bluuebunny/crossref_metadata_2025 huggingface dataset:
Testing the hypothesis that routine sea ice coverage of 3-5 mkm2 results in a greater than 30% decline in population size of polar bears (Ursus maritimus)
Authors: Crockford Susan J
Published: January 2018

The polar bear (Ursus maritimus) was the first species to be classified as threatened with extinction based on predictions of future conditions rather than current status. These predictions were made using expert-opinion forecasts of population declines linked to modeled habitat loss – first by the International Union for the Conservation of Nature (IUCN)’s Red List in 2006, and then by the United States Fish and Wildlife Service (USFWS) in 2008 under the Endangered Species Act (ESA), based on data collected to 2005 and 2006, respectively. Both assessments predicted significant population declines of polar bears would result by mid-century as a consequence of summer sea ice extent rapidly reaching 3-5 mkm2 on a regular basis: the IUCN predicted a >30% decline in total population, while the USFWS predicted the global population would decline by 67% (including total extirpation of ten subpopulations within two vulnerable ecoregions). Biologists involved in these conservation assessments had to make several critical assumptions about how polar bears might be affected by future habitat loss, since sea ice conditions predicted to occur by 2050 had not occurred prior to 2006. However, summer sea ice declines have been much faster than expected: low ice levels not expected until mid-century (about 3-5 mkm2) have occurred regularly since 2007. Realization of predicted sea ice levels allows the ‘rapid sea ice decline = population decline’ assumption for polar bears to be treated as a testable hypothesis. Data collected between 2007 and 2015 reveal that polar bear numbers have not declined as predicted and no subpopulation has been extirpated. Several subpopulations expected to be at high risk of decline remained stable and five showed increases in population size. Another at-risk subpopulation was not counted but showed marked improvement in reproductive parameters and body condition with less summer ice. As a consequence, the hypothesis that repeated summer sea ice levels of below 5 mkm2 will cause significant population declines in polar bears is rejected, a result that indicates the ESA and IUCN judgments to list polar bears as threatened based on future risks of habitat loss were scientifically unfounded and that similar predictions for Arctic seals and walrus may be likewise flawed. The lack of a demonstrable ‘rapid sea ice decline = population decline’ relationship for polar bears also potentially invalidates updated survival model outputs that predict catastrophic population declines should the Arctic become ice-free in summer.
Macro-algae flora and succession characteristics in the mussel culture zones in Gouqi island, Zhejiang Province
Authors: Huang Yan , Sun Bin , He Pei Min
Published: January 2018

Macro-algae flora of the mussel culture zones in Gouqi island, Zhejiang Province, was surveyed from 2014 to 2015. Seventy species of macro-algae were identified, belonging to 31 genera, 21 families, 14 orders, and three phyla. Thirty-eight species from 16 genera belong to Rhodophyta, 21 species from seven genera belong to Phaeophyta, and 11 species from eight genera belong to Chlorophyta. Rhodophyta, Chlorophyta, and Phaeophyta contributed to 54.29%, 30%, and 15.71% of the total number of species, respectively. The dominant species were Undaria pinnatifida, Sargassum horneri, Grateloupia livida, Grateloupia turuturu, Ulva pertusa, Ulva lactuca, Hypnea boergesenii, Ulva linza, Cladophora utriculosa, and Amphiroa ephedraea. Seasonal alternation of macro-algae species was evident; there were 52 species in spring, 42 species in winter, 38 species in autumn, and 30 species in summer. Macro-algae biomass was highest in spring and lower in autumn > summer > and winter. The diversity of macro-algae communities also changed seasonally; the diversity index (H’) was highest in autumn and lower in summer > winter > and spring. The results of de-trended correspondence analysis suggested that temperature was the most important environmental factor affecting the distribution of the macro-algae in mussel culture zones. Wind, water currents, and human disturbances were also important factors affecting algal communities.
Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates
Authors: Sydykova Dariya K. , Wilke Claus O
Published: January 2018

Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN/dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it assigns a relative conservation score to each site in an alignment. How site-wise dN/dS values relate to Rate4Site scores is not known. Here we elucidate the relationship between these two rate measurements. We simulate sequences with known dN/dS, using either dN/dS models or mutation--selection models for simulation. We then infer Rate4Site scores on the simulated alignments, and we compare those scores to either true or inferred dN/dS values on the same alignments. We find that Rate4Site scores generally correlate well with true dN/dS, and the correlation strengths increase in alignments with higher sequence divergence and higher number of taxa. Moreover, Rate4Site scores correlate nearly perfectly with inferred dN/dS values, even for small alignments with little divergence. Finally, we verify this relationship between Rate4Site and dN/dS in a variety of natural sequence alignments. We conclude that codon-level and amino-acid-level analysis frameworks are directly comparable and yield near-identical inferences.
Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation
Authors: Odoni Dorett I , Tamayo-Ramos Juan A , Sloothaak Jasper , van Heck Ruben G A , Martins dos Santos Vitor A P , de Graaff Leo H , Suarez-Diez Maria , Schaap Peter J
Published: January 2018

The filamentous fungus Rhizopus delemar naturally accumulates relatively high amounts of fumarate. Although the culture conditions that increase fumarate yields are well established, the network underlying the accumulation of fumarate is not yet fully understood. We set out to increase the knowledge about fumarate accumulation in R. delemar. To this end, we combined a transcriptomics and proteomics approach to identify key metabolic pathways involved in fumarate production in R. delemar, and propose that a substantial part of the fumarate accumulated in R. delemar during nitrogen starvation results from the urea cycle due to amino acid catabolism.
Comprehensive model optimization in pulp quality prediction: a machine learning approach
Authors: Huang Chin-Wei , Baron Luc , Balazinski Marek , Achiche Sofiane
Published: January 2018

Feature selection in machine learning is of great interest since it is reckoned as creating more efficient predictive models in several engineering domains. It is even of special importance in the pulp and paper transformation industry as the knowledge of this particular process is generally very limited. In this paper, we first compared the performance of rule-based genetic algorithm and that of adaptive neuro-fuzzy inference system; the latter is found to be more precise in predicting the pulp quality. We then combined several data mining algorithms such as genetic algorithm-partial least square regression, along with other statistical methods, to explore the relevance of all the potential variables that could be used to predict the pulp ISO brightness, an important property that is usually linked to model performance and hence pulp quality prediction. A few highly relevant variables are thereby determined, and the full set of 79 variables obtained from a Chip Management System was trimmed down to an optimized combination of 3 inputs depending on their relevancy. Peroxide charge (P), average luminance (L) and hue (H) were chosen as the optimal subset to describe the ISO brightness of the pulp and the model was simplified without losing much of its accuracy. Finally, we derived the numbers of membership functions for each variable to further refine the fuzzy logic-based prediction model. The error then reached 2.18%. The loss on accuracy was compensated by adjusting to the fittest membership function numbers
Visitor perceptions and reliance on active and passive communication techniques in zoos
Authors: Foote Dustin J. , Louder Matthew I. M. , Balakrishnan Christopher N.
Published: January 2018

The goal of educating the public about environmental and conservation issues is found in the mission statements of almost every zoo in the world. In order to effectively teach their visitors, zoos must understand how they are communicating with their public. In this study, we attempt to quantify how Sylvan Heights Bird Park (SHBP) communicates with its visitors. SHBP is a small not-for-profit facility that specializes in birds, with a primary focus on waterfowl (Anseriformes). Located in an economically depressed eastern North Carolina county (Halifax), SHBP receives over 46,000 visitors a year. Using a survey, we collected information of visitor perceptions of the role of zoos, their reliance on different sources of information, and their retention of information provided via different modes of communication. SHBP visitors listed exhibit signage (passive communication) as the preferred method of gaining information. Interestingly, however, we found that reliance on signage varied with age and gender and we found no difference in information retention between visitors that experienced only passive communication (signage) versus those that experienced active communication. Just over half (51%) of visitors viewed the primary purpose of a zoo to be entertainment but this view changed with age and gender. Although almost all respondents identified the role of zoos in maintaining biodiversity, we found a disconnect between this view and an understanding of how zoos might contribute to species conservation.
The genetic history of the Indian subcontinent
Authors: Mahal David G.
Published: January 2018

The human male specific Y-chromosome passes from father to son essentially unchanged, but occasionally a random change, known as a mutation, occurs. These mutations, also called markers, serve as beacons and can be mapped. When geneticists identify a mutation in a DNA test, they try to determine when it first occurred and in which part of the world. Thus, the Y-chromosome haplogroup, which is a population group descended from a common ancestor, can be used to trace the paternal lines of men. The poster describes a research project that aims to identify the ancient geographical origins of key ethnic communities of the Indian subcontinent, based on their Y-DNA haplogroups.
Effect of Phalaris aquatica on the abundance and diversity of vertebrate animals in Mediterranean coastal grasslands in California
Authors: Joseph Angela , Nazal Basma , Saini Neha , Sajadi Farwa , Ye Ryan
Published: January 2018

Harding grass (Phalaris aquatica), an invasive non-native species of bunchgrass, has been introduced to grasslands in many regions of California, particularly those with a history of disturbance, such as tilling and grazing. Due do the invasive nature of Harding grass, we sought to examine whether it has an effect on small animal abundance and diversity in the grasslands, Rancho Marino Reserve (RM) and Fiscalini Ranch Preserve (FR) in California. Both grasslands have similar climate and geographic location but differ in management history. Two transects were created in each site, with eight plots per transect. Animal cameras were deployed over the course of three nights to examine the abundance and diversity of small animals. Due to the history of tilling and planting of RM, and its increase in P. aquatica coverage, there was less animal abundance and diversity compared to FR. The results indicated that the untilled/unplanted areas had more animal abundance and diversity compared to tilled/planted due to the lack of Harding Grass. This can be due to factors such as diminished soil quality, difficulty in maneuvering in the tall grass, and adaptability to native vegetative state. Invasive plants have the ability to increase rapidly in space and potentially lead to ecosystem degradation. This adds further knowledge in the relationship between small animals and their habitats and helps conservation biologists ensure mammalian populations remain stable.
Evolutionary response to the Qinghai-Tibetan Plateau uplift: Phylogeny and biogeography of Ammopiptanthus and tribe Thermopsideae (Fabaceae)
Authors: Shi Wei , Liu Pei-Liang , Duan Lei , Pan Bo-Rong , Su Zhi-Hao
Published: January 2018

Based on sequence data from the nuclear ITS and four cpDNA regions (matK, trnH-psbA, trnL-trnF, rbcL), phylogeny of the tribe Thermopsideae was inferred. Our analyses supported this tribe being merged into a monophyletic Sophoreae in a broad sense, with exclusion of Pickeringia. Genera of Sophoreae were separated into the Thermopsoid clade and Sophoroid clade. Monophyly of Anagyris, Baptisia and Piptanthus were basically supported in the Thermopsoid clade. Ammopiptanthus, consisting of A. mongolicus and A. nanus, nested within the Sophoroid clade, with Salweenia as its sister. Ammopiptanthus and Salweenia disjunctively distributed in desert of Northwestern China and Hengduan Mountains, respectively. Divergence age was estimated based on the ITS phylogenetic analysis. Emergence of the common ancestor of Ammopiptanthus and Salweenia, divergence between these two genera, and split of Ammopiptanthus species occurred at approximately 26.96 Ma, 4.74 Ma and 2.04 Ma, respectively, which may be response to the second, third, fourth rapid uplift of the Qinghai-Tibetan Plateau, respectively.
Strengths and weaknesses of DNA-based monitoring: Assessing macroinvertebrates in 18 Finnish streams with metabarcoding and morphology
Authors: Elbrecht Vasco , Vamos Edith , Meissner Kristian , Aroviita Jukka , Leese Florian
Published: January 2018

1) DNA metabarcoding holds great promise for assessment of stream ecosystems with macroinvertebrates. However, few large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification.

2) We tested metabarcoding using 18 macroinvertebrate samples from Finland using four primer sets. The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. Morphological identification was performed to the taxonomic level at which identification was reliable following standardized protocols.

3) We identified over twice the number of taxa, with greater species-level resolution, using DNA metabarcoding than morphology-based identification. For each sample, we detected more taxa by metabarcoding than by previous morphological methods, and all four primer sets showed similarly good performance. There was a significant linear correlation between sequence abundance and the number of taxa in each sample, but the scatter was up to two orders of magnitude. Ecological status assessment indices calculated from morphological and DNA metabarcoding datasets were mostly similar, with a few exceptions. With the recent drop in sequencing costs per sample, both methods identification are currently equally expensive.

4) We used actual samples for monitoring to demonstrate that DNA metabarcoding can achieve similar results and better taxonomic resolution than current morphological identification methods. Metabarcoding has thus already become a viable and reliable invertebrate identification method for stream assessment. However, to unlock the full potential of DNA metabarcoding for ecosystem assessment key problems in current laboratory protocols and reference databases, specified in this work, will require further attention.
Assessing strengths and weaknesses of DNA metabarcoding based macroinvertebrate identification for routine stream monitoring
Authors: Elbrecht Vasco , Vamos Edith , Meissner Kristian , Aroviita Jukka , Leese Florian
Published: January 2018

1) DNA metabarcoding holds great promise for the assessment of macroinvertebrates in stream ecosystems. However, few large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification.

2) We performed metabarcoding using four primer sets on macroinvertebrate samples from 18 stream sites across Finland. The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. Specimens were morphologically classified, following standardized protocols, to the lowest taxonomic level for which identification was feasible in the routine national monitoring.

3) DNA metabarcoding identified more than twice the number of taxa than the morphology-based protocol, and also yielded higher taxonomic resolution. For each sample, we detected more taxa by metabarcoding than by the morphological method, and all four primer sets exhibited comparably good performance. Sequence read abundance and the number of specimens per taxon (proxy for biomass) were significantly correlated in each sample, although adjusted R2 were low. With a few exceptions, the ecological status assessment metrics calculated from morphological and DNA metabarcoding datasets were similar. Given the recent reduction in sequencing costs, metabarcoding is currently approximately equal priced per sample to morphology-based identification.

4) Using samples obtained in the field, we demonstrated that DNA metabarcoding can achieve similar assessment results as those of current protocols for morphological identification. Thus, metabarcoding represents a feasible and reliable method to identify macroinvertebrates in stream bioassessment, and offers powerful advantage over morphological identification in providing identification for taxonomic groups that are unfeasible to identify in routine protocols. To unlock the full potential of DNA metabarcoding for ecosystem assessment, however, it will be necessary to address key problems with current laboratory protocols and reference databases.
Angle stability and outflow in excisional ab interno trabeculectomy with active versus passive chamber management
Authors: Wang Chao , Dang Yalong , Waxman Susannah , Loewen Nils A
Published: January 2018

Purpose: To compare the intraoperative angle stability and the postoperative outflow of two ab interno trabeculectomy devices that excise the trabecular meshwork. The newer device has an active aspiration and irrigation port while the older requires viscoelastic to maintain the anterior chamber. We hypothesized that anterior segment optical coherence tomography (ASOCT) allows quantifying the intraoperative behavior in a microincisional glaucoma surgery (MIGS) pig eye training model. Methods: Twelve freshly enucleated porcine eyes were measured with ASOCT at baseline, at the beginning of the procedure and at its conclusion to determine the anterior chamber depth (ACD) and the nasal angle
Nutritional values of flamboyant (Delonix regia) seeds obtained in Akure, Nigeria
Authors: Abulude Francis Olawale , Adejayan Adewale Wright
Published: January 2018

The nutritional and antinutritional compositions (phytochemical, proximate, mineral, digestibility, functional properties, phytate, tannins and oxalate.) of Delonix regia seed were determined. The results showed that the sample, has high protein content, Ca, Na, Mg, K and Fe. Biological value (BV) - 76.24, net protein utilization (NPU) - 60.99 and net protein value (NPV) - 46.50, WAC 200%, OAC 98%, FC 4.3% and LGC 7%. The sample showed the presence of some bioactive substances, the implication of this is that the extract may be suitable for treatment of several ailments in human and animals. The results also depicted the presence of antinutrients; it would be advisable to properly process the seed before consumption. The implications of the results were discussed.
High definition video loggers provide new insights into behaviour, physiology, and the oceanic habitat of marine top predators
Authors: Mattern Thomas , McPherson Michael D , Ellenberg Ursula , van Heezik Yolanda , Seddon Philipp J
Published: January 2018

Camera loggers are increasingly used to examine behavioural aspects of free-ranging animals. However, often video loggers are deployed with a focus on specific behavioural traits for which it suffices to use cameras that are small but often have a limited field of view, poor light performance and video quality. Yet the rapid developments in consumer electronics provide new devices with much improved visual data which allows a wider scope for studies employing this novel methodology. We developed a camera logger that records full HD video through a wide-angle lens, providing high resolution footage with a greater field of view than other camera loggers. Main goal was the analysis of foraging behaviour of a marine top-predator, the Yellow-eyed penguin in New Zealand, with regards habitat characteristics. Yet, visual data recorded proved to contain much broader information than anticipated. Frame-by-frame analysis allowed accurate timing of prey pursuits and time spent over certain seafloor types. Similarly, it was possible to time breathing intervals between dives and quantify exhalation events during prey events, a previously undescribed behaviour. Using screen overlays we analysed flipper angles and beat frequencies throughout the various phases of a dive. The recorded video footage showed that prey species were associated with certain seafloor types, revealed different predator evasion strategies by benthic fishes, and highlighted varying energetic consequences for penguins pursuing certain types of prey. Flipper movements analysis confirmed decreasing effort during descent phases as the bird gained depth, and that ascent was principally passive. Breathing episodes between dives were short (<1 s) while the majority of the time was devoted to subsurface scanning with a submerged head. Video data recorded on free-ranging animals not only provides a wealth of information recorded from a single deployment but also necessitates new approaches with regards to analysis of visual data. In this paper, we demonstrate the diversity of information that can be gleaned from video logger data, provide various analysis approaches to visual data and highlight the importance of video quality and field of view significantly increase quality of the resulting data.
Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
Authors: Budnik Bogdan , Levy Ezra , Slavov Nikolai
Published: January 2018

Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these limitations, we developed Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), and validated its ability to identify distinct human cancer cell types based on their proteomes. We used SCoPE-MS to quantify over a thousand proteins in differentiating mouse embryonic stem (ES) cells. The single-cell proteomes enabled us to deconstruct cell populations and infer protein abundance relationships. Comparison between single-cell proteomes and transcriptomes indicated coordinated mRNA and protein covariation. Yet many genes exhibited functionally concerted and distinct regulatory patterns at the mRNA and the protein levels, suggesting that post-transcriptional regulatory mechanisms contribute to proteome remodeling during lineage specification, especially for developmental genes. SCoPE-MS is broadly applicable to measuring proteome configurations of single cells and linking them to functional phenotypes, such as cell type and differentiation potentials.
Correlated mutations distinguish misfolded and properly folded proteins
Authors: Woźniak Paweł , Kotulska Malgorzata , Vriend Gert
Published: January 2018

Knowledge about the three dimensional structure of proteins is crucial in order to learn about their behavior, stability, or role as a target in drug design. Unfortunately, traditional experimental methods used in structure determination such as X-ray crystallography and NMR are costly and time-consuming. Therefore, computational methods that allow for protein structure reconstruction from sequence only are greatly desired. One of these is the recently developed direct coupling analysis (DCA) method [1, 2] which achieves the best results in residue-residue contact prediction from multiple sequence alignments only. Predicted contacts are used as restraints in the reconstruction of the three-dimensional structure of a protein. Unfortunately, the accuracy of DCA methods is on the order of 40% among the 100 strongest predicted contacts, which is insufficient for ab initio protein structure reconstruction. However, the results of DCA can support protein structure reconstruction in a different way.

Our results show that DCA can indicate the best protein structure among its structural variants by the prediction of residue-residue contacts [3]. We counted the number of correctly predicted contacts within the strongest 100 DCA predictions for a set of obsolete PDB entries and their successors and for 22 proteins for which the Decoys 'R' Us database [4] provided properly folded and misfolded structures. These numbers were related to structure similarity scores, such as RMSD or TM-score [5]. DCA correctly predicts significantly more contacts for properly folded structures than for misfolded ones. Our method works much better for structures determined with X-ray crystallography than with the NMR spectroscopy [3]. The method will not detect misfolded proteins per se, but when a protein structure experimentalist needs to choose between alternative folds for the same protein, DCA can help.

[1] F. Morcos et al., Direct-coupling analysis of residue coevolution captures native contacts across many protein families, 2011, Proc Natl Acad Sci U S A 108(49):E1293-301.

[2] C. Feinauer et al., Improving contact prediction along three dimensions, 2014, PLoS Comput Biol., 10(10):e1003847.

[3] P.P. Wozniak, G. Vriend, M. Kotulska, Correlated mutations select misfolded from properly folded proteins, 2016, Bioinformatics, (article accepted).

[4] R. Samudrala, M. Levitt, Decoys 'R' Us: A database of incorrect protein conformations to improve protein structure prediction, 2000, Protein Science 9: 1399-1401.

[5] Y. Zhang, J. Skolnick, TM-align: A protein structure alignment algorithm based on TM-score, 2005, Nucleic Acids Research, 33: 2302-2309.
Postmortem succession of gut microbial communities in human cadavers
Authors: DeBruyn Jennifer M , Hauther Kathleen A
Published: January 2018

The human microbiome has demonstrated importance for health and functioning in living individuals. However the fate of the microbiome after death is poorly understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI). The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449) while diversity decreased (rs = -0.701). The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides) significantly declined while Clostridiales (Clostridium, Anaerosphaera) and the fly-associated Gammaproteobacteria Ignatzschineria and Wohlfahrtiimonas increased. A best fit multiple regression model, which included five OTUs, improved the ability to predict PMI (R2 = 0.824; p < 0.001). Our examination of human caeca microflora in decomposing cadavers adds to the growing literature on postmortem microbial communities, which will ultimately contribute to a better understanding of decomposition processes.
Pesticide mixtures in the Swedish streams: environmental risks, contributions of individual compounds and consequences of single-substance oriented risk mitigation
Authors: Gustavsson Mikael B , Kreuger Jenny , Bundschuh Mirco , Backhaus Thomas
Published: January 2018

The paper presents the ecotoxicological assessment and environmental risk evaluation of complex pesticide mixtures occurring in freshwater ecosystems in southern Sweden. The evaluation is based on the data collected between 2002 and 2013 by the Swedish pesticide monitoring program and includes 1308 individual samples, detecting mixtures of up to 54 pesticides (modal=8). The environmental risk of 77% of the samples exceeded acceptable levels, based on an assessment using Concentration-Addition and Swedish Water Quality Objectives (WQO) for the individual pesticides. Algae were the most sensitive organism group. However, the analytical detection limits, especially for insecticides, are currently insufficient to analyze concentrations at or near their WQO’s. Thus, the risk of the analyzed pesticide mixtures to crustaceans and fish is currently systematically underestimated.

Throughout the monitoring the risk associated with pesticide mixtures is often driven by only 1-3 compounds. However, the risk-drivers differ substantially between sites and samples, so that 83 of the 141 monitored pesticides need to be included in the assessment to account for 95% of the risk at all sites and years.

Single-substance oriented risk mitigation measures that would ensure that each individual pesticide is present at 95% of its individual WQO at maximum, would also reduce the mixture risk, from a median risk quotient of 2.7 to a median risk quotient of 2.3. However, acceptable total risk levels would still be exceeded in more than 70% of the samples.
Pesticide mixtures in the Swedish streams: environmental risks, contributions of individual compounds and consequences of single-substance oriented risk mitigation
Authors: Gustavsson Mikael B , Kreuger Jenny , Bundschuh Mirco , Backhaus Thomas
Published: January 2018

This paper presents the ecotoxicological assessment and environmental risk evaluation of complex pesticide mixtures occurring in freshwater ecosystems in southern Sweden. The evaluation is based on exposure data collected between 2002 and 2013 by the Swedish pesticide monitoring program and includes 1308 individual samples, detecting mixtures of up to 53 pesticides (modal=8). Pesticide mixture risks were evaluated using three different scenarios for non-detects (best-case, worst-case and using the Kaplan-Meier method). The risk of each scenario was analyzed using Swedish Water Quality Objectives (WQO) and throphic-level specific environmental thresholds.

Using the Kaplan-Meier method the environmental risk of 73% of the samples exceeded acceptable levels, based on an assessment using Concentration-Addition and WQOs for the individual pesticides. Algae were the most sensitive organism group. However, analytical detection limits, especially for insecticides, were insufficient to analyze concentrations at or near their WQO’s. Thus, the risk of the analyzed pesticide mixtures to crustaceans and fish is systematically underestimated. Treating non-detects as being present at their individual limit of detection increased the estimated risk by a factor 100 or more, compared to the best-case or the Kaplan-Meier scenario.

Pesticide mixture risks are often driven by only 1-3 compounds. However, the risk-drivers (i.e., individual pesticides explaining the largest share of potential effects) differ substantially between sites and samples, and 83 of the 141 monitored pesticides need to be included in the assessment to account for 95% of the risk at all sites and years.

Single-substance oriented risk mitigation measures that would ensure that each individual pesticide is present at a maximum of 95% of its individual WQO, would also reduce the mixture risk, but only from a median risk quotient of 2.1 to a median risk quotient of 1.8. Also, acceptable total risk levels would still be exceeded in more than 70% of the samples.
Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi
Authors: Berná Luisa , Chiribao Maria Laura , Greif Gonzalo , Rodriguez Matias , Alvarez-Valin Fernando , Robello Carlos
Published: January 2018

American trypanosomiasis is a chronic and endemic disease, which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi, amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to the different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vector, showed higher expression on genes related to energy metabolism, mainly Krebs cycle, respiratory chain and oxidative phosphorylation related genes, and anabolism related genes associated to nucleotide and steroid biosynthesis; also a general down regulation of surface glycoproteins was seen at this stage. Trypomastigotes, living extracellularly in the bloodstream of mammals, express a plethora of surface proteins and signaling genes involved in invasion and evasion of immune response. Amastigotes mostly express membrane transporters and genes involved in regulation of cell cycle, an also express a specific subset of surface glycoproteins coding genes. In addition, these results allowed to improve the annotation of Dm28c genome, identifying new ORFs and set the stage for construction of networks of co-expression, which can give clues about coded proteins of unknown functions.
Characterization of Chilean Pseudomonas syringae pv actinidiae strains isolated from infected orchards
Authors: Parada Juan Pablo , Orellana Matias , Amaza Leticia , Pérez-Martínez Isabel , Holuigue Loreto , Salinas Paula
Published: January 2018

Pseudomonas syringae pv. actinidiae (PSA) strain is a major problem for the kiwifruit industry worldwide. So far, 5 biovars of PSA have been identified, of which the most virulent form is biovar 3. This is the only biovar that has been detected in Chile, which is the third kiwifruit exporter country and is currently suffering from canker disease produced by PSA. Single nucleotide polymorphisms (SNPs) analyses have classified the biovar 3 strain into three groups: the European, the New Zealander and the Chilean groups, which have evolved from a common Chinese PSA ancestor. Although Chilean strains have been used in phylogenetic analysis, there is no information about genomic diversity within this group or whether they present microbiological characteristics that could affect its virulence. In this work we studied 15 Chilean bacterial isolates collected from orchards with canker disease symptoms, and classified them as PSA using a different PCR techniques. To gain more information on the relationship between the isolates we sequenced part of three conserved genes widely used to classify bacterial strains: gtl (Citrate Synthase), rpoD (Sigma subunit of RNA polymerase II) and gyrB (Gyrase B). Using these sequences we performed a phylogenetic analysis that included some PSA reference sequences. Fourteen PSA Chilean isolates were grouped with PSA reference strains and three of them formed a subgroup within the PSA clade, suggesting clear differences at the genomic level among the isolates. We evaluated three microbiological traits in all the isolates: motility (swimming and swarming), and ability to induce a hypersensitive response in tobacco plants. All the isolates were able to induce the hypersensitive response in tobacco plants and were also able to perform both types of movements in appropriated growing conditions.
What an entangled Web we weave: An information-centric approach to socio-technical systems
Authors: Luczak-Roesch Markus , Tinati Ramine , O'Hara Kieron
Published: January 2018

Motivated by the increasing amount of voices who ask for careful consideration of what context-rich data analysis methods can tell us about the activities of human collectives, we contribute an argumentation that employs a dialectic of literature on the philosophy of truth and science as well as analytical methods for the study of information diffusion, Web graphs and social networks in order to make a case for changing the current view to the actions of human collectives in the digital. We strengthen our meta argument by a case study about one particular method that breaks with the causality assumption that is inherent in many of today’s methods and allows to capture novel dimensions of complexity of information sharing from a macroscopic cross-system perspective. We discuss whether this kind of analysis may generically suit to underpin the field of socio-technical systems with a novel information-centric theory.
Facial emotion recognition using Min-Max similarity classifier
Authors: Krestinskaya Olga , James Alex Pappachen
Published: January 2018

Recognition of human emotions from the imaging templates is useful in a wide variety of human-computer interaction and intelligent systems applications. However, the automatic recognition of facial expressions using image template matching techniques suffer from the natural variability with facial features and recording conditions. In spite of the progress achieved in facial emotion recognition in recent years, the effective and computationally simple feature selection and classification technique for emotion recognition is still an open problem. In this paper, we propose an efficient and straightforward facial emotion recognition algorithm to reduce the problem of inter-class pixel mismatch during classification. The proposed method includes the application of pixel normalization to remove intensity offsets followed-up with a Min-Max metric in a nearest neighbor classifier that is capable of suppressing feature outliers. The results indicate an improvement of recognition performance from 92.85% to 98.57% for the proposed Min-Max classification method when tested on JAFFE database. The proposed emotion recognition technique outperforms the existing template matching methods.
Diverse habitat use during two life stages of the critically Endangered Bahama Oriole (Icterus northropi): Community structure, foraging, and social interactions
Authors: Price Melissa R , Hayes William K
Published: January 2018

Our ability to prevent extinction in declining populations often depends on effective management of habitats that are disturbed through wildfire, logging, agriculture, or development. In these disturbed landscapes, the juxtaposition of multiple habitat types can be especially important to fledglings and young birds, which may leave breeding grounds in human-altered habitat for different habitats nearby that provide increased foraging opportunities, reduced competition, and higher protection from predators. In this study, we sought to better understand the importance of habitat diversity to two life stages of the critically endangered Bahama Oriole ( Icterus northropi ), a synanthropic songbird endemic to Andros, The Bahamas. First, we determined the avian species composition and relative abundance of the oriole among three major vegetation types on Andros: Caribbean pine ( Pinus caribaea ) forest, coppice (broadleaf dry forest), and anthropogenic areas, dominated by nonnative vegetation (farmland and developed land). We then compared the foraging strategies and social interactions of two age classes of adult orioles in relation to differential habitat use. Bird surveys late in the oriole’s breeding season indicated avian s pecies richness and oriole density were highest in coppice. Some bird species occurring in the coppice and pine forest were never observed in agricultural or residential areas, and may be at risk if human disturbance of pine forest and coppice increases, as is occurring at a rapid pace on Andros. During the breeding season, second-year (SY) adult orioles foraged in all vegetation types, whereas after-second-year (ASY) adults were observed foraging only in anthropogenic areas, where the species nested largely in introduced coconut palms ( Cocos nucifera ). Additionally, SY adults foraging in anthropogenic areas were often observed with an ASY adult, suggesting divergent habitat use for younger, unpaired birds. Other aspects of foraging (vegetation features, food-gleaning behavior, and food items) were similar for the two age classes. Older orioles exhibited relatively higher rates of social interactions (intraspecific and interspecific pooled) in anthropogenic areas, and won more interaction outcomes compared to youngeradults. Our findings concur with those of other studies indicating dry broadleaf forest is vitally important to migrating, wintering, and resident birds, including the critically endangered Bahama Oriole, which appears to depend heavily on this vegetation type during certain life stages.
CodonGenie: optimised ambiguous codon design tools
Authors: Swainston Neil , Currin Andrew , Green Lucy , Breitling Rainer , Day Philip J , Kell Douglas B
Published: January 2018

CodonGenie, freely available from http://codon.synbiochem.co.uk, is a simple web application for designing ambiguous codons to support protein mutagenesis applications. Ambiguous codons are derived from specific heterogeneous nucleotide mixtures, which create sequence degeneracy when synthesised in a DNA library. In directed evolution studies, such codons are carefully selected to encode multiple amino acids. For example, the codon NTN, where the code N denotes a mixture of all four nucleotides, will encode a mixture of phenylalanine, leucine, isoleucine, methionine and valine. Given a user-defined target collection of amino acids matched to an intended host organism, CodonGenie designs and analyses all ambiguous codons that encode the required amino acids. The codons are ranked according to their efficiency in encoding the required amino acids while minimising the inclusion of additional amino acids and stop codons. Organism-specific codon usage is also considered.
Survey methods for seed system network analysis
Authors: Buddenhagen Christopher E , Andersen Kelsey F , Fulton James C , Garrett Karen A
Published: January 2018

We present survey questions useful for describing agricultural seed systems. The questions are designed so that they can be used for standardized comparisons among seed systems, addressing both networks for seed movement and networks for the communication of information related to variety selection and integrated pest management. This approach provides information that can be used in multilayer network analyses of how information influences seed system success. Also provided are example data sheets with field descriptors that should provide for straightforward statistical analysis after data collection.
Analysis of RecA-independent recombination events between short direct repeats related to a genomic island and to a plasmid in Escherichia coli K12
Authors: Azpiroz María F , Laviña Magela D
Published: January 2018

RecA-independent recombination events between short direct repeats, leading to deletion of the intervening sequences, were found to occur in two genetic models in the Escherichia coli K12 background. The first model was a small E. coli genomic island which had been shown to be mobile in its strain of origin and, when cloned, in the E. coli K12 context too. However, it did not encode a site-specific recombinase as mobile genomic island usually do. Then, it was deduced that the host cells should provide the recombination function. This latter was searched for by means of a PCR approach to detect the island excision in E. coli K12 mutants affected in a number of recombination functions, including the 16 E. coli K12 site-specific recombinases, the RecET system, and multiple proteins that participate in the RecA-dependent pathways of homologous recombination. None of these appeared to be involved in the island excision. The second model, analyzed in a RecA deficient context, was a plasmid construction containing a short direct repeat proceeding from Saccharomyces cerevisiae, which flanked the cat gene. The excision of this gene by recombination of the DNA repeats was confirmed by PCR and through the detection, recovery and characterization of the plasmid deleted form. In sum, we present new evidence on the occurrence of RecA-independent recombination events in E. coli K12. Although the mechanism underlying these processes is still unknown, their existence suggests that RecA-independent recombination may confer mobility to other genetic elements, thus contributing to genome plasticity.
Membrane and luminal proteins reach the apicoplast by different trafficking pathways in the malaria parasite Plasmodium falciparum
Authors: Chaudhari Rahul , Dey Vishakha , Narayan Aishwarya , Sharma Shobhona , Patankar Swati
Published: January 2018

The secretory pathway in Plasmodium falciparum has evolved to transport proteins to the host cell membrane and to an endosymbiotic organelle, the apicoplast. The latter can occur via the ER or the ER-Golgi route. Here, we study these three routes using proteins Erythrocyte Membrane Protein-1 (PfEMP1), Acyl Carrier Protein (ACP) and glutathione peroxidase-like thioredoxin peroxidase (PfTPxGl) and inhibitors of vesicular transport. As expected, the G protein dependent vesicular fusion inhibitor AlF4- and microtubule destabilizing drug vinblastine block the trafficking of PfEMP-1, a protein secreted to the host cell membrane. However, while both PfTPxGl and ACP are targeted to the apicoplast, only ACP trafficking remains unaffected by these treatments. This implies that G-protein dependent vesicles do not play a role in classical apicoplast protein targeting. Unlike the soluble protein ACP, we show that PfTPxGl is localized to the outermost membrane of the apicoplast. Thus, the parasite apicoplast acquires proteins via two different pathways: first, the vesicular trafficking pathway appears to handle not only secretory proteins, but an apicoplast membrane protein, PfTPxGl. Second, trafficking of apicoplast luminal proteins appear to be independent of G-protein coupled vesicles.