bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation and development of freshwater invertebrate metabarcoding COI primers for Environmental Impact Assessment
Authors: Elbrecht Vasco , Leese Florian
Published: January 2018

A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an ideal group for Environmental Impacts Assessment (EIA). However, generating accurate macroinvertebrate inventories based on larval morphology is difficult and error-prone. Here, DNA metabarcoding provides new opportunities. Its potential to accurately identify invertebrates in bulk samples at the species level, has been demonstrated in several case studies. However, DNA based identification is often limited by primer bias, potentially leading to taxa in the sample remaining undetected. Thus, the success of DNA metabarcoding as an emerging technique for EIA critically relies on carefully evaluating primers.

We used the R package PrimerMiner to obtain and process cytochrome c oxidase I (COI) sequence data for the 15 most globally relevant freshwater invertebrate groups in EIAs. Using these sequence alignments, we developed four primer combinations optimized for freshwater macrozoobenthos. All primers were evaluated by sequencing ten mock community samples each consisting of 52 freshwater invertebrate taxa. Additionally, popular metabarcoding primers from the literature and the developed primers were tested in silico against the 15 relevant invertebrate groups.

The developed primers varied in amplification efficiency and the number of detected taxa, yet all detected more taxa than standard ‘Folmer’ barcoding primers. Two new primer combinations showed more consistent amplification than a previously tested ribosomal marker (16S) and detected all 42 insect taxa present in the mock community samples. In silico evaluation revealed critical design flaws in some commonly used primers from the literature.

We demonstrate a reliable strategy to develop optimized primers using the tool PrimerMiner. The developed primers detected almost all taxa present in the mock samples, and we argue that high base degeneracy is necessary to decrease primer bias as confirmed by experimental results and in silico primer evaluation. We further demonstrate that some primers currently used in metabarcoding studies may not be suitable for amplification of insect and freshwater taxa. Therefore, careful primer evaluation and more region / ecosystem specific primers are needed before DNA metabarcoding can be used for routine EIA of freshwater ecosystems.
Accumulation of DNA in an anoxic sediment – rDNA and rRNA presence of members of the microbial community from Landsort Deep, the Baltic Sea
Authors: Thureborn Petter , Hu Yue O.O. , Franzetti Andrea , Sjöling Sara , Lundin Daniel
Published: January 2018

Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms. To further elucidate which taxa may contribute to ecosystem function at this site, we here present three different datasets – rDNA amplicons, rDNA reads from a shotgun metagenome and expressed rRNA from a shotgun metatranscriptome. By comparing the three datasets and the ratios between rRNA and rDNA we seek to estimate the protein synthesis potential of the community members in order to provide an indication of what taxa may have cellular activity and metabolic potential. The variation in protein synthesis potential was large, both within and between taxa, in the sediment community. Many typically anaerobic taxa, e.g. from Deltaproteobacteria and Euryarchaeota, showed a high protein synthesis potential, while typical aerobes like Flavobacteria showed a low protein synthesis potential. More surprisingly, some common Baltic Sea surface water bacteria also displayed a high protein synthesis potential, suggesting they have an active role in the anoxic sediment ecosystem at 460 m depth. Both filamentous and unicellular Cyanobacteria exhibited very high protein synthesis potential, which implies a more complex role of these bacteria in carbon cycling in the Baltic Sea than previously suggested. Moreover, Mycobacteria, that were abundant in Landsort Deep sediment metagenome compared with other marine sediment metagenomes, showed protein synthesis potentials consistent with a functional role in the sediment community. Our results provide a new window of insight into the complexities of the microbial community of Landsort Deep with implications for the understanding of other anoxic accumulation sediments.
Accumulation of DNA in an anoxic sediment – rDNA and rRNA presence of members of the microbial community from Landsort Deep, the Baltic Sea
Authors: Thureborn Petter , Hu Yue O.O. , Franzetti Andrea , Sjöling Sara , Lundin Daniel
Published: January 2018

Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms in the Landsort Deep sediment. To further elucidate which taxa may contribute to ecosystem function at this site, we here present three different datasets – rDNA amplicons, rDNA reads from a shotgun metagenome and expressed rRNA from a shotgun metatranscriptome. By comparing the three datasets and the ratios between rRNA and rDNA we seek to estimate the protein synthesis potential of the community members in order to provide an indication of what taxa may have cellular activity and metabolic potential. The variation in protein synthesis potential was large, both within and between taxa, in the sediment community. Many typically anaerobic taxa, e.g. from Deltaproteobacteria and Euryarchaeota, showed a high protein synthesis potential, while typical aerobes like Flavobacteria showed a low protein synthesis potential. More surprisingly, some common Baltic Sea surface water bacteria also displayed a high protein synthesis potential, suggesting they have an active role in the anoxic sediment ecosystem at 460 m depth. Both filamentous and unicellular Cyanobacteria exhibited very high protein synthesis potential, which implies a more complex role of these bacteria in carbon cycling in the Baltic Sea than previously suggested. Moreover, Mycobacteria, that were abundant in Landsort Deep sediment metagenome compared with other marine sediment metagenomes, showed protein synthesis potentials consistent with a functional role in the sediment community. Our results provide a new window of insight into the complexities of the microbial community of Landsort Deep with implications for the understanding of other anoxic accumulation sediments.
Percentile curves for peripheral and truncal skinfold thickness for Canadian children and youth
Authors: Kuhle Stefan , Ashley-Martin Jillian , Maguire Bryan , Hamilton David C
Published: January 2018

Background: Skinfold thickness (SFT) measurements are a reliable and feasible method for assessing body fat in children but their use and interpretation is hindered by the scarcity of reference values in representative populations of children. The objectives of the present study were to develop age- and sex-specific percentile curves for five SFT measures (biceps, triceps, subscapular, suprailiac, medial calf) and to describe body fat composition in a representative population of Canadian children and youth. Methods: We analyzed data from 3938 children and adolescents between 6 and 19 years of age who participated in the Canadian Health Measures Survey cycles 1 (2007/2009) and 2 (2009/2011). Standardized procedures were used to measure SFT. Age- and sex-specific centiles for skinfolds and body fat were calculated using the GAMLSS method. Results: Percentile curves were materially different in absolute value and shape for boys and girls. Percentile girls in girls steadily increased with age whereas percentile curves in boys were characterized by a pubertal centered peak. Median body fat percentage at age 18 was 13.2 and 25.4% among boys and girls, respectively. Conclusions: The current study has presented for the first time percentile curves for five SFT measures and body fat in a representative sample of Canadian children and youth.
Evaluating the effects of habitat condition, climate and predator density on Shiras moose demography
Authors: Oates Brendan , Monteith Kevin , Merkle Jerod , Fralick Gary , Courtemanch Alyson B , Smith Douglas , Stahler Daniel , Dewey Sarah , Jimenez Michael , Goheen Jacob , Kauffman Matthew
Published: January 2018

Over the past two decades, populations of Shiras moose (Alces alces shirasi) in western Wyoming have declined. Recent work on the Jackson herd in northwest Wyoming suggests that the 1988 Yellowstone fires and regional drought contributed to a considerable decline in calf recruitment, which coincided with the recovery of grizzly bears (Ursus arctos horribilis) and gray wolves (Canis lupus occidentalis) to the Greater Yellowstone Ecosystem (GYE). Predation is also presumed to have contributed to declines in calf recruitment, but the relative influence of these predators has yet to be evaluated. We analyzed a time series of vital rates to identify the spatial extent and intensity at which predator density, habitat condition, and interacting abiotic factors limit population growth. We focused on neonate and winter calf survival because calves are the most vulnerable age class and because calf recruitment been shown to be one of the most important vital rates influencing population dynamics in large herbivores. Variables affecting calf survival were calculated at the seasonal home range scale from 100 individuals in the Jackson herd, and 90 individuals in an adjacent herd directly to the south, where moose are exposed to markedly lower predator density. We detected negative effects of grizzly bear density and habitat condition on neonate survival. Wolf density negatively influenced winter calf survival, but the effect was weak. Our spatial analysis of individual fitness in these two herds suggests that Shiras moose in the GYE have struggled to cope simultaneously with the effects of sub-optimal habitat conditions and predator density, highlighting the need to prioritize efforts to conserve Shiras moose as climate change continues to progress.
Morphological evidence for introgressive hybridization between Feirana quadranus and Feirana taihangnica in Qinling Mountains, China
Authors: Song Yang , Sui Xin , Bian Yuhong , Zhang Junfang , Zheng Junqiang , Li Pipeng
Published: January 2018

Background. Feirana quadranus and Feirana taihangnica, two species of frogs inhabiting in waterbodies in the Qinling Mountains, China, are believed to be sister species that diverged 4.6 million years ago. In their sympatric area, morphological variations found between the two species imply that the two species had inter-bred. Additionally, F. taihangnica’s polyandrous breeding behavior, without amplexus, would not hinder the potential hybridization. Methods. To verify the hybridization, 117 specimens of F. quadranus and F. taihangnica were collected from eight sampling sites in their sympatric area, and 110 of the specimens were classified morphologically into VV, vw&wv, and ww, representing the putative parental and suspected hybrid types. Their maternal bloodlines were identified using a phylogenetic tree based on a region of the mitochondrial 16S rRNA gene. In total, 34 morphometric indices were selected to analyze the morphological variation between 16S-types or among morphotypes. A principal component analysis (PCA) and linear discriminant analysis (LDA) were conducted on total or partial indices for females, males, and total specimens, as well as simulated populations with falsified morphotypes. The most important indices for differentiation among morphotypes were revealed with the assistance of heat-maps. Results. In the mitochondrial DNA tree, most of the VV were in the same clade as the reference F. quadranus, labeled as Q, while most of the ww and vw&wv were grouped with the reference F. taihangnica, labeled as T. According to the PCA, there was a clear differentiation between VV and ww, while vw&wv specimens were in the middle area close to ww. According to the LDA, VV, vw&wv, and ww were clustered into three separate groups. An ambiguous differentiation between Q and T was shown both in mtDNA tree and in multivariate analyses. Seven of the specimens with conflicting classifications blurred the morphological boundary between Q and T. In both the PCA and LDA, indices that were based on the extent of bumps and skin coloration discriminated VV, vw&wv, and ww better than ratio indices that were derived from measurements. Discussion. The distribution of VV, vw&wv, and ww in multivariate spaces, especially vw&wv being scattered between VV and ww, demonstrated an introgressive hybridization pattern. The extents of bumps in the shape of an inverted "V" between the shoulder blades, spot pattern on the back, and large bumps above the anal region were the most important characteristics for differentiating between three morphotypes or between F. quadranus and F. taihangnica.
The modulatory effect of Moringa oleifera leaf extract on endogenous antioxidant systems and inflammatory markers in acetaminophen-induced nephrotoxic mice model
Authors: Karthivashan Govindarajan , Kura Aminu Umar , Arulselvan Palanisamy , Md. Isa Norhaszalina , Fakurazi Sharida
Published: January 2018

N-Acetyl-p-Aminophenol (APAP), aka acetaminophen, is the most commonly used over-the counter analgesic and antipyretic medication. However, its overdose leads to both liver and kidney damage. APAP-induced toxicity is considered as one of the primary causes of acute liver failure; numerous scientific reports have focused majorly on APAP hepatotoxicity. Alternatively, not many works approach APAP nephrotoxicity focusing on both its mechanisms of action and therapeutic exploration. Moringa oleifera (MO) is pervasive in nature and is reported to possess surplus amount of nutrients, and is enriched with several bioactive candidates including trace elements that act as curatives for various clinical conditions. In this study, we evaluated the nephro-protective potential of MO leaf extract against APAP nephrotoxicity in male Balb/c mice. A single-dose acute oral toxicity design was implemented in this study. Group 2, 3, 4 and 5 received a toxic dose of APAP (400 mg/kg of bw, i.p) and after an hour, these groups were administered with saline (10 mL/kg), silymarin - positive control (100 mg/kg of bw, i.p), MO leaf extract (100 mg/kg of bw, i.p), and MO leaf extract (200 mg/kg bw, i.p) respectively. Group 1 was administered saline (10 mL/kg) during both the sessions. APAP-treated mice exhibited a significant elevation of serum creatinine, blood urea nitrogen, sodium, potassium and chloride levels. A remarkable depletion of antioxidant enzymes such as SOD, CAT and GSH-Px with elevated MDA levels has been observed in APAP treated kidney tissues. They also exhibited a significant raise in pro-inflammatory cytokines (TNF-α, IL-1β, IL-6) and decreased anti-inflammatory (IL-10) cytokine level in the kidney tissues. Disorganized glomerulus and dilated tubules with inflammatory cell infiltration was clearly observed in the histology of APAP treated mice kidneys. All these pathological changes were reversed in a dose dependent manner after MO leaf extract treatment. Therefore, MO leaf extract has demonstrated some therapeutic effectiveness against APAP-induced nephrotoxicity through enhancement of endogenous antioxidant system and modulatory effect on specific inflammatory cytokines in kidney tissues.
The Durand Adaptive Psychopathic Traits Questionnaire: development and validation
Authors: Durand Guillaume
Published: January 2018

While the term ‘‘psychopathy’’ is embedded with negativity, evidence points to the existence of another form of psychopathy, which involves adaptive traits such as stress and anxiety immunity, remarkable social skills, noteworthy leadership ability, and an absence of fear. The newly developed Durand Adaptive Psychopathic Traits Questionnaire (DAPTQ) aims to assess adaptive traits known to correlate with the psychopathic personality. Validation of the questionnaire among 765 individuals from the community gave support to a 10-factor solution: Leadership, Logical Thinking, Composure, Creativity, Fearlessness, Money Smart, Focus, Extroversion, Consequentialism, and Management. The DAPTQ and its 10 subscales demonstrated good internal consistency reliability in a community sample (0.64 - 0.88). Good convergent and divergent validity was confirmed by administering the DAPTQ alongside established measures of the psychopathic personality. Subscales validation against well-established personality assessments further confirms the DAPTQ’s strength. These findings support the potential of the DAPTQ as an instrument for measuring psychopathy-associated adaptive traits. Limitations of the present study and potential directions for future research are also discussed. Further studies are needed to validate the DAPTQ and its subscales against a wider range of personality traits and behaviors.
Silviculture approaches to restoring a predator-prey system: examples from the LiDea project in Boreal Alberta
Authors: Cody Michael , McNay Scott , Sutherland Glenn D. , Sherman Geoff
Published: January 2018

The issue of Woodland caribou decline has been identified corporately as a top environmental priority for Cenovus energy Inc. Pursuant to this priority, a habitat centric environmental strategy and performance commitments have been developed. Beginning in 2008, Cenovus began applied investigation into the use of silviculture techniques for accelerated restoration, emphasizing the bog and fen forest site types that are characteristic of Boreal caribou habitat. In a larger scale project called LiDea, restoration treatments were ultimately applied to linear features throughout an area of 370 km 2 within the Cold Lake herd range. As indicated by metrics at the site level, as well as GPS collar re-locations, plant and animal response to restoration treatment are positive from a caribou perspective. Results from the LiDea series of projects have been strong enough to warrant the extension of these forest habitat restoration methods to the landscape scale.
Bacteria surface charge in layers: revealed by wash buffers of different ionic strength
Authors: Ng Wenfa
Published: January 2018

Bacteria surface charge derives its meaning from the cell’s environment; thus, there is no specific surface charge. Determining the surface charge of bacteria in its native environment requires measuring the proxy variable, zeta potential, using cells obtained from field studies. However, lack of adequate cell mass and concerns over measurement of a mixed species consortia rather than a specific species meant that bacteria surface charge measurement require biomass obtained from pure culture. Often grown in rich medium where myriad proteins and ions nonspecifically adsorbed onto the cell envelope or peptidoglycan layer, standard procedures for preparing the cell mass incorporate repeated steps of washing and centrifugation with various wash buffers, the efficacies of which are poorly understood. This report describes a systematic study on how wash buffers of different composition and salinity affect the efficiency of removing nonspecifically adsorbed biomolecules and ions from Escherichia coli DH5α (ATCC 53868) cultured aerobically (shake flask, 37 oC and 230 rpm) in LB Lennox medium. Using zeta potential-pH profiles over pH 1 to 12 as readout, proxy measurement of wash buffers’ efficacies showed that efficiency of removing nonspecifically adsorbed ions and metabolites positively correlates with wash buffer ionic strength. More importantly, 0.15M ionic strength (i.e., 9 g/L NaCl and phosphate buffer saline) seems to be the minimum below which there appeared to be little removal of nonspecifically adsorbed biomolecules. On the other hand, high ionic strength of 0.6M (e.g., 0.1M sodium citrate) significantly changed the point of zero charge (pHzpc), a reference marker for removing ions intrinsic to the cell envelope; thus, indicating significant cell surface damage. Collectively, results obtained inform wash buffer choice with regards to preserving cell envelope integrity. But, is there a true cell surface charge? Yes, but how do we define it in number of “layers” of adsorbed biomolecules? Philosophically, cells in culture broth are coated with layers of metabolites, proteins and ions; hence, desire to reveal the true surface charge is essentially a decoating process, where wash buffers of increasing ionic strength remove each layer via charge screening. However, where is the endpoint? This research offers a different perspective and answer: i.e., ionic strength of wash buffers chosen should be similar to that of the environment the research is seeking to address. Imagine a single bacterium suspended in LB medium, where there is constant adsorption and desorption of biomolecules as the cell grows: what is its relevant surface charge? It is the one where the loosely associated ions and metabolites is removed. Thus, deionized water wash provides a good estimate of the bacteria surface charge as grown in specific medium.
Automation in clinical data collection in obstetrics - Enabling pooled IPD studies for fetal heart rate and activity monitoring
Authors: Weber Christopher , Saalfeld Maximilian , Harboeck Christian , Lobmaier Silvia M , Weyrich Joy , Grundmann Holger J , Daumer Martin
Published: January 2018

Cardiotocography is currently the standard surveillance tool during labour. For this reason, there are large cardiotography datasets available. Several studies gathering additional information of computerized CTG data aiming to improve surveillance during delivery and birth outcome are currently performed. Manual data collection and analysis takes a lot of human resources, is error-prone and study parameters can hardly be adjusted later on. Therefore, a software based approach was chosen to minimize the effort of preparation. The software called “CTG and patient information matcher” (CAPIM) collects relevant CTG signals for a specified patient dataset and under recognition of several parameters. CAPIM was tested with the patient database of Frauenklinik und Poliklinik of Technische Universität München (Munich, Germany). Further hospitals will follow. The cases received from CAPIM will be used to do feasibility studies for two innovative signal processing techniques as „phase-rectified signal averaging“ method on fe­tal heart rate raw data and „deceleration area“ me­thod to improve prediction of birth outcome.
Metagenomics accelerates species discovery and unravel great biodiversity of benthic invertebrates in marine sediments in Campos basin, Brazil
Authors: Schettini Milena Marcela D P , Cardenas Raony G C C L , Detoni Marcella A A , Rebelo Mauro F
Published: January 2018

Sediment fauna characterization and monitoring are mandatory requirements for obtaining oil and gas (O&G) environmental licensing for exploration and production (E&P) activities. Currently, for environmental characterizations and monitoring, biodiversity is assessed through morphological taxonomy, a time-consuming process. Taxonomists are constantly failing to meet the demands for biodiversity assessment required in monitoring programs. Thus, we combined three different phylogenetic markers(rDNA 18S, rDNA 28S and COI), HTS and Bioinformatics to identify benthic invertebrate organisms from sediment samples collected in five stations in the Campos Basin in southeast Brazil, an important oil extraction area and one of the best-studied marine biota in Brazil. Our results obtained with metagenomics were compared to morphology data provided by the Habitats Project whereas the database Global Biodiversity Information Facility ( www.gbif.org ) was used for organism localization. We obtained around 4.83 μg of DNA from 15 samples. A total of 3.3 million sequences were clustered in Operational Taxonomic Units and more than 1.6 million sequences (about 50% of all reads) were assigned to 957 prokaryotes and 577 eukaryotes. BLAST identified 23 phyla, 60 classes, 62 orders, 70 families, 67 genus and 46 species of eukaryotes. Our metagenomic analysis identified phyla that are traditionally found in samples of marine benthos, such as Annelida, Arthropoda, Mollusca and Chordata, as well as more rarely found phyla such as Bryozoa, Cnidaria, Echinodermata, Nematoda, Nemertea, Platyhelminthes, Porifera and Priapulida; and even more rare phyla like Entoprocta and Gastrotricha. The low availability of genetic markers for Brazilian species in Genebank impaired our ability to compare our findings with those obtained morphologically for which no sequences were found in Genebank. Our study shows that metagenomics can be applied for environmental characterization and monitoring programs and, with the possibility of automating the method, may reduce from years to few months the time currently required for species identification and biodiversity determination, which will certainly accelerate species discovery.
Mapping ecologically important virus-host interactions in geographically diverse solar salterns with metagenomics
Authors: Moller Abraham G , Liang Chun
Published: January 2018

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns and related them to carbon cycling. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested most dihydroxyacetone kinase genes affiliate to Halorubrum and Haloquadratum while most glycerol-3-phosphate dehydrogenase genes affiliate to Salinibacter. We identified CRISPR spacers in the metagenomes with two different methods and found more spacers in the Halobacteriaceae-dominated IC21 and C34 salterns compared with the Haloquadratum-dominated SS19, SS33, and SS37 salterns, suggesting low CRISPR diversity and possibly a high rate of CRISPR loss in the Haloquadratum-dominated salterns. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments linked viruses to Haloquadratum walsbyi, there were clusters of interactions with less abundant Haloarcula and Haloferax. Further examination of the dimer and codon usage differences between paired viruses and their hosts and detection of cas genes in the salterns confirmed both the plausibility of virus-host interactions and the possibility of CRISPR activity. Taken together, our studies suggest CRISPR loss in archaeal hosts controls the level of virus proliferation and the nutrient turnover viruses induce in these environments.
The Ecology of Stress: linking life-history traits with physiological control mechanisms in free-living guanacos
Authors: Ovejero Aguilar Ramiro J.A. , Jahn Graciela A , Soto-Gamboa Mauricio , Novaro Andrés , Carmanchahi Pablo
Published: January 2018

Background-Providing the context for the evolution of life-history traits, habitat features constrain successful ecological and physiological strategies. In vertebrates, a key response to life's challenges is the activation of the Stress (HPA) and Gonadal (HPG) axes. Much of the interest in stress ecology is motivated by the desire to understand the physiological mechanisms in which the environment affects fitness. As reported in the literature, several intrinsic and extrinsic factors affect variability in hormone levels. In both social and non-social animals, the frequency and type of interaction with conspecifics, as well as the status in social species, can affect HPA axis activity, resulting in changes in the reproductive success of animals. We predicted that a social environment can affect both guanaco axes by increasing the secretion of testosterone (T) and Glucocorticoid (GCs) in response to individual social interactions and the energetic demands of breeding. Assuming that prolonged elevated levels of GCs over time can be harmful to individuals, it is predicted that the HPA axis suppresses the HPG axis and causes T levels to decrease, as GCs increase.

Methods-All of the data for individuals were collected by non-invasive methods (fecal samples) to address hormonal activities. This is a novel approach in physiological ecology because feces are easily obtained through non-invasive sampling in animal populations.

Results- As expected, there was a marked adrenal (p-value= .344e-12) and gonadal (p-value= 0.002656) response due to seasonal variation in Lama guanicoe. No significant differences were found in fecal GCs metabolites between males/females*season for the entire study period (p-value= 0.2839). Despite the seasonal activity variation in the hormonal profiles, our results show a positive correlation (p-value= 1.952e-11,COR=0.50) between the adrenal and gonadal system. The marked endocrine (r2 = 0.806) and gonad (r2 = 0.7231) response due to seasonal variation in male guanaco individuals highlights the individual’s energetic demands according to life-history strategies. This is a remarkable result because no inhibition was found between the axes as theory suggests. Finally, the dataset was used to build a reactive scope model for guanacos.

Discussion-Guanacos cope with the trade-off between sociability and reproductive benefits and costs, by regulating their GCs and T levels on a seasonal basis, suggesting an adaptive role of both axes to different habitat pressures. The results presented here highlight the functional role of stress and gonad axes on a critical phase of a male mammal's life—the mating period—when all of the resources are at the disposal of the male and must be used to maximize the chances for reproductive success.
Walking on the Moon
Authors: Schlacht Irene Lia , Rittweger Jörn , Foing Bernard H. , Daumer Martin , Masali Melchiorre
Published: January 2018

How high do we jump on the Moon? Should we build architecture with steps or should we support climbing? The hypogravity will lead to vestibular system malfunction, loss of muscular mass, and stiffness of the legs, negatively affecting a person’s balance: Yes, we can climb, but we can also easily lose our balance and trip up.

To avoid all of this, we need to better understand gait and balance on the Moon. This research will investigate a methodology that focuses on the collection of basic anthropometrical and postural data needed to develop interfaces for the Moon and Mars gravity environments and habitat.
Construction and use of a Cupriavidus necator H16 soluble hydrogenase promoter (P SH ) fusion to gfp (green fluorescent protein)
Authors: Jugder Bat-Erdene , Welch Jeffrey , Braidy Nady , Marquis Christopher P
Published: January 2018

Hydrogenases are metalloenzymes that reversibly catalyse the oxidation or production of molecular hydrogen (H2). Amongst a number of promising candidates for application in the oxidation of H2 is a soluble [Ni-Fe] uptake hydrogenase (SH) produced by Cupriavidus necator H16. In the present study, molecular characterisation of the SH operon, responsible for functional SH synthesis, was investigated by developing a green fluorescent protein (GFP) reporter system to characterise PSH promoter activity using several gene cloning approaches. A PSH promoter-gfp fusion was successfully constructed and inducible GFP expression driven by the PSH promoter under de-repressing conditions in heterotrophic growth media was demonstrated in the recombinant C. necator H16 cells. Here we report the first successful fluorescent reporter system to study PSH promoter activity in C. necator H16. The fusion construct allowed for the design of a simple screening assay to evaluate PSH activity. Furthermore, the constructed reporter system can serve as a model to develop a rapid fluorescent based reporter for subsequent small-scale process optimisation experiments for SH expression.
Assessment of spectral properties of Apollo 12 landing site
Authors: Chemin Yann H , Crawford Ian A , Grindrod Peter , Alexander Louise
Published: January 2018

The geology and mineralogy of the Apollo 12 landing site has been the subject of recent studies that this research attempts to complement from a remote sensing point of view using the Moon Mineralogy Mapper (M3) sensor data, onboard the Chandrayaan-1 lunar orbiter. It is a higher spatial-spectral resolution sensor than the Clementine UVVis sensor and gives the opportunity to study the lunar surface with a comparatively more detailed spectral resolution.

The M3 signatures are showing a monotonic featureless increment, with very low reflectance, suggesting a mature regolith. The regolith maturity is splitting the landing site in a younger Northwest and older Southeast. The mineral identification using the lunar sample spectra from within the Relab database found some similarity to a basaltic rock/glass mix. The spectrum features of clinopyroxene have been found in the Copernican rays and at the landing site. Lateral mixing increases FeO content away from the central part of the ray. The presence of clinopyroxene in the pigeonite basalt in the stratigraphy of the landing site brings forth some complexity in differentiating the Copernican ray’s clinopyroxene from the local source, as the spectra are twins but for their vertical shift in reflectance, reducing away from the central part of the ray.

Spatial variations in mineralogy were not found mostly because of the pixel size compared to the landing site area. The contribution to stratigraphy is limited to the topmost layer which is a clinopyroxene-dominated basalt belonging to the most remote tip of a Copernican ray and its resulting local regolith mix.
Observation analysis tool for the FREEWAT GIS environment for water resources management
Authors: Cannata Massimiliano , Neumann Jakob , Cardoso Mirko , Rossetto Rudy , Foglia Laura
Published: January 2018

The Observation Analysis Tool was developed for the FREEWAT GIS environment in order to integrate the data offered by state-of-the-art monitoring systems directly into numerical simulations for water resources management. Time-series are an important aspect of environmental modelling, and are becoming more available through the requirements of the water framework directive as well as more important with the advancement of numerical simulation techniques and increased model complexity. OAT enables time-series visualisation, pre-processing of data for model development, and post-processing of model results. The tool contains an expandable Python library of processes, incorporating a participatory approach to development. As well as processing MODFLOW results, OAT can act as a pre-processor for calibration observations, and will be expanded to incorporate its processing capabilities directly into the calibration process.
Observation analysis tool for the FREEWAT GIS environment for water resources management
Authors: Cannata Massimiliano , Neumann Jakob , Cardoso Mirko , Rossetto Rudy , Foglia Laura
Published: January 2018

Time-series are an important aspect of environmental modelling, and are becoming more available through the requirements of the water framework directive as well as more important with the advancement of numerical simulation techniques and increased model complexity. For this reason, within the H2020 FREEWAT project, which aims at facilitating the adoption of modeling for water resource management, the integration of a tool for time-series analysis and processing has been foreseen. As a result the Observation Analysis Tool was developed to enable time-series visualisation, pre-processing of data for model development, and post-processing of model results. Observation Analysis Tool can act as a pre-processor for calibration observations, and will be expanded to incorporate its processing capabilities directly into the calibration process. The tool consists in an expandable Python library and in an interface integrated in the QGIS FREEWAT plug-in which include a large number of modelling capabilities, hydro-chemical data management tools and calibration capacity. The tool has been extensively used and tested in different european institutions, to collect a number of indications to drive the future development.
Using Python® language for the validation of the CCI soil moisture products via SM2RAIN
Authors: Ciabatta Luca , Massari Christian , Brocca Luca , Reimer Christoph , Hann Sebastian , Paulik Christoph , Dorigo Wouter , Wagner Wolfgang
Published: January 2018

Remote sensing techniques provide a new way to obtain hydrological variables (i.e. rainfall and soil moisture), mainly in poorly instrumented areas that are fundamental for natural hazard assessment and mitigation. The ever increasing availability of satellite derived products characterized by high temporal and spatial coverage requires the development of techniques and instruments for big data volume managing. Moreover, the use of open source systems is highly encouraged in order to increase their use by the scientific community. In this study, the application of the SM2RAIN algorithm to the CCI soil moisture product is proposed as a case study. A number of Python® classes and methods have been developed for this purpose, with the aim of creating an open-source web validation tool for SM dataset, within the Earth Observation Data Centre for Water Resources Monitoring (EODC).
LISAM: an open source GIS-based model for liveability spatial assessment
Authors: Antognelli Sara , Vizzari Marco
Published: January 2018

Ecosystem Services (ES) and Urban Services (US) influence place liveability in a comparable manner so that assessing landscape liveability considering both types of services can result effective for landscape planning and policy-making purposes. Considering that liveability is strongly dependent also on landscape perception by local population, stakeholder involvement results essential for a more coherent liveability assessment. In this study, a Spatial Multicriteria Decision Aiding (S-MCDA) approach guided the development of a LIveability Spatial Assessment Model (LISAM). Using a combination of GIS techniques (euclidean distance, kernel density estimation, network analysis, viewshed analysis), implemented in open-source geo-spatial software (QGIS, PostGIS and PostgreSQL), consistent and comparable ES and US spatial indices were calculated in a study area located in central Italy. These indices, according to the Analytical Hierarchy Process (AHP), were integrated with their percentage weights on liveability deriving from stakeholders interviews. Then, to investigate the liveability levels of local population, main statistics of liveability values were calculated per census section. Results include overall liveability indices at a local scale, and key statistics of liveability related to resident population. The work highlights the effectiveness of LISAM to assess local liveability and to deliver important information for policy-makers. Results show a strong, nonlinear correlation between local liveability and population density. Both the tendency to attribute higher importance to US than ES, and to the underestimation of ES quantity has emerged. The future integration in LISAM of ecosystem and urban disservices would be relevant to consider those landscape factors that reduce the overall level of place liveability.
Contribution of prosthetic treatment considerations for dental extractions of permanent teeth
Authors: Fernández-Barrera Miguel Ángel , Medina-Solís Carlo Eduardo , Casanova-Rosado Juan Fernando , Mendoza-Rodríguez Martha , Escoffié-Ramírez Mauricio , Casanova-Rosado Alejandro José , Navarrete-Hernández José de Jesús , Maupomé Gerardo
Published: January 2018

Background: Tooth loss is an easily identifiable outcome that summarizes a complex suite of factors in an individual’s history of dental disease and its treatment by dental services over a lifetime. Assessment of overall tooth loss data is essential for evaluating epidemiologically the adequacy of dental care provided at a systems level, as well as for placing in context tooth loss for non-disease causes. For example, when derived from prosthetic treatment planning; the latter may unfortunately lead to some teeth being extracted (pulled) for the sake of better comprehensive clinical results. The objective of the present manuscript was to identify the contribution to overall tooth loss, by extraction of permanent teeth because of prosthetic treatment reasons. Material and Methods: A cross-sectional study included sex, age, total number of extractions performed by subject, sextant (anterior vs. posterior), group of teeth (incisors, canines, premolars and molars), upper or lower arch, and the main reason underlying extraction (extraction for any reason vs. prosthetic treatment), in patients 18 years of age and older seeking care a dental school clinic in Mexico. A multivariate logistic regression model was generated. Results: A total of 749 teeth were extracted in 331 patients; 161 teeth (21.5% of total) were extracted for explicit prosthetic treatment indications. As age increased, the likelihood of having an extraction for prosthetic reasons increased 3% (OR=1.03, p<0.001). Women (OR=1.57, p<0.05) were more likely to be in this situation, and molars (OR=2.70, p<0.001) were most at risk. As the total number of extractions increased, the risk of having an extraction for prosthetic reasons decreased (OR=0.94, p<0.05). Conclusions: A significant amount (21.5%) of the extractions of permanent teeth were performed for prosthetic reasons in this dental school clinical environment; age, sex, type of tooth, and the total number of extractions moderated such pattern.
Structural models of the human iron exporter ferroportin in the inward- and outward- open states
Authors: Tortosa Valentina , Polticelli Fabio
Published: January 2018

Motivation

Ferroportin (Fpn) is a membrane protein belonging to the Major Facilitator Superfamily of transporters. It is the only vertebrate iron exporter known so far. Several Fpn mutations lead to the so-called ‘ferroportin disease’ or type 4 haemochromatosis, characterized by two distinct iron accumulation phenotypes depending on whether the mutations affects the protein’s activity or its degradation pathway (1). Despite a general agreement of the scientific community on a 12 transmembrane helices topology, no experimental data are available on human Fpn (HsFpn) three-dimensional structure. Thus, important features of HsFpn remain to be clarified. Recently, the crystal structures of a HsFpn homologue from the predatory Gram-negative bacterium Bdellovibrio bacteriovorus (BbFPN), in both the outward- (Figure 1 A) and inward-open states (Figure 1 B), has been reported (2). The residues essential for iron binding and transport in HsFpn are conserved in BbFPN (3). The conservation of these functionally relevant residues prompted us to exploit the two BbFPN structures to construct reliable models of HsFPN.

Methods

The structural models of HsFpn in were built in both the outward- and inward-open states through the ab initio/threading strategy implemented in the I-TASSER server (4). The overall quality of the models generated has been evaluated using PROCHECK (5) and the model quality parameters provided in the I-TASSER output, such as the C-score. Putative iron binding sites have been detected using LIBRA (6).

Results

The models display the typical fold of MFS proteins with 12 TMs spanning the membrane and the N- and C-termini located on the intracellular side (Figure 1). LIBRA analysis of the models has led to the identification of potential iron binding sites in the inward-open state allowing to propose an iron traslocation mechanism. Further, the outward-open model uncovers details of the interaction site of the peptide hormone hepcidin, a regulator of HsFpn function. Fin ally, the HsFPN models provide a mechanistic interpretation for the disease-related mutations that cause hereditary hemochromatosis.
The effect of pleasant touch on nose skin temperature, heart rate and heart rate variability: preliminary results in a male laboratory rhesus monkey
Authors: Grandi Laura Clara , Heinzl Eugenio L
Published: January 2018

Human and animal studies emphasize the importance of affiliative touch among conspecifics, both from the behavioral and physiological perspectives. Among non-human primates, allogrooming, and in particular the pleasant sweeping motion occurring during it, could be considered analogous to human social affiliative touch. Despite the evidences of the effects of affiliative touch in terms of heart rate (HR) and heart rate variability (HRV), both in humans and non-human primates, the physiological consequences have never been investigated in respect to the body temperature changes through infrared thermography (IRT). The aim of the present study was to investigate for the first time in a male rhesus monkey, the physiological effects of sweeping the back at different speeds in terms of nose skin temperature changes, and to explore the possible relationship with the HR and HRV. The preliminary results underline that sweeping the back at a speed of 5–10 cm/sec determined an increment of the nose skin temperature and HRV, together with a decrement of the HR. These preliminary data represent the first evidence of the body temperature changes manifesting during affiliative touch at the speed of 5–10 cm/sec in non-human primates and the existence of a possible relationship among the body temperature, HR and HRV. This study represents an important starting point in order to investigate the affiliative pleasant social touch by means of non-invasive techniques (e.g. the IRT), and to deeply examine the correlation between body temperature and cardiac changes, both in humans and non-human primates.