multinomial data
Authors: Jensen Greg
Published: January 2018

Kernel-based smoothers have enjoyed considerable success in the estimation of both probability densities and event frequencies. Existing procedures can be modified to yield a similar kernel-based estimator of instantaneous probability over the course of a binomial or multinomial time series. The resulting nonparametric estimate can be described in terms of one bandwidth per outcome alternative, facilitating both the understanding and reporting of results relative to more sophisticated methods for binomial outcome estimation. Also described is a method for sample size estimation, which in turn can be used to obtain credible intervals for the resulting estimate given mild assumptions. One application of this analysis is to model response accuracy in tasks with heterogeneous trial types. An example is presented from a study of transitive inference, showing how kernel probability estimates provide a method for inferring response accuracy during the first trial following training. This estimation procedure is also effective in describing the multinomial responses typical in the study of choice and decision making. An example is presented showing how the procedure may be used to describe changing distributions of choices over time when eight response alternatives are simultaneously available.
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flasks: Part 1
Authors: Ng Wenfa
Published: January 2018

Sufficient quantities of cells of consistent characteristics are needed for studying biologicalprocesses (at the population level ) in many areas of applied microbiology. However, generating the requisite biomass by cell culture is usually the rate-limiting step of a project given the relatively low biomass yield of many commercial culture media in shake flask culture systems. This work reports the formulation of a semi-defined medium that enabled aerobic high cell density cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. The formulated medium (FM) comprises: a buffer system (K2HPO4 : 12.54 g/L and KH2 PO4 : 2.31 g/L); vitamins and trace elements (yeast extract: 12.0 g/L); salts (NaCl: 5.0 g/L and MgSO4 : 0.24 g/L); and carbon and nitrogen sources (D-Glucose: 6.0 g/L and NH4Cl: 1.5 g/L). Notable characteristics of this medium are: high buffer capacity (89 mM phosphate), 1:1 molar ratio between D-Glucose and NH4Cl, and yeast extract providing trace elements and a secondary source of carbon and nitrogen. Preliminary data revealed an OD 600nm of 9 after 24 hours of cultivation at 37 oC, presumably with glucose and NH4Cl as the main nutrients. At 48 hours, an OD 600nm of 11 was attained with yeast extract providing the necessary nutrients for cell growth and biomass formation. The broth’s pH varied between 5.5 and 7.8 during cultivation. On the other hand, the maximum OD 600nm of E. coli grown in three commonly used complex media: Nutrient Broth, LB Lennox, and Tryptic Soy Broth (TSB) were 1.4, 3.2 and 9.2, respectively, under identical culture conditions. Finally, FM maintained the viability of a larger population of cells for three days, compared to a population collapse in TSB broth after one day. Collectively, the results suggested that the formulated medium might find use as a high cell density aerobic growth medium for E. coli in shake flasks. Part 2 of this work describes improvements in medium performance ; specifically, higher cell yield as well as a shorter diauxic lag phase and total culture period achieved through a small reduction in D-Glucose and NH4Cl concentrations in the medium composition. An abstract preprint of Part 2 is available at https://peerj.com/preprints/117/
LecoS - A QGIS plugin for automated landscape ecology analysis
Authors: Jung Martin
Published: January 2018

The quantification of landscape structures is an important part in many ecological analysis dealing with GIS derived satellite data. This paper introduces a new free and open-source tool for conducting landscape ecology analysis. LecoS is able to compute a variety of basic and advanced landscape metrics in an automatized way by iterating through an optional provided vector layer. It is integrated into the QGIS processing framework and can thus be used as a stand-alone tool or within bigger complex models.
Contemporary premature feather loss (PFL) among common tern chicks in Lake Ontario: the return of an enigmatic developmental anomaly
Authors: Arnold Jennifer M. , Tyerman Donald J. , Crump Doug , Williams Kim L. , Oswald Stephen A.
Published: January 2018

In July 2014, we observed premature feather loss (PFL) among non-sibling, common tern Sterna hirundo chicks between 2 and 4 weeks of age at Gull Island in northern Lake Ontario, Canada. Rarely observed in wild birds, to our knowledge PFL has not been recorded in terns since 1974, despite the banding of tens of thousands of tern chicks across North America since then. The prevalence (5% of chicks) and extent of feather loss was more extreme than in previous reports but was not accompanied by other aberrant developmental or physical deformities. Complete feather loss from all body areas (wing, tail, head and body) occurred over a period of a few days but all affected chicks appeared vigorous and quickly began to grow replacement feathers. All but one (recovered dead and submitted for post-mortem) most likely fledged 10-20 days after normal fledging age. Secondary covert feather samples were collected from PFL chicks (n=6; including shed feathers and re-growing live feathers) and normal individuals (n=8; plucked live feathers) and were analyzed for corticosterone concentrations. There was striking temporal association between the onset of PFL and persistent strong southwesterly winds that caused extensive mixing of near-shore surface water with cool, deep lake waters. We found no evidence of feather dystrophy, concurrent developmental abnormalities or nutritional shortfall among affected chicks. Thus, the PFL we observed among common terns in 2014 was largely of unknown origin but may have been caused by unidentified pathogens or toxins welling up from these deep waters along the shoreline. PFL was not observed among common terns at Gull Island in 2015, although we did observe similar feather loss in a herring gull Larus argentatus chick in that year. Comparison with sporadic records of PFL in other seabirds suggests that PFL may be a rare, but non-specific response to a range of potential stressors. Its reemergence in penguins, and now gulls and terns, may indicate widespread environmental changes that could lead to health risks for birds and other wildlife.
Application of Graph Theory to the elaboration of personal genomic data for genealogical research
Authors: Palleschi Vincenzo , Pagani Luca , Pagnotta Stefano , Amato Giuseppe , Tofanelli Sergio
Published: January 2018

In this communication a representation of the links between DNA-relatives based on Graph Theory is applied to the analysis of personal genomic data to obtain genealogical information. The method is tested on real data and discussed its applicability to the field of genealogical research. We envisage the proposed approach as a valid tool for a streamlined application to the publicly available data generated by many online personal genomic companies. By this way, anonymized matrices of pairwise genome sharing counts will enable to improve the retrieval of genetic relationship between customers who provided explicit consent to the treatment of their data.
Psychedelics and creativity: a review of the quantitative literature
Authors: Baggott Matthew J
Published: January 2018

After a 40-year hiatus, the question of whether psychedelics can increase creativity is being asked with renewed vigor. This article critically reviews the conceptual issues of studying psychedelic-induced creativity by summarizing the limited evidence on the question and suggesting two broader frameworks. There are two important challenges to researchers on this topic. One is to separate creativity from other effects of the drug that may be mistaken for creativity. The second is to develop operational measures to quantify it. This article reviews the major studies assessing creativity (or related constructs) induced by psychedelics, including a reanalysis of raw data from one study. Results are modest and inconclusive but are consistent with reports that psychedelics give rise to unusual or novel thoughts. Given the lack of robust changes in creativity measures, I suggest creativity may be too specific of a construct to accurately and fully characterize the putatively beneficial cognitive changes that psychedelic users report. Feelings of creativity may be an inconsistent result of a more general effect of these drugs, such as alterations in availability of mental representations or changes in Bayesian inference. Ultimately, creativity may not be a sufficiently creative construct to capture the beneficial effects of psychedelics.
Amplikyzer: Automated methylation analysis of amplicons from bisulfite flowgram sequencing
Authors: Rahmann Sven , Beygo Jasmin , Kanber Deniz , Martin Marcel , Horsthemke Bernhard , Buiting Karin
Published: January 2018

The Roche 454 GS Junior sequencing platform allows locus-specific DNA methylation analysis using deep bisulfite amplicon sequencing. However, bisulfite-converted DNA reads may contain long T homopolymers, and the main sources of errors on pyrosequencing platforms are homopolymer over- and undercalls. Furthermore, existing tools do not always meet the analysis requirements for complex assay designs with multiple regions of interest (ROIs) from multiple samples. We have developed the amplikyzer software package to address the above challenges. It directly aligns the intensity sequences from standard flowgram files (SFF format) to given amplicon reference sequences, without converting to nucleotide FASTA format first, avoiding information loss by rounding flow intensities, and taking special measures to correctly process long homopolymers. It offers a variety of options to analyze complex multiplexed samples with several regions of interest and outputs useful statistics and publication-quality analysis plots without mandatory manual interaction. This allows our software to be used as part of automated pipelines as well as interactively. The underlying analysis algorithms, using a novel hybrid flowgram-DNA sequence representation are described in detail. We also discuss configuration options and use cases of our open source amplikyzer software and present exemplary results. The software, including required libraries, is available at https://bitbucket.org/svenrahmann/amplikyzer/downloads.
Identifying Genetic Interactions Associated with Late-Onset Alzheimer’s Disease
Authors: Floudas Charalampos S , Um Nara , Kamboh M. Ilyas , Barmada Michael M , Visweswaran Shyam
Published: January 2018

Background Identifying genetic interactions in data obtained from genome-wide association studies (GWASs) can help in understanding the genetic basis of complex diseases. The large number of single nucleotide polymorphisms (SNPs) in GWASs however makes the identification of genetic interactions computationally challenging. We developed the Bayesian Combinatorial Method (BCM) that can identify pairs of SNPs that in combination have high statistical association with disease. Results We applied BCM to two late-onset Alzheimer’s disease (LOAD) GWAS datasets to identify SNP-SNP interactions between a set of known SNP associations and the dataset SNPs. For evaluation we compared our results with those from logistic regression, as implemented in PLINK. Gene Ontology analysis of genes from the top 200 dataset SNPs for both GWAS datasets showed overrepresentation of LOAD-related terms. Four genes were common to both datasets: APOE and APOC1, which have well established associations with LOAD, and CAMK1D and FBXL13, not previously linked to LOAD but having evidence of involvement in LOAD. Supporting evidence was also found for additional genes from the top 30 dataset SNPs. Conclusion BCM performed well in identifying several SNPs having evidence of involvement in the pathogenesis of LOAD that would not have been identified by univariate analysis due to small main effect. These results provide support for applying BCM to identify potential genetic variants such as SNPs from high dimensional GWAS datasets.
Astrocyte activation in the anterior cingulate cortex and altered glutamatergic gene expression during paclitaxel-induced neuropathic pain in mice
Authors: Masocha Willias
Published: January 2018

Spinal astrocyte activation contributes to the pathogenesis of paclitaxel-induced neuropathic pain (PINP) in animal models. We examined glial fibrillary acidic protein (GFAP; an astrocyte marker) immunoreactivity and gene expression of GFAP, glutamate transporters and receptor subunits by real time PCR in the anterior cingulate cortex (ACC) at 7 days post first administration of paclitaxel, a time point when mice had developed thermal hyperalgesia. The ACC, an area in the brain involved in pain perception and modulation, was chosen because changes in this area might contribute to the pathophysiology of PINP. GFAP transcripts levels were elevated by more than fivefold and GFAP immunoreactivity increased in the ACC of paclitaxel-treated mice. The 6 glutamate transporters (GLAST, GLT-1 EAAC1, EAAT4, VGLUT-1 and VGLUT-2) quantified were not significantly altered by paclitaxel treatment. Of the 12 ionotropic glutamate receptor subunits transcripts analysed 6 (GLuA1, GLuA3, GLuK2, GLuK3, GLuK5 and GLuN1) were significantly up-regulated, whereas GLuA2, GLuK1, GLuK4, GLuN2A and GLuN2B were not significantly altered and GLuA4 was lowly expressed. Amongst the 8 metabotropic receptor subunits analysed only mGLuR8 was significantly elevated. In conclusion, during PINP there is astrocyte activation, no change in glutamate transporter expression and differential up-regulation of glutamate receptor subunits in the ACC. Thus, targeting astrocyte activation and the glutamatergic system might be another therapeutic avenue for management of PINP.
Effects of phenolic antioxidants extraction from four selected seaweeds obtained from Sabah
Authors: Fu Carmen Wai Foong , Ho Chun Wai , Yong Wilson Thau Lym , Abas Faridah , Tan Chin Ping
Published: January 2018

Algal have attracted attention from biomedical scientists as they are a valuable natural source of secondary metabolites that exhibit antioxidant activities. In this study, single-factor experiments were conducted to investigate the best extraction conditions (ethanol concentration, solid-to-solvent ratio, extraction temperature and extraction time) in extracting antioxidant compounds and capacities from four species of seaweeds (Sargassum polycystum, Eucheuma denticulatum , Kappaphycus alvarezzi variance Buaya and Kappaphycus alvarezzi variance Giant) from Sabah. Total phenolic content (TPC) and total flavonoid content (TFC) assays were used to determine the phenolic and flavonoid concentrations, respectively, while 2,2-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and 2,2-diphenyl-1-picylhydrazyl (DPPH) radical scavenging capacity assays were used to evaluate the antioxidant capacities of all seaweed extracts. Results showed that extraction parameters had significant effect (p < 0.05) on the antioxidant compounds and antioxidant capacities of seaweed. Sargassum polycystum portrayed the most antioxidant compounds (37.41 ± 0.01 mg GAE/g DW and 4.54 ± 0.02 mg CE/g DW) and capacities (2.00 ± 0.01 µmol TEAC/g DW and 0.84 ± 0.01 µmol TEAC/g DW) amongst four species of seaweed. Single-factor experiments were proven as an effective tool to determine and quantify the relationship between a single factor and a single response variable.
Inter simple sequence repeats (ISSRs): Neglected DNA markers for molecular dissection of Plasmodium species in long-tailed Macaque (Macaca fascicularis)
Authors: Khajeaian Parastoo , Tan Soon Guan , Valdiani Alireza , Yong Christina Seok Yien , Zareian Jahromi Mohammad , Alitheen Noorjahan Banu , Rovie-Ryan Jeffrine Japning
Published: January 2018

Understanding the genetic variation of the Plasmodium parasites could play an important role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR) markers have successfully been tested for investigating the genetic diversity of malaria vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic variation of Plasmodium species, as well. To illustrate the genetic diversity of two infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium cynomolgi, infected and uninfected monkey blood samples were separately collected on filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of three clusters. However, the most significant result of the cluster analysis was revealing the high efficiency of ISSR markers in the discrimination of the two Plasmodium species from each other. The cluster analysis showed a wide range of genetic diversity among both Plasmodium and the long-tailed Macaque accessions. The principal component analysis (PCA) also confirmed the cluster analysis results.
Implanted intracortical electrodes as chronic neural interfaces to the central nervous system
Authors: Henderson Peter
Published: January 2018

Recent developments in neural interfaces show that it is possible to have fine control of a robotic prosthetic by interfacing with the motor cortex of the human brain. Development of long term systems for this purpose is a challenging task with many different possibilities. Intracortical implants have shown the most promise in providing enough signal selectivity and throughput for complex control systems with many degrees of freedom. Intracortical systems generally fall into two categories: MEMS devices and bundle of wire systems. While both show promise, MEMS systems have been greatly popularized due to their reproducibility. In particular, the Michigan probe and Utah microarray are often used as a base for construction of more complex intracortical systems. However, these systems still carry many downsides. Their long-term viability is questionable, with mixed results. The effects of damage from implantation are still inconclusive and immune responses remain a problem for long-term use. While there is some promising research in the use of bioactive molecules and biocompatible materials to prevent immune responses, more controlled study is needed before intracortical systems become widespread.
Hydrogeomorphic and biotic drivers of instream wood differ across sub-basins of the Columbia River Basin, USA
Authors: Hough-Snee Nate , Kasprak Alan , Rossi Rebecca K , Bouwes Nicolaas , Roper Brett B , Wheaton Joseph
Published: January 2018

Instream wood promotes habitat heterogeneity through its influence on flow hydraulics and channel geomorphology. Within the Columbia River Basin, USA, wood is vital for the creation and maintenance of habitat for threatened salmonids. However, our understanding of the relative roles of the climatic, geomorphic, and ecological processes that source wood to streams is limited, and making it difficult to identify baseline predictions of instream wood and create targets for stream restoration. Here we investigate how instream wood frequency and volume differ between seven sub-basins of the Columbia River Basin and what processes shape these differences within these sub-basins. We collected data on wood volume and frequency, discharge and stream power, and riparian and watershed forest structure for use in modeling wood volume and frequency. Using random forest models, we found that mean annual precipitation, riparian tree cover, and the individual watershed were the most important predictors of wood volume and frequency. Within sub-basins, we used linear models, finding that some basins had unique predictors of wood. Discharge, watershed area or precipitation often combined with forest cover, riparian conifer and/or large tree cover in models of instream large wood volume and frequency. In many sub-basins, models showed at least one hydrologic variable, indicative of transport capacity and one ecological variable, indicative of the reach or upstream watershed’s ability to grow measurable instream wood. We conclude that basin-specific models yield important insights into the hydrologic and ecological processes that influence wood loads, creating tractable hypotheses for building predictive models of instream wood.
Developing appropriate conservation measures for the seasonal whale shark feeding aggregation in Seychelles using ecological modeling tools
Authors: French Georgia C.A. , Bluemel Joanna K , Rowat David
Published: January 2018

Background: The whale shark feeding aggregation in the Seychelles has been studied in detail since 2002, including aerial survey and collection of environmental data. In these coastal waters previous tagging studies have shown whale sharks spend considerable time in the top 10m of water (44-60% of daylight hours). Although protected locally there is currently no management structure to conserve them outside of protected areas. This is the first attempt to develop Temporary Protected Areas using statistical modeling of their ecological distribution to conserve the aggregation.

Methods: Data on whale shark occurrence and distribution were collected via standardized aerial surveys from microlight aircraft that also recorded locations of surface-feeding schools of fish and environmental variables. These data were input into Geographical Information System (GIS) software to create density distribution maps; further layers generated included distance from the coastline, and chlorophyll-a (Chl-a) concentration (from MODIS satellite imagery). MAXENT ecological modeling software and Kernel Density Estimate analysis were used to produce a habitat suitability map and probability distribution estimate. The MAXENT model was tested using pseudo-absence data in a binomial generalized linear model.

Results: Chl-a concentration, distance from coast and fish schools were all found to influence whale shark presence and Maxent results closely matched those from the Kernel Density Estimate analysis. Predictions of suitable habitat for whale sharks avoided higher Chl-a concentrations, but showed positive correlations with schools of fish, possibly acting as a direct indication of zooplankton abundance. Whale sharks preferentially selected feeding areas close to the coast.

Conclusion: Maxent and Kernel Density Estimates can provide useful tools to guide the development of appropriate conservation and management of this species that take into consideration temporal behavior and ecology.
Modeling biological oscillations: integration of short reaction pauses into a stationary model of a negative feedback loop generates sustained long oscillations
Authors: Yang Louis , Yang Ming
Published: January 2018

Sustained oscillations are frequently observed in biological systems consisting of a negative feedback loop, but a mathematical model with two ordinary differential equations (ODE) that has a negative feedback loop structure fails to produce sustained oscillations. Only when a time delay is introduced into the system by expanding to a three-ODE model, transforming to a two-DDE model, or introducing a bistable trigger do stable oscillations present themselves. In this study, we propose another mechanism for producing sustained oscillations based on periodic reaction pauses of chemical reactions in a negative feedback system. We model the oscillatory system behavior by allowing the coefficients in the two-ODE model to be periodic functions of time – called pulsate functions – to account for reactions with go-stop pulses. We find that replacing coefficients in the two-ODE system with pulsate functions with micro-scale (several seconds) pauses can produce stable system-wide oscillations that have periods of approximately one to several hours long. We also compare our two-ODE and three-ODE models with the two-DDE, three-ODE, and three-DDE models without the pulsate functions. Our numerical experiments suggest that sustained long oscillations in biological systems with a negative feedback loop may be an intrinsic property arising from the slow diffusion-based pulsate behavior of biochemical reactions.
Examining the role of red background in magnocellular contribution to face perception
Authors: Awasthi Bhuvanesh , Williams Mark A , Friedman Jason
Published: January 2018

This study examines the role of the magnocellular system in the early stages of face perception, in particular sex categorization. Utilizing the specific property of magnocellular suppression in red light, we investigated visually guided reaching to low and high spatial frequency hybrid faces against red and grey backgrounds. The arm movement curvature measure shows that reduced response of the magnocellular pathway interferes with the low spatial frequency component of face perception. This is the first definitive behavioral evidence for magnocellular contribution to face perception.
Simultaneous gene finding in multiple genomes
Authors: König Stefanie , Romoth Lars , Gerischer Lizzy , Stanke Mario
Published: January 2018

As whole genome sequencing is taking on ever-increasing dimensions, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or – if not – where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on a whole-genome alignment of 12 Drosophila species and its accuracy evaluated on D. melanogaster. The method is being implemented as an extension to the gene finder AUGUSTUS.
Efficient duplicate rate estimation from subsamples of sequencing libraries
Authors: Schröder Christopher , Rahmann Sven
Published: January 2018

In high-throughput sequencing (HTS) projects, the sequenced fragments’ duplicate rate is a key quality metric. A high duplicate rate may arise from a low amount of input DNA and many PCR cycles. Many methods for downstream analyses require that duplicates be removed. If the duplicate rate is high, most of the sequencing effort and money spent would have been in vain. Therefore, it is of considerable interest to estimate the duplicate rate after sequencing only a small subsample at low depth (multiplexed with other libraries) for quality control before running the full experiment. In this article, we provide an elementary mathematical framework and an efficient computational approach based on quadratic and linear optimization to estimate the true duplicate rate from a small subsample. Our method is based on up-sampling the occupancy distribution of the reads’ copy numbers. Compared to an existing approach, we use an explicit and easily explained mathematical model that accurately inverts the sub-sampling process. We evaluate the performance of our approach in comparison to that of the existing method on several artificial and real datasets. The same ideas can be used for diversity estimation in general. Software implementing our approach is available under the MIT license.
Retrieving the Hemodynamic Response Function in resting state fMRI: methodology and applications
Authors: Wu Guo-Rong , Marinazzo Daniele
Published: January 2018

Retrieving the hemodynamic response function (HRF) in fMRI data is important for several reasons. Apart from its use as a physiological biomarker, HRF can act as a confounder in connectivity studies. In task-based fMRI is relatively straightforward to retrieve the HRF since its onset time is known. This is not the case for resting state acquisitions. We present a procedure to retrieve the hemodynamic response function from resting state (RS) fMRI data. The fundamentals of the procedure are further validated by a simulation and with ASL data. We then present the modifications to the shape of the HRF at rest when opening and closing the eyes using a simultaneous EEG-fMRI dataset. Finally, the HRF variability is further validated on a test-retest dataset.