bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenetic transfer of knowledge for biological networks
Authors: Zhang Xiuwei , Ye MIn , Moret Bernard
Published: January 2018

Advances in biotechnology have enabled researchers to study molecular biology from the point of view of systems, from focused efforts at functional annotation to the study of pathways, regulatory networks, protein-protein interaction networks, etc. However, direct observation of these systems has proved difficult, time-consuming, and often unreliable. Thus computational methods have been developed to infer such systems from high-throughput data, such as sequences, gene expression levels, ChIP-Seq signals, etc. For the most part, these methods have not yet proved accurate and reliable enough to be used in automated analysis pipelines. Most methods used to infer biological networks rely on data for a single organism; a few attempt to leverage existing knowledge about some related organisms. Today, however, we have data about a large variety of organisms as well as good consensus about the evolutionary relationships among these organisms, so that the latter can be used to integrate the former in a well founded manner, thereby gaining significant power in the analysis. We have coined the term Phylogenetic Transfer of Knowledge (PTK) for this approach to inference and analysis. A PTK analysis considers a family of organisms with known evolutionary relationships and "transfers" biological knowledge among the organisms in accordance with these relationships. The output of a PTK analysis thus includes both predicted (or refined) target data (such as networks) for the extant organisms and inferred details about their evolutionary history. While a few ad hoc inference methods used a PTK approach almost a dozen years ago, we first provided a global perspective on such methods just six years ago. The last few years have seen a significant increase in research in this area, as well as new applications. The time is thus right for a review of recent work that falls under this heading, a characterization of the solutions proposed, and a description of remaining challenges.
Phylogenetic evidence suggests a later origin of the DRD2l and DRD4rs dopamine receptor gene lineages
Authors: Opazo Juan C , Zavala Kattina , Miranda-Rottmann Soledad , Araya Roberto
Published: January 2018

Dopamine receptors are integral membrane proteins whose endogenous ligand is dopamine. They play a fundamental role in the central nervous system and dysfunction of dopaminergic neurotransmission is responsible for the generation of a variety of neuropsychiatric disorders. From an evolutionary standpoint, phylogenetic relationships among the DRD1 class of dopamine receptors are still a matter of debate as in the literature different tree topologies have been proposed. In contrast, phylogenetic relationships among the DRD2 group of receptors are well understood. Understanding the time of origin of the different dopamine receptors is also an issue that needs further study, especially for the genes that have restricted phyletic distributions (e.g. DRD2l and DRD4rs). Thus, the goal of this study was to investigate the evolution of dopamine receptors, with emphasis on shedding light on the phylogenetic relationships among the D1 class of dopamine receptors and the time of origin of the DRD2l and DRD4rs gene lineages. Our results recovered the monophyly of the two groups of dopamine receptors. Within the DRD1 group the monophyly of each paralog was recovered with strong support, and phylogenetic relationships among them were well resolved. Within the DRD1 class of dopamine receptors we recovered the sister group relationship between the DRD1C and DRD1E, and this clade was recovered sister to a cyclostome sequence. The DRD1 clade was recovered sister to the aforementioned clade, and the group containing DRD5 receptors was sister to all other DRD1 paralogs. In agreement with the literature, among the DRD2 class of receptors, DRD2 was recovered sister to DRD3, whereas DRD4 was sister to the DRD2/DRD3 clade. According to our phylogenetic tree, the DRD2l and DRD4rs gene lineages would have originated in the ancestor of gnathostomes between 615 and 473 mya. Conservation of sequences required for dopaminergic neurotransmission and small changes in regulatory regions suggest a functional refinement of the dopaminergic pathways along evolution.
Functional connectivity in task-negative network of the Deaf: effects of sign language experience
Authors: Malaia Evie , Talavage Thomas M , Wilbur Ronnie B
Published: January 2018

Prior studies investigating cortical processing in Deaf signers suggest that life-long experience with sign language and/or auditory deprivation may alter the brain’s anatomical structure and the function of brain regions typically recruited for auditory processing (Emmorey et al., 2010; Pénicaud, et al., 2012 inter alia). We report the first investigation of the task-negative network in Deaf signers and its functional connectivity – the temporal correlations among spatially remote neurophysiological events. We show that Deaf signers manifest increased functional connectivity between posterior cingulate/precuneus and left medial temporal gyrus (MTG), but also inferior parietal lobe and medial temporal gyrus in the right hemisphere- areas that have been found to show functional recruitment specifically during sign language processing. These findings suggest that the organization of the brain at the level of inter-network connectivity is likely affected by experience with processing visual language, although sensory deprivation could be another source of the difference. We hypothesize that connectivity alterations in the task negative network reflect predictive/automatized processing of the visual signal.
­­Ensemble-based network aggregation improves the accuracy of gene network reconstruction
Authors: Allen Jeffrey D. , Xie Yang , Xiao Guanghua
Published: January 2018

Reverse engineering approaches to construct context-specific gene regulatory networks (GRNs) based on genome-wide mRNA expression data have led to significant biological findings. However, the reliability and reproducibility of the reconstructed GRNs needs to be improved. Here, we propose an ensemble-based network aggregation approach to improve the accuracy of the network topology constructed from mRNA expression data. To evaluate the performance of different approaches, we created dozens of simulated networks and also tested our methods on three Escherichia coli datasets. We demonstrate three novel applications from this development. First, bootstrapping can be done on the available samples, turning any network reconstruction approach into an ensemble method. Second, this aggregation approach can be used to combine GRNs from different network inference methods, creating a novel network reconstruction approach that consistently outperforms any constituent method. Third, the approach can be used to effectively integrate GRNs constructed from different studies – producing more accurate networks. We are releasing an implementation of these techniques as an R package “ENA” which is able to run network inference in parallel across multiple servers. We made all of the code and data used in our simulations and analysis available online at https://github.com/QBRC/ENA-Research to ensure the reproducibility of our results.
HIV-positive parents disclosure-related preparation activities in Kenya
Authors: Gachanja Grace , Burkholder Gary J , Ferraro Aimee
Published: January 2018

Background. HIV disclosure from parent to child is a complex and challenging issue that needs to be approached carefully. Little is known about how parents prepare for and perform disclosure to children in resource-poor nations and what resources are needed. This study was conducted to describe the lived experiences of HIV-positive parents and their children during the disclosure process in Kenya.

Methods. This qualitative phenomenological study's data was collected using in-depth semi-structured interviews with 34 participants consisting of HIV-positive parents, HIV-positive and negative children, and healthcare professionals. The Van Kaam method was used to analyze the data.

Results. Parents take years to prepare for disclosure, proceeding when they perceive themselves capable and ready; and their children are receptive to the news. Preparation activities include thinking about and making disclosure plans, reading information, teaching children about the disease without disclosure while improving the parent-child relationship, praying regularly and attending religious activities, seeking counseling, and attending support group meetings.

Conclusion. Parents perform a number of activities to get themselves and their children ready for disclosure. These activities are crucial in the timely delivery of disclosure. Understanding the importance of these activities helps healthcare professionals assist parents to deliver disclosure faster after diagnosis of illness.
Darwin and Fisher meet at biotech: On the potential of computational molecular evolution in industry
Authors: Anisimova Maria
Published: January 2018

Today computational molecular evolution and bioinformatics are vibrant research areas that flourish on large amounts of complex datasets generated by new generation technologies – from full genomes and proteomes to microbiomes, metabolomes and epigenomes. Yet the foundations for successful mining and the analyses of such data were established long before the structure of the DNA was discovered. Darwin’s theory of evolution by means of natural selection not only remains relevant today, but also provides solid ground for computational research with a variety of applications. The data size and its complexity require empirical scientists to work in close collaboration with experts in computational science, modeling and statistics, as Sir R. Fisher has beautifully demonstrated in early 20th century. Particularly, modern computational methods for evaluating selection in molecular sequences are very useful for generating biological hypotheses and candidate gene sets for follow-up experiments. Evolutionary analyses of selective pressures in genomic data have high potential for applications, since natural selection is a leading force in function conservation, in adaptation to emerging pathogens, new environments, and plays key role in immune and resistance systems. At this stage, pharma and biotech industries can successfully use this potential, taking the initiative to enhance their research and development with the state-of the art bioinformatics approaches. This mini-review provides a quick “why-and-how” guide to the current approaches that apply the evolutionary principles of natural selection to real life problems – from drug target validation, vaccine design and protein engineering to applications in agriculture, ecology and conservation.
Natural selection increases mutational robustness in complex diseases: Mendelian evidence from early versus late onset common diseases
Authors: Baysal Bora E
Published: January 2018

Background. Natural selection operates on genetically influenced phenotypic variations that confer differential survival or reproductive advantages. Common diseases are frequently associated with increased mortality and disability and complex heritable factors play an important role in their pathogenesis. Hence, common diseases should trigger the process of natural selection with subsequent population genetic response. However, empirical impact of natural selection on genetics of complex diseases is poorly understood. In this paper, I hypothesize that negative selection of diseased individuals leads to systemic genetic differences between common diseases that primarily occur before or during the reproductive years (early onset) and those that occur after the reproductive years (late onset).

Methods. To test this hypothesis, a comprehensive literature survey of highly penetrant (80% or more) nonpleiotropic, nonsyndromic susceptibility genes (hereafter defined as Mendelian phenocopies) was completed for early versus late onset common diseases, organized using the World Health Organization (WHO) ICD-10 classification scheme. An average age at sporadic disease onset of 30 years was selected for dividing early versus late onset common diseases.

Results. Mendelian phenocopies were identified for 16 primarily late onset common diseases from 9 distinct WHO diagnostic categories. Late onset common diseases with Mendelian phenocopies include papillary renal carcinoma, obesity, Alzheimer disease, Parkinson disease, frontotemporal dementia, amyotrophic lateral sclerosis, primary open angle glaucoma, age-related hearing loss, coronary artery disease, stroke, pancreatitis, thrombotic thrombocytopenic purpura, systemic lupus erythematosus, inclusion body myositis, Paget's disease of bone and focal segmental glomerulosclerosis (steroid resistant). In contrast, no Mendelian phenocopy was found for any primarily early onset common disease (p<5.8x10-4). Thus, highly predictive rare variants are present for a subset of late onset common diseases, but not for early onset common diseases.

Discussion. These findings suggest that genetic architecture of early onset common diseases is more robust against the phenotypic expression of highly penetrant predisposing mutations than is the case for late onset common diseases. The primary candidate for increased genetic robustness in early onset common diseases is proposed to be natural selection.
Sequencing at sea: Challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition
Authors: Lim Yan Wei , Cuevas Daniel A , Silva Genivaldo Gueiros Z. , Aguinaldo Kristen , Dinsdale Elizabeth , Haas Andreas F , Hatay Mark , Sanchez Savannah E , Kelly Linda W. , Dutilh Bas E. , Harkins Timothy T. , Lee Clarence C , Tom Warren , Sandin Stuart A , Smith Jennifer , Zgliczynski Brian , Vermeij Mark JA , Rohwer Forest , Edwards Robert
Published: January 2018

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phospohonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.
Restore: An R of sustainability that can tame the “conundrum”
Authors: Bindewald Eckart
Published: January 2018

The environmental benefits of sustainability efforts can be rendered less effective due to economic feedback mechanisms. As a remedy against such rebound effects, a reinvestment strategy towards environmental causes has been suggested. Here, a practical implementation of such a reinvestment strategy is presented. It involves a) estimating the financial savings resulting from sustainability efforts, b) informing the participants that the environmental benefit of the efforts is reduced by economic feedback mechanisms and c) asking them to donate a fraction of the expected savings towards environmental causes. An easy-to-use methodology for estimating rebound effects of sustainability efforts is presented in order to quantify the efficacy of this approach. CO2 emission offsets are used as an example of donations towards environmental causes. It is shown, that donating even a small amount (less than 1% of financial savings obtained from conservation or engineering savings) of donated carbon offsets can more than eliminate the estimated rebound effects. This then leads to the restore principle, that states that the environmental benefit of reducing activities with average environmental impact is dramatically improved if a fraction of the resulting financial savings is applied towards environmental causes. This approach is made practical by augmenting the common reduce, reuse, recycle motto with a fourth component: reduce, reuse, recycle and restore.
Building an ecological knowledge of virtual worlds
Authors: Montiglio Pierre-Olivier , Céré Julien
Published: January 2018

Virtual worlds supporting massively multiplayer games have become so complex that they exhibit temporal and spatial dynamics mostly driven by interactions between players. In this respect, virtual worlds resemble closely natural ecosystems. Studying the ecology of virtual worlds is an outstanding opportunity for ecologists as well as the game industry to collaborate in order to test several aspects of ecological theory difficult to study in nature, and build manageable, resilient virtual worlds.
Retaining the double dimension of species diversity: Application of partially ordered set theory and Hasse diagrams
Authors: Kampichler Christian , Wieland Ralf
Published: January 2018

The measurement of species diversity has been a central task of community ecology from the mid 20th century onward. The conventional method of designing a diversity index is to combine values for species richness and assemblage evenness into a single composite score. The literature abounds with such indices. Each index weights richness and evenness in a different fashion. The conventional approach has repeatedly been criticized since there is an infinite number of potential indices which have a minimum value when S (species richness) = 1 and a maximum value when S = N (number of individuals). We argue that partial order theory is a sound mathematical fundament and demonstrate that it is an attractive alternative for comparing and ranking biological diversity without the necessity of combining values for species richness and evenness into an ambiguous diversity index. The general principle of partial ordering is simple: one particular assemblage is regarded as more diverse than another when both its species richness and its evenness are higher. Assemblages are not comparable with each other when one has a higher value for species richness and a lower value for evenness. Hasse diagrams can graphically represent partially ordered communities. Linear extensions and rank-frequency distributions reveal the potential of partial order theory as a means to support decisions when assemblage ranking is desired.
A Biologist’s Guide to Impact Factors
Authors: Rosenberg Michael S
Published: January 2018

Personal impact factors (e.g., the h-index) are becoming more and more important in evaluations of faculty with respect to job hiring, promotion, and tenure, but they are largely poorly understood by the community at large. The purpose of this study is to educate biologist and other scientists about some of the wide literature about impact factors, including highlighting their strengths and weaknesses. This includes a thorough exploration of dozens of such indices by comparing how they perform through repeated calculation of data representing 15 years of scientific output of a single individual from beginning through mid-career. Indices are examined with respect to factors such as interpretability, consistency, and stability.
Spatial genetic structure across a hybrid zone between European rabbit subspecies
Authors: Alda Fernando , Doadrio Ignacio
Published: January 2018

The Iberian Peninsula is the only region in the world where the two existing subspecies of the European rabbit (Oryctolagus cuniculus) naturally occur and hybridize. In this study we explore the relative roles of historical and contemporary processes in shaping the spatial genetic structure of the rabbit across its native distribution range, and how they differently affect each subspecies and the hybrid zone. For that purpose multilocus genotypes and mitochondrial DNA data were obtained for 771 rabbits across most of the species’ distribution range in Spain. Nuclear markers defined a hierarchical genetic structure firstly comprised by two genetic groups, largely congruent with the mitochondrial lineages and subspecies distributions (O. c. algirus and O. c. cuniculus), which were subsequently subdivided into seven genetic groups probably shaped by environmental or ecological factors. Geographic distance alone emerged as an important factor explaining genetic differentiation across the whole range, without the need to invoke for the effect for geographical barriers. Thus, when considering the overall genetic structure, differences at a local level seem to be of greater importance. The significantly positive spatial correlation up to a distance of only 100 km supported this hypothesis. However, northern populations of O. c. cuniculus showed more spatial genetic structure and differentiation than O. c. algirus, which could be due to local geographic barriers, limited resources, soil type and/or social behaviours limiting dispersal. The hybrid zone showed similar genetic structure to the southern populations but a larger introgression from the northern lineage genome. These differences have been attributed to selection against the hybrids rather than to behavioural differences between subspecies. Ultimately, the genetic structure of the rabbit in its native distribution range is the result of an ensemble of factors, from geographical and ecological, to behavioural and molecular, that hierarchically interact in time and space.
Advances and limits of using population genetics to understand local adaptation
Authors: Tiffin Peter , Ross-Ibarra Jeffrey
Published: January 2018

Local adaptation is an important process shaping within species diversity. In recent years, population genetic analyses, which complement organismal approaches in advancing our understanding of local adaptation have become widespread. Here we focus on using population genetics to address some key questions in local adaptation: What traits are involved? What environmental variables are most important? Does local adaptation target the same genes in related species? Do loci responsible for local adaptation exhibit tradeoffs across environments? After discussing these questions we highlight important limitations to population genetic analyses including challenges with obtaining high quality data, deciding which loci are targets of selection, and limits to identifying the genetic basis of local adaptation.
On the measurement of running style
Authors: Daumer Martin , Trost Michael , Subkowski Paul , Schneider Andreas , Mrowca Damian , Ding Rui , Gao Han , Walther Markus , Lederer Christian
Published: January 2018

The measurement of running style must be ecologically valid. The individual running style has an impact on the running performance as well as the running injury risk. In order to increase the performance and lower the injury risk, runners should be educated towards a healthy running style. But before advice can be made it is crucial to distinguish running styles from each other. Thus, it is interesting to detect and optimize the running style of individuals. The goal is to evaluate the possibility for a running style app using accelerometry data, which is able to track and display the user’s current running style by using accelerometry data, based on which advice can be given for a healthy and efficient running style with the help of gaming tools (meta product). To validate the approach, a gold standard with outdoor running acceleration data has to be created.
Temporal variability is a personalized feature of the human microbiome
Authors: Flores Gilberto E , Caporaso J Gregory , Henley Jessica B , Rideout Jai Ram , Domogala Daniel , Chase John , Leff Jonathan W , Vázquez-Baeza Yoshiki , Gonzalez Antonio , Knight Rob , Dunn Robert R , Fierer Noah
Published: January 2018

Background: It is now apparent that the complex microbial communities found on and in the human body (the human microbiome) vary across individuals. What has largely been missing from previous studies is an understanding of how these communities vary over time within individuals. To the extent to which it has been considered, it is often assumed that temporal variability is negligible for healthy adults. Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over three months.

Results: We found that skin (forehead and palm) varied most in the number of taxa present, whereas gut and tongue communities varied more in the relative abundances of taxa. Within each body habitat, there was a wide range of temporal variability across the study population, with some individuals consistently harboring more variable communities than others. The best predictor of these differences in variability across individuals was microbial diversity; individuals with more diverse gut or tongue communities were less variable than individuals with less diverse communities.

Conclusions: This expanded sampling allowed us to observe consistently high levels of temporal variability in both diversity and community structure in all body habitats studied. These findings suggest that temporal dynamics may need to be considered when attempting to link changes in microbiome structure to changes in health status.Furthermore, our findings show that, not only is the composition of an individual’s microbiome highly personalized, but their degree of temporal variability is also a personalized feature.
The CombineArchive Toolkit - facilitating the transfer of research results
Authors: Scharm Martin , Wendland Florian , Peters Martin , Wolfien Markus , Theile Tom , Waltemath Dagmar
Published: January 2018

Sharing in silico experiments is essential for the advance of research in computational biology. Consequently, the COMBINE archive was designed as a digital container format. It eases the management of numerous files, fosters collaboration, and ultimately enables the exchange of reproducible research results. However, manual handling of COMBINE archives is tedious and error prone. We therefore developed the CombineArchive Toolkit. It supports scientists in promoting and publishing their work by means of creating, exploring, modifying, and sharing archives.
Loss of CITED1, an MITF regulator, drives a phenotype switch in vitro and can predict clinical outcome in primary melanoma tumours
Authors: Howlin Jill , Cirenajwis Helena , Lettiero Barbara. , Staaf Johan , Lauss Martin , Saal Lao , Borg Åke , Gruvberger-Saal Sofia K , Jönsson Göran B
Published: January 2018

CITED1 is a non-DNA binding transcriptional co-regulator whose expression can distinguish the ‘proliferative’ from ‘invasive’ signature in the phenotype-switching model of melanoma. We have found that CITED1 expression is repressed by TGFβ in addition to other ‘proliferative’ signature genes while the ‘invasive’ signature genes are upregulated. In agreement, CITED1 positively correlates with MITF expression and can discriminate the MITF-high/pigmentation tumor molecular subtype in a large cohort (120) of melanoma cell lines. Interestingly, CITED1 overexpression significantly suppressed MITF promoter activation, mRNA and protein expression levels while MITF was transiently upregulated following siRNA mediated CITED1 silencing. Conversely, MITF siRNA silencing resulted in CITED1 downregulation indicating a reciprocal relationship. Whole genome expression analysis identified a phenotype shift induced by CITED1 silencing and driven mainly by expression of MITF and a cohort of MITF target genes that were significantly altered. Concomitantly, we found changes in the cell-cycle profile that manifest as transient G1 accumulation, increased expression of CDKN1A and a reduction in cell viability. Additionally, we could predict survival outcome by classifying primary melanoma tumors using our in vitro derived ‘CITED1-silenced’ gene expression signature. We hypothesize that CITED1 acts a regulator of MITF, functioning to maintain MITF levels in a range compatible with tumourigenesis.
Action and cognition in task oriented coping: Factor structure and internal consistency of the CISS-21 with an Indian sample
Authors: Golpelwar Mayank
Published: January 2018

Objective : Although the Coping Instrument for Stressful Situations – 21 item scale (CISS-21) offers excellent psychometric stability in samples from various countries, data about its validity and reliability among Indian samples is not easily accessible. The current study presents these data from a sample consisting of urban Indians working in the global service sector.

Method : Two hundred and seventy four professionals working in highly paying service sector jobs in India completed the CISS-21. The data was analyzed using principal factor analysis and reliability analysis.

Results : Instead of the three-factor structure consisting of emotion-oriented, avoidance-oriented, and task-oriented coping strategies, a four-factor structure emerged. This resulting structure indicates that the current Indian sample perceived the task-oriented coping strategy as comprising of two distinct sub-factors: One involving cognitive-appraisal based mechanisms and another where a direct action-based approach is preferred.

Conclusion : among the Indian sample involved in the current study, CISS-21 appears to be a reliable and valid scale, albeit with a four instead of three factor structure. Naïve dialecticism and Biculturalism are presented and discussed as possible reasons for this unique factor structure.
MRA-Wavelet subspace architecture for logic, probability, and symbolic sequence processing
Authors: Greenhoe Daniel J.
Published: January 2018

The linear subspaces of a multiresolution analysis (MRA) and the linear subspaces of the wavelet analysis induced by the MRA, together with the set inclusion relation, form a very special lattice of subspaces which herein is called a "primorial lattice". This paper introduces an operator R that extracts a set of 2^{N-1} element Boolean lattices from a 2^N element Boolean lattice. Used recursively, a sequence of Boolean lattices with decreasing order is generated---a structure that is similar to an MRA. A second operator, which is a special case of a "difference operator", is introduced that operates on consecutive Boolean lattices L_2^n and L_2^{n-1} to produce a sequence of orthocomplemented lattices. These two sequences, together with the subset ordering relation, form a primorial lattice P. A logic or probability constructed on a Boolean lattice L_2^N likewise induces a primorial lattice P. Such a logic or probability can then be rendered at N different "resolutions" by selecting any one of the N Boolean lattices in P and at N different "frequencies" by selecting any of the N different orthocomplemented lattices in P. Furthermore, P can be used for symbolic sequence analysis by projecting sequences of symbols onto the sublattices in P using one of three lattice projectors introduced. P can be used for symbolic sequence processing by judicious rejection and selection of projected sequences. Examples of symbolic sequences include sequences of logic values, sequences of probabilistic events, and genomic sequences (as used in "genomic signal processing").
Representing SSR molecular marker profiles using concepts from Andean khipus
Authors: Simon Reinhard , Carhuapoma Pablo , Hualla Vilma , Ghislain Marc , de Mendiburu Felipe , Gomez Rene , Zorilla Cinthya , Roca William , de Haan Stef , Bonierbale Merideth
Published: January 2018

Genebanks increasingly use molecular markers for routine characterization of ex-situ collections and farmer managed diversity. The International Potato Center presently uses a SSR marker-kit to create molecular profiles for potato accessions. We identified a need for a compact graphical representation that allows comparative presentation of molecular diversity and accession characteristics - thereby permitting biologists and collection curators to have a simple means to interpret molecular data. Inspired by the ancient Andean qipus we devised a graph that standardizes representation while leaving room for updates of the marker kit and the collection of accessions. The molecular khipu permits combining and annotating a set of SSR loci with allele frequency and allele size distribution information. The design is flexible to incorporate updates on genetic diversity information. Graphical means facilitate reading of allele diversity information. As a compact graphical view it facilitates information storage and exchange. The SSR khipu will be useful to other genebanks and breeders. Software to create graphics in single or batch mode is available as R package ’khipu’.
GenomePeek - An online tool for prokaryotic and metagenome analysis
Authors: McNair Katelyn , Edwards Rob
Published: January 2018

As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach; where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.
The association between shame and substance misuse in young people: A review of the literature
Authors: Rahim Masuma , Patton Robert
Published: January 2018

BACKGROUND: Shame has been associated with a range of maladaptive behaviours, including substance abuse. Young people may be particularly vulnerable to heightened shame sensitivity, and substance abuse is a significant problem amongst UK adolescents. Although there appears to be a relationship between shame and substance abuse, the direction of the relationship remains unclear. AIM: We reviewed the literature relating to shame and substance abuse amongst young people. METHOD: Five electronic databases were searched for articles containing terms related to ‘adolescence’, ‘shame’ and ‘substance abuse’. Of the two hundred and twelve articles identified in the first sweep, six were included in the final analyses. RESULTS: Sexual abuse is indicated as a predictor of shame-proneness. Substance abuse may be a mechanism by which individuals cope with negative feelings. In general, there is a lack of literature investigating the shame-substance abuse relationship among adolescents. The available literature associates shame-proneness with poorer functioning and suggests that this may lead to psychopathology and early-onset substance misuse. Scant attention has been paid to the cognitive and emotional processes implicated. Further research is required to ascertain the strength of the shame-substance abuse relationship in young people and to develop appropriate interventions for this population.
Piecing together the biogeographic history of Chenopodium vulvaria L. using botanical literature and collections
Authors: Groom Quentin J
Published: January 2018

This study demonstrates the value of legacy literature and historic collections as a source of data on environmental history. Chenopodium vulvaria L. has declined in Northern Europe and is of conservation concern in several countries, whereas in other countries it has naturalised and is considered an alien weed. It is hypothesised that much of its former distribution was the result of repeated introductions from its native range in southern Europe and that its decline in northern Europe is the result of habitat change and a reduction in number of propagules imported to the north. An historical analysis of its ecology and distribution was conducted by mining legacy literature and historic botanical collections. Text analysis of habitat descriptions written on specimens and published in botanical literature covering a period of more than 200 years indicate that the habitat and introduction pathways of C. vulvaria have changed with time. Using the naturalised alien range in a climate niche model it is possible to project the range in Europe. By comparing this predicted model with a similar model created from all observations it is clear that there is a large discrepancy between the realised and predicted distributions. It is concluded that if C. vulvaria was native to northern Europe, then it was only ever a rare species, however it was more common in the 18th and 19th centuries due to a combination of repeated introductions and the creation of suitable habitats by people.
The first occurrence of the enigmatic archosauriform Crosbysaurus Heckert 2004 from the Chinle Formation of Southern Utah
Authors: Gay Robert J , St. Aude Isabella
Published: January 2018

Originally identified as an ornithischian dinosaur, Crosbysaurus harrisae has been found in New Mexico, Arizona, and its type locality in Texas, as well as in North Carolina. The genus has been reassessed by other workers in light of reinterpretations about the postcrania of another putative Triassic ornithischian, Revueltosaurus. The understanding of Triassic dental faunas has become more complicated by the extreme convergence between pseudosuchian archosaurs and ornithischian dinosaur dental morphologies. We report here on a new specimen of Crosbysaurus (MNA V10666) from the Chinle Formation at Comb Ridge in southeastern Utah. This new specimen is assigned to Crosbysaurus sp. on the basis of the unique compound posterior denticles, labiolingual width, and curvature. While MNA V10666 does not help resolve the affinities of Crosbysaurus, it does represent the extension of the geographic range of this taxon for approximately 250 kilometers. This is the first record of the genus Crosbysaurus in Utah and as such it represents the northernmost known record of this taxon. This indicates that Crosbysaurus was not limited to the southern area of the Chinle/Dockum deposition but instead was widespread across the Late Triassic paleoriver systems of western Pangea. The reported specimen was found in close association with a typical Late Triassic Chinle fauna, including phytosaurs, metoposaurs, and dinosauromorphs.
Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array
Authors: Zhang Xu , Mu Wenbo , Liu Cong , Zhang Wei
Published: January 2018

Genetic admixture has been utilized as a tool for identifying loci associated with complex traits and diseases in recently admixed populations such as African Americans. In particular, admixture mapping is an efficient approach to identifying genetic basis for those complex diseases with substantial racial or ethnic disparities. Though current advances in admixture mapping algorithms may utilize the entire panel of SNPs, providing ancestry-informative markers (AIMs) that can differentiate parental populations and estimate ancestry proportions in an admixed population may particularly benefit admixture mapping in studies of limited samples, help identify unsuitable individuals (e.g., through genotyping the most informative ancestry markers) before starting large genome-wide association studies (GWAS), or guide larger scale targeted deep re-sequencing for determining specific disease-causing variants. Defining panels of AIMs based on commercial, high-throughput genotyping platforms will facilitate the utilization of these platforms for simultaneous admixture mapping of complex traits and diseases, in addition to conventional GWAS. Here, we describe AIMs detected based on the Shannon Information Content (SIC) or Fst for African Americans with genome-wide coverage that were selected from ~2.3 million single nucleotide polymorphisms (SNPs) covered by the Affymetrix Axiom Pan-African array, a newly developed genotyping platform optimized for individuals of African ancestry.
Three-dimensional anatomy of the knee joint of ostriches (Struthio camelus)
Authors: Chadwick Kyle P , Regnault Sophie , Allen Vivian , Hutchinson John R.
Published: January 2018

The three-dimensional anatomy of the ostrich (Struthio camelus) knee (femorotibial, femorofibular, and femoropatellar) joint has scarcely been studied, and could elucidate certain mechanobiological properties of sesamoid bones. The adult ostrich is unique in that it has double patellae, while another similar ratite bird, the emu, has none. Understanding why these patellae form and what purpose they may serve is dually important for future studies on ratites as well as understanding mechanobiological characteristics of sesamoid bone development. For this purpose, we present a three-dimensional anatomical study of the ostrich knee joint, detailing osteology, ligaments and menisci, and myology. We have identified seven muscles which connect to the two patellae and compare our findings to past descriptions. These descriptions can be used to further study the biomechanical loading and implications of the double patella in the ostrich.
Distinct root-associated bacterial communities on three wild plant species growing in a common field
Authors: Aleklett Kristin , Leff Jonathan W , Fierer Noah , Hart Miranda
Published: January 2018

Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We sampled endophytic and epiphytic bacteria in root tissues from a population of a wild, clonal plant (Orange hawkweed – Pilosella aurantiaca) as well as two neighboring plant species (Oxeye daisy – Leucanthemum vulgare and Alsike clover – Trifolium hybridum) to determine if plant species hosted unique root microbiota. Our results show that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae) were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where gamma Proteobacteria and Acidobacteria occupied a larger portion of the community. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be explored.
BioNames: linking taxonomy, texts, and trees
Authors: Page Roderic D M
Published: January 2018

BioNames is a web database of taxonomic names for animals, linked to the primary literature and, wherever possible, to phylogenetic trees. It aims to provide a taxonomic "dashboard" where at a glance we can see a summary of the taxonomic and phylogenetic information we have for a given taxon and hence provide a quick answer to the basic question "what is this taxon?" BioNames combines classifications from the Global Biodiversity Information Facility (GBIF) and GenBank, imagery from the Encyclopedia of Life (EOL), animal names from the Index of Organism Names (ION), and bibliographic data from multiple sources including the Biodiversity Heritage Library (BHL) and CrossRef. The user interface includes display of full text articles, interactive timelines of taxonomic publications, and zoomable phylogenies. It is available at http://bionames.org.
Phylogenetic patterns of extinction risk: the need for critical application of appropriate datasets
Authors: Gereau Roy E. , Burgess Neil D. , Fjeldså Jon , Hall Jaclyn , Hemp Andreas , Jump Alistair S. , Kajuni Asukile R. , Marchant Robert A. , Marshall Andrew R. , Platts Philip J. , Taylor Charlotte M. , Tibazarwa Flora I.
Published: January 2018

In order to conduct a replicable analysis of the possible phylogenetic patterns of extinction risk, one must first formulate a clear set of definitions of ecosystem boundaries and risk categories. Subsequently, a robust and internally consistent dataset that includes all the available information on species distributions and risk assessments must be assembled. Here, we review the dataset and methodology of a recent paper focused on phylogenetic patterns of plant extinction risk in the Eastern Arc Mountains of Kenya and Tanzania and point out some of the limitations of inferring such patterns from inadequate and biased data. We show that bias in the dataset is probably responsible for the conclusion that Vulnerable species are more closely related than expected by chance, and provide guidelines for the construction of an appropriate dataset for such an analysis.
Association between intrinsic disorder and serine/threonine phosphorylation in Mycobacterium tuberculosis
Authors: Singh Gajinder P
Published: January 2018

Serine/threonine phosphorylation is an important mechanism to regulate protein function. In eukaryotes phosphorylation occurs predominantly in intrinsically disordered regions of proteins. While serine/threonine phosphorylation and protein disorder are much less prevalent in prokaryotes, M. tuberculosis has both high serine/threonine phosphorylation and disorder. Here I show that, similar to eukaryotes, serine/threonine phosphorylation sites in M. tuberculosis are highly enriched in intrinsically disordered regions, indicating similarity in substrate recognition mechanism of eukaryotic and M. tuberculosis kinases. Serine/threonine phosphorylation has been linked to the pathogenicity and survival of M. tuberculosis, thus better understanding of how its kinases recognize their substrates could have important implications in understanding and controlling the biology of this deadly pathogen.
Using empirical and simulated data to study the influence of environmental heterogeneity on fish species richness in two biogeographic provinces
Authors: Massicotte Philippe , Proulx Raphael , Cabana Gilbert , Rodriguez Marco
Published: January 2018

Loss of species richness in aquatic ecosystems is occurring rapidly and many factors, including habitat heterogeneity, have been suggested to affect the diversity of aquatic communities. We used fish community data (> 200 species) from extensive surveys conducted in two biogeographic provinces (extent > 1000 km) in North America to test the hypothesis that fish species richness is greater in more heterogeneous habitats (grain < 10 km2). Our tests are based on samples collected at nearly 800 stations over a period of five years. Using a set of environmental variables routinely measured by monitoring programs and a random placement model of community assembly, we demonstrate that fish species richness in coastal ecosystems is associated locally with the spatial heterogeneity of environmental variables but not with their magnitude. The observed effect of heterogeneity on species richness was substantially greater than that generated by simulations. Our modeling framework opens avenues for targeted conservation of habitat heterogeneity at broader temporal and spatial scales.