bluuebunny/crossref_metadata_2025 huggingface dataset:
Constraints on vertebrate athleticism: The temperature dependence of red blood cell volume
Authors: Gillooly James JF , Zenil-Ferguson Rosana
Published: January 2018

The ability to perform at high levels of aerobic activity (i.e. athletic ability) increases with temperature among vertebrates. These differences in species’ activity levels, from highly active to sedentary, are reflected in their ecology and behavior. Yet, the changes in the cardiovascular system that allow for greater oxygen supply rates at higher temperatures, and thus greater activity levels, remain unclear. Here we show that vertebrates provide more oxygen to tissues at higher temperatures in part by increasing the total volume of red blood cells in the body. Across 60 species of vertebrates (fishes,amphibians, reptiles, birds and mammals), whole-body red blood cell volume increases exponentially with temperature after controlling for effects of body size and taxonomy. These changes are accompanied by increases in relative heart mass, an indicator of athletic ability. The results help explain how temperature-dependent changes in cardiovascular design allow species to overcome the constraints of passive diffusion on oxygen supply.
The challenges to inferring the regulators of biodiversity in deep time
Authors: Ezard Thomas H , Quental Tiago B , Benton Michael J
Published: January 2018

Attempts to infer the ecological drivers of macroevolution have long drawn inspiration from work on extant systems, but long-term evolutionary and geological changes complicate the simple extrapolation of such theory into a deep-time setting. Recent efforts to incorporate a more informed ecology into macroevolution have moved beyond the descriptive to attempts that seek to isolate the generating mechanisms of dynamic signatures to produce testable hypotheses of how species and larger groups usurp or co-exist alongside one another over vast spans of time. The papers of this Theme Issue exemplify this progress, providing a series of case studies of how novel modelling approaches are helping infer the regulators of biodiversity in deep time. In this Introduction, we aim to discuss the challenges associated with this area. We break our Introduction into four main areas. First, we discuss how our choices of biological units for study have implications for the conclusions subsequently drawn. Second, we emphasize the need to embrace the interdependence of biotic and abiotic change, because no living organism ignores its environment. Third, in the light of parts 1 and 2, we discuss the set of dynamic signatures that we might expect to observe in the fossil record. Finally, we ask whether these signatures are the most ecologically informative foci for research efforts aimed at inferring the regulators of biodiversity in deep time. The papers in this Theme Issue contribute in each of these areas.
What is the effect of ammonium sulfate on the heart rate of Daphnia magnia?
Authors: Ng Qin Xiang
Published: January 2018

Ammonium sulfate [(NH4)2SO4] is one of the most widely used nitrogen-based fertilizer in agriculture, and has been produced for over 150 years. However, limited research has been done to investigate the eco-toxic effects of ammonium sulfate, commonly present in surface runoff. This study therefore aimed to investigate the effects of varying ammonium sulfate concentrations on the normal physiology of Daphnia magna through a modified acute toxicity testing. Concentrations of ammonium sulfate solutions at 0M, 0.05M, 0.10M, 0.15M, 0.20M, 0.25M, and 0.30M were prepared and tested on 10 D. magna for each concentration of ammonium sulfate solution. The bioassay test was done by observing the effects of different concentrations of ammonium sulfate solution on the heart rate of D. magna. The percentage increase in average heart rate of D. magna after exposure to the respective concentrations of ammonium sulfate solution were calculated and a relationship between varying concentrations of ammonium sulfate concentration and the heart rate of D. magna was illustrated by plotting a graph using the respective data points obtained. Results indicated that increasing concentrations of ammonium sulfate solution resulted in an increase in the heart rate of D. magna per minute, up till 0.20M concentration. Increasing concentrations of ammonium sulfate solution beyond 0.20M resulted in a decrease in the heart rate of D. magna per minute. It was also discovered that specifically, the ammonium ions present when ammonium sulfate dissociates in water, is responsibility for toxicity, and not the sulfate ions. It is reasonable to conclude that ammonium sulfate poses significant eco-toxic effects as D. magna is a common primary consumer in many freshwater aquatic ecosystems, any change in its population quality or quantity can cause irreparable effects to the populations of other aquatic organisms.
PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
Authors: Stephens Timothy G , Bhattacharya Debashish , Ragan Mark A , Chan Cheong Xin
Published: January 2018

A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, such as robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for sorting phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa, with customisable options to assess clades within the context of the whole tree. PhySortR is a command-line tool that is freely available, highly scalable, and easily automatable.
Poppr: an R package for genetic analysis of populations with clonal or partially clonal reproduction
Authors: Kamvar Zhian N , Tabima Javier F , Grünwald Niklaus J
Published: January 2018

Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal or partially clonal. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, and/or mixed populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.
Bayesian multinomial ordered categorical response model for the analysis of length of hospital stay
Authors: Kazembe Lawrence N
Published: January 2018

Length of hospital stay (LOS) is of primary importance in health services research because it is directly related to health care management and cost of health care. In some epidemiological settings the actual length of stay is not directly observed but it is known to have happened in a particular interval or for simple epidemiological interpretation time is categorized into ordered categorical responses. In this paper, we focus our attention on cumulative regression models for ordinal responses to analyze length of hospital stay for children admitted to a paediatric ward for malaria. Such models exploit the ordered scale of the outcomes. We approach our analysis using a Bayesian probit model. Our model incorporated random effects for hospital specific heterogeneity, while simultaneously investigating nonlinear effects in covariates within the general framework of semi-parametric regression models. Findings indicate children who died had relatively shorter LOS, which suggest worse prognosis at admission. Calendar time effects indicated changing seasonal effects with high peaks in wet season and low peak in dry season, largely explained by malaria transmission patterns. Age showed deviation from linearity, and early discharge was associated with much older children than infants.
Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results
Authors: Weber Jessica A. , Aldana Rafael , Gallagher Brendan D. , Edwards Jeremy S.
Published: January 2018

Sentieon DNAseq Software is a suite of tools for running DNA sequencing secondary analyses. The Sentieon DNAseq Software produces identical results to the Genome Analysis Toolkit (GATK) Best Practice Workflow using HaplotypeCaller, with more than a 20-fold increase in processing speed on the same hardware.

This paper presents a benchmark analysis of the GATK and Sentieon DNAseq software packages using publically available datasets from the 1000 genomes database, and includes speed comparisons and output concordance analyses.
Effects of range, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds
Authors: Ndihokubwayo Noel , Nguyen Viet - Thang , Cheng Dandan
Published: January 2018

Invasive plants colonize new environments, become pests and cause biodiversity loss, economic loss and health damage. Senecio vulgaris (Common groundsel, Asteraceae), a cosmopolitan weed wildly distributes in the temperate area, is reported with large populations in the north–eastern and south–western parts, but not in southern, central, northern or north-western part of China. We studied the germination behavior of S. vulgaris to explain the distribution and the biological invasion of this species in China. We used seeds originated from 12 populations in native and invasive range (six populations in each range) to conduct germination experiments in a climate chamber and ambient condition. When incubated in climate chamber (15°C) seeds from the majority of population showed >90% germination percentage (GP) and the GP was equal for both ranges. The mean germination time (MGT) was significant different among the populations. Under ambient conditions, significant effect of range, storage conditions (stored at 4 or 27°C) and seasons (in summer or autumn) were observed on the GP while the MGT was only affected by the season. In autumn, the GP was higher (38.6%) and the MGT was slightly longer than that in summer (4.5%). In autumn, seeds stored at 4°C showed higher GP than those stored at 27°C, and seeds from invasive population revealed higher GP than those from native populations. High GP and short time for seed emergence demonstrated that in S. vulgaris seeds checked in this study were from Senecio vulgaris ssp vulgaris, the non – dormancy subspecies. The results also implied that the high temperature exceeds the threshold for S. vulgaris to germinate and storage at high temperature cause S. vulgaris seeds lost the viability greatly. This demonstrates the reason why in Wuhan S.vulgaris can’t establish natural and viable populations, and also explain why S.vulgaris is scattered in China.
A comparison of clustering methods for biogeography with fossil datasets
Authors: Vavrek Matthew J
Published: January 2018

Cluster analysis is one of the most commonly used methods in palaeoecological studies, particularly in studies investigating biogeographic patterns. Although a number of different clustering methods are widely used, the approach and underlying assumptions of many of these methods are quite different. For example, methods may be hierarchical or non-hierarchical in their approaches, and may use Euclidean distance or non-Euclidean indices to cluster the data. In order to assess the effectiveness of the different clustering methods as compared to one another, a simulation was designed that could assess each method over a range of both cluster distinctiveness and sampling intensity. Additionally, a non-hierarchical, non-Euclidean, iterative clustering method implemented in the R Statistical Language is described. This method, Non-Euclidean Relational Clustering (NERC), creates distinct clusters by dividing the data set in order to maximize the average similarity within each cluster, identifying clusters in which each data point is on average more similar to those within its own group than to those in any other group. While all the methods performed well with clearly differentiated and well-sampled datasets, when data are less than ideal the linkage methods perform poorly compared to non-Euclidean based k-means and the NERC method. Based on this analysis, Unweighted Pair Group Method with Arithmetic Mean and neighbor joining methods are less reliable with incomplete datasets like those found in palaeobiological analyses, and the k-means and NERC methods should be used in their place.
The effect of weight controllability beliefs on prejudice and self-efficacy
Authors: Thorsteinsson Einar B , Loi Natasha M , Breadsell Dana
Published: January 2018

An experiment was conducted to test for the presence of prejudice towards obesity and whether weight controllability beliefs information reduces this prejudice and impacts on a person’s own healthy eating self-efficacy. The experiment randomly allocated 346 participants (49 males) into one of three conditions: controllable contributors toward obesity condition (e.g., information about personal control about diet and exercise); uncontrollable contributors toward obesity condition (e.g., information about genes, factors in society); and a control condition with no information given. Prejudice was present in 81% of the sample. High prejudice was predicted by low self-efficacy for exercise and weight. Weight controllability beliefs information had no significant effect on prejudice levels or exercise or healthy eating self-efficacy levels. Increasing self-efficacy for exercise and weight my help reduce prejudice towards obese individuals.
Development and validation of a direct real-time PCR assay for Mycobacterium bovis and implementation into the United States national surveillance program
Authors: Dykema Philip E , Stokes Kevin D , Beckwith Nadine R , Mungin James W , Xu Lizhe , Vickers Deborah J , Reising Monica M , Bravo Doris M , Thomsen Bruce V , Robbe-Austerman Suelee
Published: January 2018

Abattoir surveillance for bovine tuberculosis, which consists of identifying and submitting granulomas for histopathology and mycobacterial culture was the primary means for detecting new cases in the United States. Mycobacterial culture is expensive, labor intensive and identifies cases weeks after slaughter, hampering trace back efforts. To address this inefficiency, the United States Department of Agriculture replaced culture with real-time PCR for screening granulomas. The objectives of this paper were to describe the development and validation of this PCR as well as the performance of the assay during the first year of implementation. Using archived culture and histologically positive tissue, the sensitivity was 0.96 (95% CI: 0.89, 0.99) for the Mycobacterium tuberculosis complex primer-probe set and 0.89 (95% CI: 0.80, 0.95) for the Mycobacterium bovis specific primer-probe set. Specificity, estimated during by side by side testing was 0.998 (95% CI: 0.994, 1.000). After implementation, 6124 samples over 54 weeks were tested and all 36 histopathology positive samples were detected including 2 additional cases initially misclassified by histopathology. It appeared that specificity may have declined during post validation testing with 47/6086 signaling positive but not confirmed by either histopathology or culture. While PCR implementation has significantly improved the efficiency of the US slaughter surveillance program, careful attention must be paid to prevent and address cross contamination in the laboratory.
Extending MetAMOS - new methods and new integrations
Authors: Siwiak Marian , Bogdanowicz Albert , Hajduk Agnieszka , Krassowski Michał , Jankowski Paweł , Savenko Mariia , Pyzik Adam AP , Szczęsny Paweł
Published: January 2018

Biodiversity analysis of metagenomic and metatranscriptomic data acquired from next-generation sequencing (NGS) requires following multiple analytic steps, often independent from each other with exception of passing output files of previous step as input for the following. If parameterization of steps following one after another is independent from one another, they may be pipelined. There are three most popular pipelines used for NGS analyses: QIIME, mothur and MetAMOS. In this work we describe our extensions to the latter. One is supplementing MetAMOS’ default modes with taxonomic and metabolic biodiversity using metagenomics and metatranscriptomics data and the other provides a web-based interface to run predefined analyses that is easy to integrate with laboratory information management systems.
Asymmetric connectivity of spawning aggregations of a commercially important marine fish using a multidisciplinary approach
Authors: Munguia-Vega Adrian , Erisman Brad , Jackson Alexis , Marinone Silvio Guido , Moreno-Baez Marcia , Giron Alfredo , Pfister Tad , Aburto-Oropeza Octavio , Torre Jorge
Published: January 2018

Understanding patterns of larval dispersal is key in determining whether no-take marine reserves are self-sustaining, what will be protected inside reserves and where the benefits of reserves will be observed. However, explicitly incorporating dispersal data into designing reserves for fisheries and conservation is still uncommon in many places around the world. We followed a multidisciplinary approach that merged detailed descriptions of fishing zones and spawning time at 17 sites distributed in the Midriff Island region of the Gulf of California (GC) with a biophysical oceanographic model that simulated larval transport at Pelagic Larval Duration (PLD) 14, 21 and 28 days for the most common and targeted predatory reef fish (leopard grouper Mycteroperca rosacea). M. rosacea is endemic to the GC and considered ‘Vulnerable’ according to World Conservation Union. We described metapopulation dynamics using graph theory and employed empirical sequence data from a subset of 10 sites at two mitochondrial genes to verify the model predictions. Our approach made sense of seemingly chaotic patterns of genetic diversity and structure, and provided a mechanistic explanation of the location of fishing zones. Most of the connectivity patterns observed were strictly asymmetric, except for a small region in the Southeast. The best-supported gene flow model confirmed a pulse of larvae from the Baja Peninsula, across the GC and northward up the Sonoran coastline, in agreement with the cyclonic gyre present at the peak of spawning (May). We found support that genetic diversity increased in sink sites that concentrated larvae from many sources at the time of larval flexion (PLD 14 days), while diversity decreased at important gateways identified at PLD 28 days with high betweenness centrality that are key for multigenerational dispersal and population resilience. Heavily targeted fished areas seem to be sustained by high levels of local retention, contribution of larvae from upstream sites and oceanographic patterns that concentrate larval density from all over the region. The general asymmetry in marine connectivity observed highlights that benefits from reserves are biased towards particular directions, that no-take areas need to be located upstream of targeted fishing zones, and that some fishing localities might not directly benefit from avoiding fishing within reserves located adjacent to their communities. We discuss the implications of marine connectivity for the current network of marine protected areas and no-take zones, and identify ways of improving it.
Healthcare professionals' perspectives on HIV disclosure of a parent's and a child's illness in Kenya
Authors: Gachanja Grace , Burkholder Gary J , Ferraro Aimee
Published: January 2018

Background: Many HIV-affected families have both parent(s) and child(ren) infected. HIV disclosure to children continues to be a great global challenge for HIV-positive parents and healthcare professionals (HCPs); parents and HCPs differ on how and when to disclose to children. Methods: Six HCPs including a physician, clinical officer, psychologist, registered nurse, social worker, and a peer educator participated in a larger qualitative phenomenological study conducted to describe the lived experiences of HIV-positive parents and their children during the disclosure process in Kenya. Each HCP underwent an in-depth, semi-structured interview; transcribed data were analyzed using the modified Van Kaam method in NVivo8. Results: Despite HCPs providing parents with regular advice on the benefits of HIV disclosure, fear of stigma, discrimination, and disclosure consequences caused parents to delay disclosure of a parent’s and/or a child’s illness to their HIV-negative and positive children respectively for lengthy periods. While awaiting parental consent for full disclosure, HCPs were forced to provide age-appropriate disease-related information to children. HCPs preference however, was to fully disclose to children in their parents’ presence at the clinic, when children started asking questions and/or displayed maturity and understanding of the illness. Conclusion: Parents are known to prefer disclosing to their children at a time and place of their choosing. Conversely, it appears that HCPs may prefer to disclose to children when they judge the time as being right. For favorable disclosure outcomes, further studies are needed to reconcile the most suitable timing, setting, and person to disclose to HIV-positive and negative children.
On a general definition of the set of native conformations for globular polypeptides
Authors: Jeff-Eke Imadol V
Published: January 2018

Here we question the generality of the conventional definition of a native conformation –as the 3-dimensional conformation of an entire globular polypeptide molecule. Although considered common knowledge, and thus not explicitly stated in modern writings, this definition of native conformations has a history as old as the protein folding problem. We attempt a more applicable definition that better correlates with functional activity and thus may be a more suitable substitute for the current convention.
Connecting laboratory behavior to field function through stable isotope analysis
Authors: Glon Mael G , Larson Eric R , Pangle Kevin L
Published: January 2018

Inherent difficulties of tracking and observing organisms in the field often leave researchers with no choice but to conduct behavioral experiments under laboratory settings. However, results of laboratory experiments do not always translate accurately to natural conditions. A fundamental challenge in ecology is therefore to scale up from small area and short-duration laboratory experiments to large areas and long-durations over which ecological processes generally operate. In this study, we propose that stable isotope analysis may be a tool that can link laboratory behavioral observations to past field interactions or function of individual organisms. We conducted laboratory behavioral assays to measure dominance of invasive rusty crayfish, Orconectes rusticus, and used stable isotope analysis to hindcast trophic positions of these crayfish under preceding natural conditions. We hypothesized that more dominant crayfish in our assays would have higher trophic positions if dominance were related to competitive ability or willingness to pursue high-risk, high-reward prey. We did not find a relationship between crayfish dominance and trophic position, and therefore infer that laboratory dominance of crayfish may not necessarily relate to their ecology in the field. However, this is to our knowledge the first attempt to directly relate laboratory behavior to field performance via stable isotope analysis. We encourage future studies to continue to explore a possible link between laboratory and field behavior via stable isotope analysis, and propose several avenues to do so.
Physiological stress associated with physical trauma during transportation of the Norway lobster, Nephrops norvegicus
Authors: Powell Adam , Cowing Daniel M , Eriksson Susanne P , Johnson Magnus L
Published: January 2018

The Norway lobster, Nephrops norvegicus is a valuable European decapod, particularly when sold live, although along the supply chain lobsters experience a range of extreme stressors during and immediately after capture, and onward transportation. To improve quality and quantity of live product, laboratory experiments and transport simulations have investigated the effect of stress, particularly emersion and temperature, on physiology and the immune system, typically via blood (haemolymph) assays. This study investigated a relatively neglected stressor, physical trauma during transport (i.e. prolonged vibrations) via a simulated transport experiment, following anecdotal evidence that additional cushioning reduced post-transport mortality of N. norvegicus by up to ca. 20%. Baseline (BS) lobsters were sampled shortly after creel capture, and subsamples emersed for 1h, with additional experimental shaking (ES) or as immobile controls (EM). Both emersed treatments showed increased THC and serum glucose, lactate and ammonium, although serum protein and refractive index did not change significantly. Compared to the EM treatment, ES lobsters had significant increases in serum ammonium and glucose. In addition to emersion stress, physical trauma during transport is confirmed as an additional stressor that needs to be considered in transport simulations, whilst straightforward and cheap mitigation of physical trauma (e.g. road vibrations) could improve welfare, survival and recovery.
Daniel Goodman’s empirical approach to Bayesian statistics
Authors: Gerrodette Tim , Ward Eric J , Taylor Rebecca L , Schwartz Lisa K , Eguchi Tomoharu , Wade Paul R , Himes Boor Gina K
Published: January 2018

Bayesian statistics, in contrast to classical statistics, uses probability to represent uncertainty about the state of knowledge. Bayesian statistics has often been associated with the idea that knowledge is subjective and that a probability distribution represents a personal degree of belief. Dr. Daniel Goodman considered this viewpoint problematic for issues of public policy. He sought to ground his Bayesian approach in data, and advocated the construction of a prior as an empirical histogram of “similar” cases. In this way, the posterior distribution that results from a Bayesian analysis combined comparable previous data with case-specific current data, using Bayes’ formula. Goodman championed such a data-based approach, but he acknowledged that it was difficult in practice. If based on a true representation of our knowledge and uncertainty, Goodman argued that risk assessment and decision-making could be an exact science, despite the uncertainties. In his view, Bayesian statistics is a critical component of this science because a Bayesian analysis produces the probabilities of future outcomes. Indeed, Goodman maintained that the Bayesian machinery, following the rules of conditional probability, offered the best legitimate inference from available data. We give an example of an informative prior in a recent study of Steller sea lion spatial use patterns in Alaska.
Exact pattern matching: Adapting the Boyer-Moore algorithm for DNA searches
Authors: Allmer Jens
Published: January 2018

Exact pattern matching aims to locate all occurrences of a pattern in a text. Many algorithms have been proposed, but two algorithms, the Knuth-Morris-Pratt (KMP) and the Boyer-Moore (BM), are most widespread. It is the basis of some approximate string matching algorithms like BLAST, and in many cases it is desirable to locate an exact rather than approximate matches. Although several studies included measures with small alphabets, none of them specifically designed an algorithm to target nucleotide sequences. Since there are also no application programming interfaces available for pattern matching in nucleotide sequences, these two issues were aimed to be resolved. A portion of the Chlamydomonas reinhardtii genome (30 mega bases) was searched with queries ranging from 10 to 2000 nucleotides and an alternating number of matches between one and 25000. The results indicate that the use of two of the algorithms developed in this study is sufficient to efficiently cover the complete search space as presented in the experiment conducted here. Thus the aim of implementing an algorithm specifically targeting pattern matching in nucleotide sequences and making it available to the general public as an advanced programming interface was achieved. All algorithms are freely available at: http://bioinformatics.iyte.edu.tr/supplements/peerj/.
Glutamate, GABA and Serotonin concentrations in the cerebrospinal fluid and primary somatosensory cortex of birth-enucleated rats: Searching for S1 intrinsic and extrinsic epigenetic regulatory signals modulating neonatal cross-modal plasticity
Authors: Martínez-Méndez Raquel , Padilla-Cortés Patricia , Gómez-Chavarín Margarita , Gutiérrez-Ospina Gabriel
Published: January 2018

Neonatal eye loss leads to an expansion of the primary somatosensory cortex (S1) in rodents. In blind rats, S1 expansion results from the predisplacement of S1 formation during the first three days of life, a process modulated by epigenetic factors. Some of these factors might be local and some others may come from extra-S1 sources such as the cerebrospinal fluid (CSF). Thus, we evaluated the concentration of glutamate, GABA and serotonin in the CSF and S1 of control and birth-enucleated rat pups. These neurotransmitters modulate through epigenetic mechanisms several aspects of brain development and also regulate S1 formation. Our results show, first, that axon segregation during barrel formation is discreetly predisplaced in birth-enucleated rats. Second, S1 glutamate, GABA and serotonin concentrations were similar in control and birth-enucleated rats during S1 formation. Lastly, CSF glutamate concentration decreased in birth-enucleated rats during S1 formation. Overall, our results open the possibility that neurochemical shifts in the CSF might modulate S1 expansion in enucleated rats. Further studies are needed to establish causal links.
A low-cost auditory multi-class brain-computer interface based on pitch, spatial and timbre cues
Authors: Vamvakousis Zacharias , Ramirez Rafael
Published: January 2018

P300-based brain-computer interfaces (BCIs) are especially useful for people with illnesses, which prevent them from communicating in a normal way (e.g. brain or spinal cord injury). However, most of the existing P300-based BCI systems use visual stimulation which may not be suitable for patients with sight deterioration (e.g. patients suffering from amyotrophic lateral sclerosis). Moreover, P300-based BCI systems rely on expensive equipment, which greatly limits their use outside the clinical environment. Therefore, we propose a multi-class BCI system based solely on auditory stimuli, which makes use of low-cost EEG technology. We explored different combinations of timbre, pitch and spatial auditory stimuli (TimPiSp: timbre-pitch-spatial, TimSp: timbre-spatial, and Timb: timbre-only) and three inter-stimulus intervals (150ms, 175ms and 300ms), and evaluated our system by conducting an oddball task on 7 healthy subjects. This is the first study in which these 3 auditory cues are compared. After averaging several repetitions in the 175ms inter-stimulus interval, we obtained average selection accuracies of 97.14%, 91.43%, and 88.57% for modalities TimPiSp, TimSp, and Timb, respectively. Best subject’s accuracy was 100% in all modalities and inter-stimulus intervals. Average information transfer rate for the 150ms inter-stimulus interval in the TimPiSp modality was 14.85 bits/min. Best subject’s information transfer rate was 39.96 bits/min for 175ms Timbre condition. Based on the TimPiSp modality, an auditory P300 speller was implemented and evaluated by asking users to type a 12-characters-long phrase. Six out of 7 users completed the task. The average spelling speed was 0.56 chars/min and best subject’s performance was 0.84 chars/min. The obtained results show that the proposed auditory BCI is successful with healthy subjects and may constitute the basis for future implementations of more practical and affordable auditory P300-based BCI systems.
Electronic tagging data and habitat envelope modeling used to monitor spatial persistency and possible relocation of spawning grounds for the bluefin tuna in the East Atlantic and the Mediterranean Sea
Authors: Ospina-Alvarez Andres , Sainz Trápaga Susana , Tudela Sergi , Di Natale Antonio , Quílez-Badia Gemma
Published: January 2018

A spawning habitat envelope has been created for bluefin tuna in its traditional spawning ground in the Mediterranean Sea by combining environmental variables and species behavior. We used logistic regressions through a generalized linear model (GLM) approach to determine whether reproduction was affected by spawning habitat characteristics and individual behavior. Results from the implementation of the model predicted a high probability of occurrence of reproductive events associated with 17 tagged tuna. Some of them matched the already well known spawning grounds in the Mediterranean Sea (the area around the Balearic Islands, the Tyrrhenian Sea and the Gulf of Sirte). The model also proposed some other areas seldom or not at all mentioned in the bibliography in both, the Mediterranean and the Atlantic Ocean, such as the Alboran Sea, the Catalan Sea, the Gulf of Lions and the Bay of Biscay. This model provides an objective methodology to predict and adapt spawning areas, and to identify other potential but unknown, or even new, spawning areas and periods for the species. Moreover, the application of the present methodology could help the implementation of an adaptive management approach for Atlantic bluefin tuna by predicting areas suitable for spawning and identifying changes in spawning areas and season in the currently highly changing ocean and climate conditions.
Contribution of insect pollinators to crop yield and quality varies with agricultural intensification
Authors: Bartomeus Ignasi , Potts Simon G , Steffan-Dewenter Ingolf , Vaissiere Bernard E , Woyciechowski Michal , Krewenka Kristin M , Tscheulin Thomas , Roberts Stuart PM , Szentgyörgyi Hajnalka , Westphal Catrin , Bommarco Riccardo
Published: January 2018

Background. Up to 75 % of crop species benefit at least to some degree from animal pollination for fruit or seed set and yield. However, basic information on the level of pollinator dependence and pollinator contribution to yield is lacking for many crops. Even less is known about how insect pollination affects crop quality. Given that habitat loss and agricultural intensification are known to decrease pollinator richness and abundance, there is a need to assess the consequences for different components of crop production. Methods. We used pollination exclusion on flowers or inflorescences on a whole plant basis to assess the contribution of insect pollination to crop yield and quality in four flowering crops (spring oilseed rape, field bean, strawberry, and buckwheat) located in four regions of Europe. For each crop, we recorded abundance and species richness of flower visiting insects in ten fields located along a gradient from simple to heterogeneous landscapes. Results. Insect pollination enhanced average crop yield between 18 and 71% depending on the crop. Yield quality was also enhanced in most crops. For instance, oilseed rape had higher oil and lower chlorophyll contents when adequately pollinated, the proportion of empty seeds decreased in buckwheat, and strawberries' commercial grade improved; however, we did not find higher nitrogen content in open pollinated field beans. Complex landscapes had a higher overall species richness of wild pollinators across crops, but visitation rates were only higher in complex landscapes for some crops. On the contrary, the overall yield was consistently enhanced by higher visitation rates, but not by higher pollinator richness. Discussion. For the four crops in this study, there is clear benefit delivered by pollinators on yield quantity and/or quality, but it is not maximized under current agricultural intensification. Honeybees, the most abundant pollinator, might partially compensate the loss of wild pollinators in some areas, but our results suggest the need of landscape-scale actions to enhance wild pollinator populations.
Should bread be targeted as a vector to reduce sodium intake in Morocco?
Authors: Derouiche Abdelfettah , Jafri Ali , ElKardi Younes , Jabari Mohammed , Habbal Rachida , El Attaoui Khalid , Alami Mohamed
Published: January 2018

Background: High blood pressure is a serious public health problem in Morocco; the national survey of cardiovascular risk factors in Morocco found a prevalence of 33.6% of people with high blood pressure (HBP) with a higher prevalence among women, also, the World Health Organization estimated the prevalence of HBP in 2008 at 41.2%. Our study aimed to evaluate the amount of salt provided by the consumption of bread, since it is a staple food, in daily food intake and compare it to the recommendations. This study aims to raise awareness about salt consumption and its impact in causing high blood pressure. Methods: We used the MOHR method to quantify sodium in bread samples from 80 professional bakeries in Casablanca. Results: Results showed that the average amount of salt used in the preparation of bread is 17.42 ± 1.28 g / kg, which is the equivalent of a daily intake of 8 to 9 g of salt through bread alone, and exceeds all recommendations. Conclusion: We can only recommend using it as a vector for the programme of awareness about salt over-consumption and its impact on raising the prevalence of hypertension.
Harmine stimulates neurogenesis of human neural cells in vitro
Authors: Dakic Vanja , de Moraes Maciel Renata , Drummond Hannah , Nascimento Juliana M , Trindade Pablo , Rehen Stevens K
Published: January 2018

Harmine is a β-carboline alkaloid present at highest concentration in the psychotropic plant decoction Ayahuasca. In rodents, classical antidepressants reverse the symptoms of depression by stimulating neuronal proliferation. It has been shown that Ayahuasca presents antidepressant effects in patients with depressive disorder. In the present study, we investigated the effects of harmine in cell cultures containing human neural progenitor cells (hNPCs, 97% nestin-positive) derived from pluripotent stem cells. After 4 days of treatment, the pool of proliferating hNPCs increased by 57%. Harmine has been reported as a potent inhibitor of the dual specificity tyrosine-phosphorylation-regulated kinase (DYRK1A), which regulates cell proliferation and brain development. We tested the effect of analogs of harmine, an inhibitor of DYRK1A (INDY) and an irreversible selective inhibitor of monoamine oxidase (MAO) but not DYRK1A (pargyline). INDY but not pargyline induced proliferation of hNPCs similarly to harmine, suggesting that inhibition of Dyrk1a is a possible mechanism to explain harmine effects upon the proliferation of hNPCs. Harmine also increased dendritic arborization, including total neurite length, number of segments, extremities and nodes in MAP2 positive neurons. Our findings show that harmine enhances neurogenesis of hNPCs in vitro, and suggest a biological activity associated with its antidepressant effects in vivo.
Use of rbcL sequences for DNA barcoding and authentication of plant drugs used in Traditional Chinese Medicine
Authors: Herrmann Florian , Wink Michael
Published: January 2018

Traditional Chinese medicine has become increasingly popular in Europe and North America.There is evidence that quality control in terms of species authentication is sometimes inappropriate. Repeated incidents of adulterations and wrong identification, some even with serious consequences have occurred recently. The necessity of a quality control for TCM drugs to avoid these incidents is given since many years. DNA barcoding was used in this study to authenticate drugs which are often used in Chinese herbal medicine. 37 plants from 28 families were identified using nucleotide sequences of the rbcL gene. Only one adulteration could be detected. Both the advantages and limitations of rbcL as a marker gene for identification were analysed and discussed. We could show that DNA barcoding is a valid and fast method to identify medicinal herbs, showing some advantages over chemical profiling because of its universal application even for unknown plant species.
Glyoxylate reductase as versatile enzymatic system for pharmaceutical and medical use
Authors: Kutner Jan , Shabalin Ivan , Matelska Dorota , Handing Katarzyna B , Gasiorowska Olga , Sroka Piotr , Ginalski Krzysztof , Minor Wladek , Wozniak Krzysztof
Published: January 2018

The chiral homogeneity of a chemical compound is the main prerequisite in safety and efficiency of drug substances and generation of single enantiomers of drug intermediates in pharmaceutical industry. Over the past several years there have been an increase wide variety of enzymes and bioengineered microorganisms used for biotransformation of chemicals with chemo- regio- and enantioselectivity. The direct evolution – a combination of biochemistry, molecular biology, structural biology and bioinformatics predictions can modulate enzyme stability, reactivity or substrate specificity. One example of enzymes used in pharmaceutical industry are enzymes from the D-2-hydroxyacid dehydrogenase (2HADH) family. They catalyze reversible reduction of 2-oxoacids to 2-hydroxyacids in an NAD(P)H dependent manner, playing a key role in metabolism of many organisms. One of the enzyme group from 2HADH family is glyoxylate reductase (GR). The advantages of these enzymes have been recently recognized by pharmaceutical and biotechnological industry, considering a possibility of highly stereospecific biotransformation of α-ketoacids into homochiral α-hydroxyacids, as important industrial intermediates. The glycolic acid, reduced by the enzyme into ethylene glycol, the smallest member of the α-hydroxy acid family, is nowadays obtained in a large-scale industrial process. The monomeric structure of the enzyme comprises two domains typical for NAD(P)-dependent dehydrogenases: the substrate-binding domain (SBD) and the nucleotide-binding domain (NBD). Several crystal X-ray structures of glyoxylate reductase from different species have been already solved, but only few of them were determined with the bound substrate and/or cofactor. Such structures are crucial in understanding the reaction mechanism and for predicting or designing the structures of new substrates for the enzyme. We will communicate the structural study of two homodimeric glyoxylate reductases from S. meliloti (SmGR1 and SmGR2). We have solved the crystal structures for SmGR1 and SmGR2 with bound oxalate and NADPH and compared them with the structures of other glyoxylate reductases subfamily members: from Rhizobium etli (with L(+)-tartaric acid and NADP) and human (with (2 R )-2,3-dihydroxypropanoic acid and NADPH). During the ligand and cofactor binding the catalytic domain rotates towards coenzyme-binding site, changing its structure from open to close conformation. Using biochemical tools and kinetics approaches we have also shown that Sm GR1 and Sm GR2 possess substrate specificity to hydroxypuryvate, hydroxylphenylpyruvate and gloxylate, providing new insights into the potential pharmaceutical and medical uses of this family of enzymes.
The fractal dimension of the tree of life
Authors: Lv Xiaofei , Wu Yuping , Ma Bin
Published: January 2018

The structure pattern of the tree of life clues on the key ecological issues; hence knowing the fractal dimension is the fundamental question in understanding the tree of life. Yet the fractal dimension of the tree of life remains unclear since the scale of the tree of life has hypergrown in recent years. Here we show that the tree of life display a consistent power-law rules for inter- and intra-taxonomic levels, but the fractal dimensions were different among different kingdoms. The fractal dimension of hierarchical structure (Dr) is 0.873 for the entire tree of life, which smaller than the values of Dr for Animalia and Plantae but greater than the values of Dr for Fungi, Chromista, and Protozoa. The hierarchical fractal dimensions values for prokaryotic kingdoms are lower than for other kingdoms. The Dr value for Viruses was lower than most eukaryotic kingdoms, but greater than prokaryotes. The distribution of taxa size is governed by fractal diversity but skewed by overdominating taxa with large subtaxa size. The proportion of subtaxa in taxa with small and large sizes was greater than in taxa with intermediate size. Our results suggest that the distribution of subtaxa in taxa can be predicted with fractal dimension for the accumulating taxa abundance rather than the taxa abundance. Our study determined the fractal dimensions for inter- and intra-taxonomic levels of the present tree of life. These results emphases the need for further theoretical studies, as well as predictive modelling, to interpret the different fractal dimension for different taxonomic groups and skewness of taxa with large subtaxa size.
Examining the foundations of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem
Authors: McGlinn Daniel J , Palmer Michael W
Published: January 2018

The conservation of disturbance-prone ecosystems such as rangelands may depend on the spatial and temporal variation in the application of disturbances. Patch-burn management approaches attempt to increase overall landscape biodiversity by creating a mosaic of habitat patches using a patchy application of fire and grazing. Three fundamental assumptions underlay the patch-burn management approach: 1) fire and grazing drive spatial patch differentiation in community structure, 2) species composition of patches diverge through time in response to disturbance, 3) high spatio-temporal variation in fire and grazing results in high compositional variation and thus high landscape-scale diversity. We tested the first two assumptions of the patch-burn approach by comparing the importance of variation in management (changes in fire frequency and grazer species) relative to inherent sources of landscape heterogeneity at the Tallgrass Prairie Preserve in Osage Co., Oklahoma, USA. We sampled 150 square 100 m2 quadrats on a 1 x 1 km UTM grid. We randomly selected 20 of those quadrats to annually resample for 12-years. We recorded visual cover of all vascular plant species rooted within each quadrat. We used variation partitioning within multiple regression and direct ordination frameworks to estimate the relative contribution of classes of variables on species richness and composition respectively.

Our results indicate that there was some support for the two assumptions underlying patch-burn management; however, independent spatial and temporal inherent landscape heterogeneity played a much larger role than management in shaping both plant richness and composition. The strength of inherent landscape heterogeneity on the plant community suggests that fine-tuning the application of fire and grazing is not critical for maintaining this community as long as fire and grazing remain part of the system. More generally, the effects of intrinsic spatiotemporal template on biodiversity may dominate even in disturbance-prone ecosystems.