bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth series of one: case studies in time-transgressive morphology
Authors: Wedel Mathew J , Kraatz Brian P , Taylor Michael P , Vendetti Jann
Published: January 2018

The study of ontogeny in the fossil record is complicated by two main factors: growth series are not available for many taxa, and correctly assigning juveniles and adults to the same taxon is often difficult, especially where several related taxa coexisted. Ontogenetic change can also be revealed in single individuals whose morphology records characters from multiple ontogenetic stages. A snail shell is an intuitive example: the shell grows by accretion at its margin, starting from the larval shell (protoconch), and moving outward. Larval shell shape varies predictably between planktotrophic and non-planktotrophic lineages; and since the protoconch is embedded in the adult shell, larval ecology can be inferred in adults from the size and morphology of the retained protoconch. In many extinct lagomorphs, the occlusal surface of the molars changed markedly over the lifespan of an individual, as features such as enamel ridges were revealed and then obliterated by wear. In this case, the complete ‘stack’ of potential occlusal morphologies was present in the adult tooth as soon as it was done mineralizing, and further change progressively erased the ontogenetically early character states. In sauropodomorph dinosaurs, morphological complexity of the vertebrae increases along the cervical series. The simple morphology of anterior cervicals reflects both earlier ontogenetic stages and more primitive character states. More posterior vertebrae reveal the sequential formation of complex structures. Individuals that record multiple ontogenetic stages can help solve palaeobiological problems, such as inferring life histories, assessing ranges of variation, and determining the origin of complex morphological characters.
Wrangling categorical data in R
Authors: McNamara Amelia , Horton Nicholas J
Published: January 2018

Data wrangling is a critical foundation of data science, and wrangling of categorical data is an important component of this process. However, categorical data can introduce unique issues in data wrangling, particularly in real-world settings with collaborators and periodically-updated dynamic data. This paper discusses common problems arising from categorical variable transformations in R, demonstrates the use of factors, and suggests approaches to address data wrangling challenges. For each problem, we present at least two strategies for management, one in base R and the other from the ‘tidyverse.’ We consider several motivating examples, suggest defensive coding strategies, and outline principles for data wrangling to help ensure data quality and sound analysis.
Using a fast clustering method for viral segment lineage determination, applied to the H9 influenza hemagglutinin.
Authors: Dalby Andrew , Tinworth Lorna , Sealy Joshua , Iqbal Munir
Published: January 2018

Lineage determination is an important part of the analysis of viral sequence data. Previously this has depended on phylogenetic analysis in order to identify distinct clades within the phylogenetic trees. This method is time consuming and dependent on a set of empirical rules for clade identification. An alternative approach is to use clustering. Clustering is commonly used to identify operational taxonomic units in next generation sequencing data. In this paper we use clustering in order to rapidly identify viral segment lineages and clades without the need for tree construction.
Minimum time required to detect population trends: the need for long-term monitoring programs
Authors: White Easton R
Published: January 2018

Long-term time series are necessary to better understand population dynamics, assess species' conservation status, and make management decisions. However, population data are often expensive, requiring a lot of time and resources. When is a population time series long enough to address a question of interest? We determine the minimum time series length required to detect significant increases or decreases in population abundance. To address this question, we use simulation methods and examine 878 populations of vertebrate species. Here we show that 15-20 years of continuous monitoring are required in order to achieve a high level of statistical power. For both simulations and the time series data, the minimum time required depends on trend strength, population variability, and temporal autocorrelation. These results point to the importance of sampling populations over long periods of time. We argue that statistical power needs to be considered in monitoring program design and evaluation. Time series less than 15-20 years are likely underpowered and potentially misleading.
Hips, tips and sweet sweptback rays: Looking beyond traditional cranial characters in Pachycormiformes
Authors: Liston Jeff , Maltese Anthony E
Published: January 2018

A focus on cranial characters for determining relatedness is a predominant trait in many datasets, however this overemphasis can lead to distortion from sampler bias. We report on revised analyses of pachycormids - a key group within Actinopterygii, as part of the Holostei-Teleostei transition, which display a phyletic trend towards reduced skeletal ossification with the increased adult size of a pachycormid taxon. This reduced preservation potential for the axial skeleton makes it difficult not to base phylogenetic assumptions primarily on the limited skull material present. However, pachycormids show a remarkable conservatism in their dermatocranial anatomy, the few differences being useful for showing the separation of genera, but of little utility in working out broader intrafamilial relationships. The combination of a paucity of postcranial characters in the Late Cretaceous pursuit predator Protosphyraena with a poor knowledge about the skulls of suspension-feeding pachycormids (SFPs) had led to the absence of Early Cretaceous predatory pachycormids being interpreted as indicating a ghost lineage between Protosphyraena and the European Upper Jurassic taxa Orthocormus and Hypsocormus over an almost 50-million-year gap. However, the inclusion of several features from the pectoral and pelvic fins, supplemented by splanchnocranial characters, produces a much clearer picture that questions the traditional perception of a single carnivore lineage: Protosphyraena emerges as secondarily carnivorous from the SFPs’ tribe, mirroring 130 years of misidentification of North American Bonnerichthys specimens as Protosphyraena. Confirmation of this will rely on the further recovery of data concerning the skull morphology of SFPs.
Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits
Authors: Kayal Ehsan , Bastian Bentlage , Pankey M Sabrina , Ohdera Aki , Medina Monica , Plachetzki David C , Collins Allen , Ryan Joseph F
Published: January 2018

The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all-possible relationships among the major lineages have been proposed. The ecological success of Cnidaria is predicated on several fascinating organismal innovations including symbiosis, colonial body plans and elaborate life histories, however, understanding the origins and subsequent diversification of these traits remains difficult due to persistent uncertainty surrounding the evolutionary relationships within Cnidaria. While recent phylogenomic studies have advanced our knowledge of the cnidarian tree of life, no analysis to date has included genome scale data for each major cnidarian lineage. Here we describe a well-supported hypothesis for cnidarian phylogeny based on phylogenomic analyses of new and existing genome scale data that includes representatives of all cnidarian classes. Our results are robust to alternative modes of phylogenetic estimation and phylogenomic dataset construction. We show that two popular phylogenomic matrix construction pipelines yield profoundly different datasets, both in the identities and the functional classes of the loci they include, but resolve the same topology. We then leverage our phylogenetic resolution of Cnidaria to understand the character histories of several critical organismal traits. Ancestral state reconstruction analyses based on our phylogeny establish several notable organismal transitions in the evolutionary history of Cnidaria and depict the ancestral cnidarian as a solitary, non-symbiotic polyp that lacked a medusa stage. In addition, Bayes factor tests of multiple origins strongly suggest that symbiosis has evolved multiple times independently across the cnidarian radiation. Cnidaria have experienced more than 600 million years of independent evolution and in the process generated an array of organismal innovations. Our results add significant clarification on the cnidarian tree of life and the histories of these innovations. Further, we confirm the existence of Acraspeda (staurozoans plus scyphozoans and cubozoans), thus reviving an evolutionary hypothesis put forward more than a century ago.
Phylogenetic relationships and genetic diversity of the Polypedates leucomystax complex in Thailand
Authors: Buddhachat Kittisak , Suwannapoom Chatmongkon
Published: January 2018

Controversy in the taxonomic evaluation of the Asian tree frog Polypedates leucomystax complex presents the challenging task of gaining insight into its biogeographical distribution and diversification. Here, we describe the dispersion and genetic relationship of these species in Thailand where we connect the population of the P. leucomystax complex of the Sunda Islands to the mainland population based on the mitochondrial cytochrome c oxidase subunit I (COI) gene, derived from 266 samples. Our maternal genealogy implies that there are four well-supported lineages in Thailand, consisting of Northern A (clade A: Polypedates sp.), Nan (clade B: P. cf. impresus), Southern (clade C: P. cf. leucomystax) and Northern B (clade D: P. cf. megacephalus), with Bayesian posterior probability >0.9. Phylogeny and haplotype networks indicate that clades A, B and D are sympatric. In contrast, clade C (P. cf. leucomystax) and clade D (P. cf. megacephalus) are genetically divergent due to the geographical barrier of the Isthmus of Kra, resulting in allopatric distribution. Climatic conditions, in particular rainfall, that differ on each side of the Isthmus of Kra may play an important role in limiting the immigration of both clades. For the within-populations of either clades C or D, there was no significant correlation between geographic and genetic distance by the isolation-by-distance test, indicating intraspecific gene flow of each clade. Population expansion occurred in clade C, whereas clade D showed a constant population. Taken together, the P. leucomystax complex in Southeast Asia may be diversified by climatic oscillation, leading to allopatric and/or sympatric speciation.
Pheromones of three ambrosia beetles in the Euwallacea fornicatus species complex: ratios and preferences
Authors: Cooperband Miriam F , Cossé Allard A , Jones Tappey H , Carrillo Daniel , Cleary Kaitlin , Canlas Isaiah , Stouthamer Richard
Published: January 2018

Three cryptic species in the Euwallacea fornicatus species complex were reared in laboratory colonies and investigated for the presence of pheromones. Collections of volatiles from combinations of diet, fungus, beetles, and galleries from polyphagous shot hole borer (Euwallacea sp. #1) revealed the presence of 2-heneicosanone and 2-tricosanone only in the presence of beetles, regardless of sex. Subsequent examination of volatiles from the other two species, tea shot hole borer (Euwallacea sp. #2) and Kuroshio shot hole borer (Euwallacea sp. #5), revealed these two ketones were present in all three species but in different ratios. In dual choice olfactometer behavioral bioassays, mature mated females were strongly attracted to a synthetic binary blend of ketones matching their own natural ratios. However, females in each species were repelled by ketone blends in ratios corresponding to the other two species. Males of each species responded similarly to females when presented with ratios matching their own or the other two species. The presence of these compounds in the three beetle species, in ratios unique to each species, and their strong species-specific attraction and repellency, suggests they are pheromones. The ecological function of these pheromones is discussed. In addition to the pheromones, the previously known attractant (1S,4R)-p-menth-2-en-1-ol (also known as quercivorol) was discovered in the presence of the fungal symbionts, but not in association with the beetles. Quercivorol was tested in a dual-choice olfactometer and was strongly attractive to all three species. This evidence suggests quercivorol functions as a kairomone for members of the E. fornicatus species complex, likely produced by the symbiotic fungi.
Parameters tuning boosts hyperSMURF predictions of rare deleterious non-coding genetic variants
Authors: Petrini Alessandro , Schubach Max , Re Matteo , Frasca Marco , Mesiti Marco , Grossi Giuliano , Castrignanò Tiziana , Robinson Peter N , Valentini Giorgio
Published: January 2018

The regulatory code that determines whether and how a given genetic variant affects the function of a regulatory element remains poorly understood for most classes of regulatory variation. Indeed the large majority of bioinformatics tools have been developed to predict the pathogenicity of genetic variants in coding sequences or conserved splice sites. Computational algorithms for the prediction of non-coding deleterious variants associated with rare genetic diseases are faced with special challenges owing to the rarity of confirmed pathogenic mutations. Indeed in this context classical machine learning methods are biased toward neutral variants that constitute the large majority of genetic variation, and are not able to detect the potential deleterious variants that constitute only a tiny minority of all known genetic variation. We recently proposed hyperSMURF, hyper-ensemble of SMOTE Undersampled Random Forests, an ensemble approach explicitly designed to deal with the huge imbalance between deleterious and neutral variants, and able to significantly outperform state-of-the-art methods for the prediction of non-coding variants associated with Mendelian diseases. Despite its successful application to the detection of deleterious single nucleotide variants (SNV) as well as to small insertions or deletions (indels), hyperSMURF is a method that depends on several learning parameters, that strongly influence its overall performances. In this work we experimentally show that by tuning hyperSMURF parameters we can significantly boost the performance of the method, thus predicting with significantly better precision and recall rare SNVs associated with Mendelian diseases.
Extending R with C++: A Brief Introduction to Rcpp
Authors: Eddelbuettel Dirk , Balamuta James Joseph
Published: January 2018

R has always provided an application programming interface (API) for extensions. Based on the C language, it uses a number of macros and other low-level constructs to exchange data structures between the R process and any dynamically-loaded component modules authors added to it. With the introduction of the Rcpp package, and its later refinements, this process has become considerably easier yet also more robust. By now, Rcpp has become the most popular extension mechanism for R. This article introduces Rcpp, and illustrates with several examples how the Rcpp Attributes mechanism in particular eases the transition of objects between R and C++ code.
Code-free bioinformatics pipeline for building biological databases used to construct cardiovascular-SNPDB: an online database for SNPs associated with cardiovascular metabolites
Authors: Tarek Mohammad M
Published: January 2018

Biological databases are of great importance for managing biological research data. Building databases has been a code-based process that requires integrative coding skills of different languages. Herein, we present a code-free pipeline that helps biologists to build their databases with no need for coding skills providing searchable downloadable and editable databases using Google Apps. We provided an example for an online tool including a database of SNPs associated with cardiovascular Metabolites, allowing basic features like browsing, downloading, filtering and printing. We also described a stepwise pipeline for building such an interactive database. Cardiovascular-SNPDB was made available at : https://sites.google.com/view/cvdsnpdb/browse/ .
Forecasting at Scale
Authors: Taylor Sean J , Letham Benjamin
Published: January 2018

Forecasting is a common data science task that helps organizations with capacity planning, goal setting, and anomaly detection. Despite its importance, there are serious challenges associated with producing reliable and high quality forecasts — especially when there are a variety of time series and analysts with expertise in time series modeling are relatively rare. To address these challenges, we describe a practical approach to forecasting “at scale” that combines configurable models with analyst-in-the-loop performance analysis. We propose a modular regression model with interpretable parameters that can be intuitively adjusted by analysts with domain knowledge about the time series. We describe performance analyses to compare and evaluate forecasting procedures, and automatically flag forecasts for manual review and adjustment. Tools that help analysts to use their expertise most effectively enable reliable, practical forecasting of business time series.
Single cell transcriptomics view of cell lineage, cell fate and cellular differentiation
Authors: Ng Wenfa
Published: January 2018

Single cell studies increasing reveal myriad cellular subtypes beyond those postulated or observed through optical and fluorescence microscopy as well as DNA sequencing studies. While gene sequencing at the single cell level offer a path towards illuminating, in totality, the different subtypes of cells present, the technique nevertheless does not offer answers concerning the functional repertoire of the cell, which is defined by the collection of RNA transcribed from the genome. Known as the transcriptome, transcribed RNA defines the function of the cell as proteins or effector RNA molecules, while the genome is the collection of all information endowed in the cell type, expressed or not. Thus, a particular cell state, lineage, cell fate or cellular differentiation is more fully depicted by transcriptomic analysis compared to delineating the genomic context at the single cell level. While conceptually sound and could be analysed by contemporary single cell RNA sequencing technology and data analysis pipelines, the relative instability of RNA in view of RNase in the environment would make sample preparation particularly challenging, where degradation of cellular RNA by extraneous factors could provide a misinterpretation of specific functions available to a cell type. Hence, RNA as the de facto functional molecule of the cell defining the proteomics landscape as well as effector RNA repertoire, meant that RNA transcriptomics at the single cell level is the way forward if the goal is to understand all available cell types, lineage, cell fate and cellular differentiation. Given that a cell state is defined by the functions encoded by functional molecules such as proteins and RNA, single cell RNA sequencing offers a larger contextual basis for understanding cellular decision making and functions, for example, proteins are increasingly known to work in concert with RNA effector molecules in enabling a function. Hence, providing a view of the diverse cell types and lineages present in a body, single cell RNA sequencing is only hampered by the high sensitivity required to analyse the small amount of RNA available in single cells, as well as the perennial problem of RNA studies: how to prevent or reduce RNA degradation by environmental RNase enzymes. Ability to reduce RNA degradation would provide the cell biologist a unique view of the functional landscape of different cells in the body through the language of RNA.
The democratization of data science education
Authors: Kross Sean , Peng Roger D , Caffo Brian S , Gooding Ira , Leek Jeffrey T
Published: January 2018

Over the last three decades data has become ubiquitous and cheap. This transition has accelerated over the last five years and training in statistics, machine learning, and data analysis have struggled to keep up. In April 2014 we launched a program of nine courses, the Johns Hopkins Data Science Specialization, which has now had more than 4 million enrollments over the past three years. Here the program is described and compared to both standard and more recently developed data science curricula. We show that novel pedagogical and administrative decisions introduced in our program are now standard in online data science programs. The impact of the Data Science Specialization on data science education in the US is also discussed. Finally we conclude with some thoughts about the future of data science education in a data democratized world.
Human-Borg dynamics during a cybernetic alien invasion
Authors: Pabico Jaderick P
Published: January 2018

We propose a series of ODE systems to model the various dynamics of human-Borg interaction during a Borg invasion. These models, progressively developed one after the other, could provide humanity and other peace-loving intergalactic species the necessary mathematical tools to develop survival strategies in the event of future alien invasion. The Borg is a race of technologically-advanced cybernetic aliens and acts as a very powerful antagonist against the peace-loving human species in various Star Trek sci-fi story lines. Cybernetics, also called cyborgs, are organic individuals implanted with intelligent electromechanical devices for the purpose of increasing the individuals' efficiency by several degrees (e.g., strength, speed, and intelligence) but in the expense of procreation. Thus, the "parasitic" Borg needs to assimilate other species in an epidemiological manner for the survival of their own race.

In these models, humans can be transformed into one of six types depending on their reaction on or resistance to Borg assimilation. These are Susceptible (\(S\)), Captured (\(C\)), Assimilated (\(A\)), Rescued (\(R\)), Educated (or Rehabilitated, \(E\)), and Defiant (\(D\)). {\em Susceptible} humans can be captured and then assimilated into being a Borg drone. The remaining humans can rescue those who were captured or assimilated. Once rescued, they will undergo rehabilitation after which they either end up (again) susceptible to or strongly defiant from being captured and assimilated.

We start by describing the SCA model which has the same (analytical and/or numerical) solution to the Susceptible-Exposed-Infected model in epidemiology. Then we move on to the SCAR model which incorporates the tendency of humans to fight back by rescuing the captured or assimilated. SCARE further models the propensity of humans to educate (or rehabilitate) those whom they have rescued. Finally, we present the SCARED model which describes the natural inclinations of humans to either "relapse" to being susceptible to or grow being defiant against assimilation after undergoing rehabilitation. The numerical solutions to all these models will be presented using a popular yet simple computer software.

The SCA, SCAR, and SCARE models are reduction from the SCARED model when all the respective coefficients of the quantities not present in the reduced model are zero. In other words, SCA reduces from SCAR; SCA and SCAR both reduce from SCARE; and SCA, SCAR, and SCARE all reduce from SCARED. The bottomline is SCA \(\subset\) SCAR \(\subset\) SCARE \(\subset\) SCARED. The dynamics in the general SCARED model is governed by the system of ODEs shown (as a teaser) in the attached addendum.
Self-efficacy, relationship satisfaction, and social support: The quality of life of maternal caregivers of children with type 1 diabetes
Authors: Thorsteinsson Einar B , Loi Natasha M , Rayner Kylie
Published: January 2018

Objectives. To examine maternal functioning and wellbeing as important aspects of a family’s adaptation to chronic paediatric conditions, in particular, children with diabetes.

Method. This cross-sectional study investigated the difference between the perceived quality of life of mothers of children with diabetes (n=63) and mothers of children without diabetes (n=114). The study also examined the role of self-efficacy, relationship satisfaction, number of social support providers, and satisfaction with social support in predicting quality of life.

Results. Mothers who had a child with diabetes had lower quality of life measured by general health, vitality, social functioning, role-emotional, and mental health than mothers that did not have a child with diabetes. Self-efficacy, relationship satisfaction, and social support were significant predictors of quality of life (mental health domain).

Conclusion. In order to enhance their psychological wellbeing, mothers of children with diabetes require adequate psychosocial support. Other implications for research and potential interventions are discussed.
Bored bones from the terrestrial middle Cretaceous Kem-Kem beds of southeast Morocco
Authors: Shears-Ozeki Christina
Published: January 2018

During the last two decades, bioerosion of bone has become more widely investigated, with the earliest identified coming from mid-Triassic strata. Bioerosion has even been identified in bone fragments from a Jurassic theropod coprolite. Although the effects of this destructive process can lead to a loss of important information form the fossil record, understanding of bone bioerosion may be useful for identifying palaeoclimatic conditions in a variety of ancient fluvial settings.

Recent examination of bones of terrestrial fauna (mostly dinosaurs) form the middle Cretaceous Kem-Kem beds (?Albian-late Cenomanian) of southeast Morocco identified several distinctive bioerosional traces (surface scratches, bite marks [up to 10cm long] and borings in the form of channels and oval shaped chambers ~5mm diameter) from indeterminate producers. One heavily bored specimen suggests successive infestation during prolonged subaerial exposure.

Silicon moulding, thin sections and SEM analysis enabled investigation of the bones to determine the producers responsible, and evaluate their role in the taphonomy of ancient fluvial systems.

The bite marks can be attributed to macro predators/ scavengers, whereas the borings and surface scratches, are comparable to traces produced by recent insects including isopterans and the larvae of coleopterans. Scratches (approximately 1-2mm long) within the chambers and channels were also identified and considered fodinichnia and domichnia in the form of feeding trails and pupation chambers.
Modeling offensive player movement in professional basketball
Authors: Wu Steven , Bornn Luke
Published: January 2018

The 2013 arrival of SportVU player tracking data in all NBA arenas introduced an overwhelming amount of on-court information - information which the league is still learning how to maximize for insights into player performance and basketball strategy. Knowing where the ball and every player on the court are at all times throughout the course of the game produces almost endless possibilities, and it can be difficult figuring out where to begin. This article serves as a step-by-step guide for how to turn a data feed of one million rows of SportVU data from one NBA game into visualizable components you can use to model any player's movement. We detail some utility functions that are helpful for manipulating SportVU data before applying it to the task of visualizing player offensive movement. We conclude with visualizations of the resulting output for one NBA game, as well as what the results look like aggregated across an entire season for three NBA stars with very different offensive tendencies.
Extended SAC: A review and new algorithms of differential cryptanalysis of 4-bit s-boxes and strict avalanche criterion of BFs and 4-bit s-boxes again with a new extension to HO-SAC criterion
Authors: Dey Sankhanil , Ghosh Ranjan
Published: January 2018

Bitwise-Xor of two 4 bit binary numbers or 4-bit bit patterns entitled 4-bit differences carries information in Cryptography. The Method to Analyze Cryptographic cipher algorithms or 4-bit substitution boxes with 4-bit differences is known as Differential Cryptanalysis. In this paper a brief review of Differential Cryptanalysis of 4-bit bijective Crypto S-Boxes and a new algorithm to analyze them using 4-bit Boolean Functions (BFs) have been introduced. A brief review of Strict Avalanche Criterion (SAC) of 4-bit bijective Crypto S-Boxes and 4-bit BFs and two new algorithms of both the aforesaid criterions have been introduced in this paper. A New algorithm entitled extended Strict Avalanche Criterion (An Extension to Higher Order SAC or HO-SAC) has also been introduced. A new Analysis of Similarity of extended HO-SAC and Differential Cryptanalysis has also been elaborated in this paper.
Effects of accelerated ageing and cryopreservation on seeds and embryonic axes of Phaseolus vulgaris L and Arachis hypogaea L. Germination and seedlings vigor
Authors: Tacán Marcelo , Tapia César , Pérez César
Published: January 2018

The effects of artificial aging and cryopreservation methods on the germination of seeds and embryonic axes of Phaseolus vulgaris and Arachis hypogaea , were studied. Aging and cryopreservation treatments in bean seeds not affect the germination percentage, reaching values not significantly different from control. Germination percentage was higher when isolated embryonic axes were studied. Aging treatments gave rise to larger bean seedlings than the controls and cryopreservation treatments affected the size depending on the explant used. In groundnut seeds, aging treatments and cryopreservation positively affected germination and vigor of seedlings, but embryonic axes from not rehydrated aging seeds not germinate. Undried groundnut seeds not survive cryopreservation, while the dried ones showed a germination behavior superior to the control. Embryonic axes tolerate immersion in liquid nitrogen but when droplet-vitrification was used, formed callus instead of seedlings. Electrolyte leakage was always higher in embryonic axes than in seeds, both in beans and groundnut, and not to have a significant effect, under the conditions studied, on germination and vigor of seedlings. The present study evidences the possibility of cryopreserving, by simple procedures, germplasm of beans and groundnut, and to verify the aging tolerance of the seeds and embryonic axes of these important species.
Documenting and evaluating Data Science contributions in academic promotion in Departments of Statistics and Biostatistics
Authors: Waller Lance A
Published: January 2018

The dynamic intersection of the field of Data Science with the established academic communities of Statistics and Biostatistics continues to generate lively debate, often with the two fields playing the role of an upstart (but brilliant), tech-savvy prodigy and an established (but brilliant), curmudgeonly expert, respectively. Like any emerging discipline, Data Science brings new perspectives and new tools to address new questions requiring new perspectives on traditionally established concepts. We explore a specific component of this discussion, namely the documentation and evaluation of Data Science-related research, teaching, and service contributions for faculty members seeking promotion and tenure within traditional departments of Statistics and Biostatistics. We focus on three perspectives: the department chair nominating a candidate for promotion, the junior faculty member going up for promotion, and the senior faculty members evaluating the promotion package. We contrast conservative, strategic, and iconoclastic approaches to promotion based on accomplishments in Data Science.
Genetic and genomic monitoring with minimally invasive sampling methods
Authors: Carroll Emma L , Bruford Michael , DeWoody J. Andrew , Leroy Gregoire , Strand Allan , Waits Lisette , Wang Jinliang
Published: January 2018

Emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g. collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically-driven declines, which are unlikely to abate without intensive management efforts that often include MIS approaches. Here we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy datasets and recommend how to address the challenges of moving between traditional and next generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
Chemical properties and fertility analysis of dredger-fill silt during soil formation: The tianjin dredge–fill project
Authors: Sui Xin , Gu Huijun , Zhang Guogang , Jia Meiqing
Published: January 2018

Dredger-fill silt has been used in the port of Tianjin, China to reclaim land; however, the dredger-fill silt has no soil ecological function. Translating the silt into soil rapidly and accelerating the soil-forming process are key to solving the ecological problems of the Dredge–Fill project. This study measured 15 chemical properties of the dredger-fill silt for 8 years of the soil forming process to explore fertility changes and the critical factors affecting soil formation. The results showed that: (1) the salinity of silt changed from severe to mild with a reduction in Na+ and Cl- concentration. Other ion concentrations changed slightly. (2) Effective nutrients significantly decreased during soil formation. Soil organic matter (SOM)，the nitrate-nitrogen, available phosphorus (A-P) and available potassium (A-K) decreased by 26.22%, 86.23%, 45.92%, 33.61% respectively, indicating severe nutrients loss. (3) Principal component analysis showed that silt fertility decreased significantly and the total soil fertility loss was severe. This study has significance for the artificial improvement of silt.
A bioinformatics and network analysis framework to find novel therapeutics for autoimmunity
Authors: Banerjee Soumya
Published: January 2018

The immune system protects a host from foreign pathogens. In rare cases, the immune system can attack the cells of the host organism causing autoimmune diseases. We outline a computational framework that combines bioinformatics and network analysis with an emerging targets platform. The computational framework presented here can be used to find drug targets for autoimmune diseases. It can also be used to find existing drugs that can be repurposed to treat autoimmune diseases based on networks of interactions or similarities between different diseases. Information on which gene regions are associated with the disease (single nucleotide polymorphisms) can be used in gene therapy when that technique becomes viable. Our analysis also revealed immune cell subtypes that are implicated in these diseases. These immune cell subtypes can be selected for immunotherapy experiments. Finally, our analysis also reveals intra-cellular and protein-protein interaction networks and pathways that can be targeted with small molecule inhibitors. The downstream off-target effects of these inhibitors can also be determined from such a network analysis. In summary, our computational framework can be used to find novel therapeutics for autoimmune diseases and potentially even other dysfunctions.
Agricultural constraints on microbial resource use and niche breadth in drainage ditches
Authors: Hunting Ellard R , Barmentlo Henrik , Schrama Maarten , van Bodegom Peter , Zhai Yujia , Vijver Martina
Published: January 2018

Background. Microorganisms govern important ecosystems processes, in particular the degradation of organic matter (OM). However, microorganisms are rarely considered in efforts to monitor ecosystem health and functioning. Evidence suggests that environmental perturbations can adversely affect microbial communities and and their ability to use available substrates. However, whether impacted microbial efficiencies in extracting and utilizing the available resources (resource niche breadth) translate to changes in organic matter (OM) degradation in natural systems remains poorly understood.

Methods. Here we evaluated effects of differences in organic matter (OM) related to agricultural land use (OM derived from ditches adjacent to grasslands, bulb fields and a pristine dune area) on microbial functioning. We specifically assessed 1) resource niche breadths of microbial communities during initial community assembly in laboratory microcosms and already established natural communities, and 2) how changes in community resource niche breadth translates to the degradation of natural OM.

Results. A disparity existed between microbial resource niche breadth in laboratory incubations and natural microbial communities. Resource utilization and niche breadth of natural microbial communities was observed to be constrained in drainage ditches adjacent to agricultural fields. This outcome coincides with retarded degradation of natural OM collected from ditches adjacent to hyacinth bulb fields. Microbial communities in bulb field ditches further showed functional redundancy when offered grassland OM of seemingly higher substrate quality.

Discussion. Results presented in this study suggest that agricultural practices can impose constraints on microbial functional diversity by reducing OM resource quality, which can subsequently translate to confined microbial resource niche differentiation and reduced organic matter degradation rates. This hints that assessments of actual microbial resource utilization and niche differentiation could potentially be used to assess the ecological health and functioning of natural communities.
Morphological convergence in ‘river dolphin’ skulls: a disparate grouping justified
Authors: Page Charlotte E , Cooper Natalie
Published: January 2018

Convergent evolution can provide insights into the predictability of, and constraints on, the evolution of biodiversity. One striking example of convergence is seen in the ‘river dolphins’. The four dolphin genera that make up the ‘river dolphins’ (Inia geoffrensis, Pontoporia blainvillei, Platanista gangetica and Lipotes vexillifer) do not represent a monophyletic group, despite being very similar in morphology. This has led many to using the ‘river dolphins’ as an example of convergent evolution. However, these morphological similarities have never been quantified. We investigate whether the skulls of the four ‘river dolphin’ genera are convergent when compared to other toothed dolphin taxa. We use geometric morphometrics to uncover shape variation in the skulls of the ‘river dolphins’ and then apply a number of phylogenetic techniques to test for convergence. We find significant convergence in the skull morphology of the ‘river dolphins’. The four genera seem to have experienced evolution in the same direction, leading to a convergent morphotype characterised by elongation of skull features. The cause of this morphological convergence remains unclear, but our results support hypotheses of shared feeding mode or diet and thus provide the foundation for future work into convergence within the Odontoceti.
PlantCV v2.0: Image analysis software for high-throughput plant phenotyping
Authors: Gehan Malia A , Fahlgren Noah , Abbasi Arash , Berry Jeffrey C , Callen Steven T , Chavez Leonardo , Doust Andrew N , Feldman Max J , Gilbert Kerrigan B , Hodge John G , Hoyer J Steen , Lin Andy , Liu Suxing , Lizárraga César , Lorence Argelia , Miller Michael , Platon Eric , Tessman Monica , Sax Tony
Published: January 2018

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.
Foliar microbiome transplants confer disease resistance in a critically-endangered plant
Authors: Zahn Geoffrey , Amend Anthony S
Published: January 2018

There has been very little effort to incorporate foliar microbiomes into plant conservation efforts even though foliar endophytes are critically important to the fitness and function of hosts. Many critically endangered plants that have been extirpated from the wild are dependent on regular fungicidal applications in greenhouses that cannot be maintained for remote out-planted populations, which quickly perish. These fungicides negatively impact potentially beneficial fungal symbionts, which may reduce plant defenses to pathogens once fungicide treatments are stopped. We conducted experiments to test total foliar microbiome transplants from healthy wild relatives onto fungicide-dependent endangered plants in an attempt to mitigate disease and reduce dependency on fungicides. Plants were treated with total microbiome transplants or cultured subsets of this community and monitored for disease severity. High-throuhgput DNA screening of fungal ITS1 rDNA was used to track the leaf-associated fungal communities and evaluate the effectiveness of transplantation methods. Individuals receiving traditionally isolated fungal treatments showed no improvement, but those receiving applications of a simple leaf slurry containing an uncultured fungal community showed significant disease reduction, to which we partially attribute an increase in the mycoparasitic Pseudozyma aphidis. These results were replicated in two independent experimental rounds. Treated plants have since been moved to a native habitat and, as of this writing, remain disease-free. Our results demonstrate the effectiveness of a simple low-tech method for transferring beneficial microbes from healthy wild plants to greenhouse-raised plants with reduced symbiotic microbiota. This technique was effective at reducing disease, and in conferring increased survival to an out-planted population of critically endangered plants. It was not effective in a closely related plant. Plant conservation efforts should strive to include foliar microbes as part of comprehensive management plans.
Effect of shinbuto and ninjinto on prostaglandin E2 production in lipopolysaccharide-treated human gingival fibroblasts
Authors: Ara Toshiaki , Sogawa Norio
Published: January 2018

Previously, we revealed that several kampo medicines which are used for the patients with excess and/or medium patterns [kakkonto (TJ-1), shosaikoto (TJ-9), hangeshashinto (TJ-14), and orento (TJ-120)] decreased prostaglandin (PG)E2 by LPS-treated human gingival fibroblasts (HGFs). Currently, we examined other kampo medicines which are used for the patients with deficiency pattern [bakumondoto (TJ-29), shinbuto (TJ-30), ninjinto (TJ-32), and hochuekkito (TJ-41)] and the herbs which construct shinbuto and ninjinto using the same experimental model. Shinbuto and ninjinto concentration-dependently decreased LPS-induced PGE2 production by HGFs, whereas hochuekkito weakly decreased and bakumondoto did not decrease PGE2 production. Shinbuto and ninjinto did not alter cyclooxygenase (COX) activities and the expressions of molecules involved in arachidonic acid cascade. Next, we examined which herbs constructing shinbuto and ninjinto decrease LPS-induced PGE2 production. Among these herbs, shokyo (Zingiberis Rhizoma) and kankyo (Zingiberis Processum Rhizoma) strongly and concentration-dependently decreased LPS-induced PGE2 production. However, both shokyo and kankyo did not alter the expressions of molecules involved in arachidonic acid cascade. These results suggest that shokyo and kankyo suppress phospholipase (PL)A2 activity. We demonstrated that kampo medicines for the patients with deficiency pattern may suppress inflammatory responses in addition to those with excess and medium patterns. Moreover, kampo medicines which contain shokyo or kankyo are considered to be effective for the treatment of the inflammatory diseases.
MTopGO: a tool for module identification in PPI Networks
Authors: Vella Danila , Marini Simone , Vitali Francesca , Bellazzi Riccardo
Published: January 2018

The increasing amount of -omics data leads to development of models to interpret and analyse them. A common approach consists in representing data as PPI Networks. These models can be very complex and informatics tools are needed to analyse them. In this abstract, we present MTopGO, an algorithm of module detection specific for PPI Network, exploiting both the network topological information and the Gene Ontology (GO) knowledge about network proteins. MTopGO output consists in a network partition, where each obtained cluster is labelled with a specific GO term describing its biological nature. In a single step, MTopGO performs a double PPI network analysis; from a topological perspective, through the individuation of a meaningful network partition and, from a biological perspective, through the selection of significant GO terms describing the biological role of network proteins.