bluuebunny/crossref_metadata_2025 huggingface dataset:
The importance of sponges and mangroves in supporting fish communities in degraded coral reefs in Caribbean Panama
Authors: Seemann Janina , Yingst Alexandra , Stuart-Smith Rick D , Edgar Graham J , Altieri Andrew H
Published: January 2018

Fish communities associated with coral reefs worldwide are threatened by overexploitation and other human impacts such as bleaching events that cause habitat degradation. We assessed the fish community on coral reefs on the Caribbean coast of Panama, as well as those associated with mangrove and seagrass habitats, to explore the influences of habitat cover, connectivity and environmental characteristics in sustaining biomass, richness and trophic structure in a degraded tropical ecosystem. Overall, 94 % of all fishes across all habitat types were of small body size (≤11 cm), with communities dominated by fishes that usually live in habitats of low complexity, such as Pomacentridae (damselfishes) and Gobiidae (gobies). Moreover, total fish biomass was very low, small fishes from low trophic levels were over-represented, and top predators were under-represented relative to other Caribbean reefs. For example, herbivorous/omnivorous/detrivorous fishes (trophic level 2-2.7) comprised 37 % of total fish biomass, with the diminutive parrotfish Scarus iseri comprising 72 % of the parrotfish biomass. However, the abundance of sponges and proximity of mangroves were found to be important positive drivers of reef fish richness, biomass and trophic structure on a given reef, presumably by promoting functional processes of ecosystems. The masked goby (Coryphopterus personata) was a strong indicator of reef degradation, apparently benefiting from the reduced density of large predators on local reefs. The damselfish Abudefduf saxatilis was more common on reefs with high sponge cover, and also to proximity to mangroves. Our study suggests that a diverse fish community can persist on degraded coral reefs, and that the availability of habitat forming organisms other than corals, including sponges and mangroves, and their arrangement on the landscape, is critical to the maintenance of functional processes in these ecosystems.
Osmotic pressure characterization of glycosaminoglycans using full-atomistic molecular models
Authors: Pando Alejandro , Rigoldi Federica , Vesentini Simone
Published: January 2018

The osmotic pressure of chondroitin sulfate glycosaminoglycans (CS-GAGs) in a simulated physiological environment of articular cartilage is thoroughly examined in silico using full atomistic models. The effects of chemical and physical properties were investigated to elucidate the molecular origins of cartilage biomechanical behavior providing single-atomistic resolution analyses which would not be attainable with in vivo or in in vitro techniques. CS-GAG chains exhibit plastic deformation behavior under compressive load in the extracellular matrix (ECM) and osmotic pressure is the main contributor in balancing external pressures. This study focuses on quantitatively expressing this contribution. Molecular dynamics was used to imitate the physiological environment experienced by GAGs inside articular cartilage by simulating a semipermeable membrane acting on the full atomistic chains during compression. To this end, a variety of validation techniques, pre-simulation tasks, and comparisons were conducted to validate the test methodology. CS-GAGs with varying lengths and sulfation positions underwent simulation under varying molar concentrations. Sulfation positioning is found to have negligible influence on GAG osmotic pressure behavior; attributed to the small distance between the position of 4- and 6- sulfation relative to the intermolecular spacing between the CS chains. However, differences between sulfated and unsulfated chains did have a significant influence on osmotic pressure. Length of disaccharides was also found to have a significant contribution to osmotic pressure. Measurements are comparable to previous coarse grained studies and experimental data.
Conceptual and empirical advances in Neotropical biodiversity research
Authors: Antonelli Alexandre , Ariza María , Albert James , Andermann Tobias , Azevedo Josué , Bacon Christine , Faurby Søren , Guedes Thais , Hoorn Carina , Lohmann Lucia , Matos-Maraví Pavel , Ritter Camila , Sanmartín Isabel , Silvestro Daniele , Tejedor Marcelo , ter Steege Hans , Tuomisto Hanna , Werneck Fernanda , Zizka Alexander , Edwards Scott
Published: January 2018

The outstanding biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in the generation of biodiversity data, many questions remain to be answered. In this review, we first summarize some of the knowns and unknowns about Neotropical biodiversity, and discuss how human impact may have drastically affected some of the patterns observed today. We then link biodiversity to landscape, and outline major advances in biogeographical research. In particular, we argue that it is crucial to test the effect of landscape and climatic evolution to biotic diversification and distribution in order to achieve a comprehensive understanding of current patterns. In this context, it is also important to consider extant and extinct taxa, as well as to use probabilistic and parametric methods that explicitly include landscape evolution models. We subsequently explore different scales in Neotropical biogeography, focusing on the intersection between biogeography and community ecology, both of which often address similar questions from different angles. The concepts of community assembly, island biogeography, neutral processes, and ecological interactions are then discussed as important components of the complex processes that determine the patterns observed today. Single-taxon and cross-taxonomic studies are complementary and greatly needed, but achieving synthesis remains challenging. Finally, we argue that phylogenetic approaches hold great potential to connect across taxonomic, spatial and temporal scales, despite current difficulties to generate and cross-analyze large volumes of molecular data. We conclude by outlining major prospects and hindrances for further advancing our knowledge on the rich Neotropical biodiversity.
Maxent-directed field surveys identify new populations of narrowly endemic habitat specialists
Authors: Rhoden Cody M , Peterman William E , Taylor Christopher A
Published: January 2018

Background. Rare or narrowly endemic organisms are difficult to monitor and conserve when their total distribution and habitat preferences are incompletely known. One method employed in determining distributions of these organisms is species distribution modeling (SDM).

Methods. Using two species of narrowly endemic burrowing crayfish species as our study organisms, we sought to ground validate Maxent, a commonly used program to conduct SDMs. We used fine scale (30 m) resolution rasters of pertinent habitat variables collected from historical museum records in 2014. We then ground validated the Maxent model in 2015 by randomly and equally sampling the output from the model.

Results. The Maxent models for both species of crayfish showed positive relationships between predicted relative occurrence rate and crayfish burrow abundance in both a Receiver Operating Characteristic and generalized linear model approach. The ground validation of Maxent led us to new populations and range extensions of both species of crayfish.

Discussion. We conclude that Maxent is a suitable tool for the discovery of new populations of narrowly endemic, rare habitat specialists and our technique may be used for other rare, endemic organisms.
Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing
Authors: Csizmár Nikolett , Mihók Sándor , Jávor András , Kusza Szilvia
Published: January 2018

Background. Hungarian draft is a horse breed with a recent mixed ancestry. The interest in their conservation and characterization has increased over the last few years. It was developed in the 1920s by crossing local mares with draught horses imported from France and Belgium. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks.

Methods. To genetically characterize the breed and to set up the basis for a conservation programme, in this present study a hypervariable region of the mithocrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed.

Results. One hundred and sixty-four haplotypes were revealed. Thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (Hd=0.954±0.004; π=0.028±0.0004) were identified in Hungarian populations, although they were higher within than among the total number of breeds (Hd =0.972±0.002; π=0.03097±0.002). Fourteen of the previously observed seventeen haplogroups were detected.

Discussion. Our samples showed a large intra- and interbreed variation. There were no clear clustering on the median joining tree. The overall information given in this work led us to consider that the genetic scenario of this breed is more likely to be due to ‘ancestrally’ different genetic backrounds. This study could contribute to the development of a detailed breeding plan of Hungarian draft horse and help to formulate its genetic conservation plan, with the aim of increasing the population size, but avoiding inbreeding while, on the other hand, also facilitating genetic exchange among the populations.
Predicting context specific enhancer-promoter interactions from ChIP-Seq time course data
Authors: Dzida Tomasz , Iqbal Mudassar , Charapitsa Iryna , Reid George , Stunnenberg Henk , Matarese Filomena , Honkela Antti , Rattray Magnus
Published: January 2018

We have developed a machine learning approach to predict context specific enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERα binding. We use the method to identify a genome-wide confident set of ERα target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERα binding proximity alone.
Comparing enzyme activity modifiers equations through the development of global data fitting templates in Excel
Authors: Walsh Ryan
Published: January 2018

The classical way of defining enzyme inhibition has obscured the distinction between inhibitory effect and the inhibitor binding constant. This article examines the relationship between the simple binding curve used to define biomolecular interactions and the standard inhibitory term (1+([I]/Ki)). By understanding how this term relates to binding curves which are ubiquitously used to describe biological processes, a modifier equation which distinguishes between inhibitor binding and the inhibitory effect, is examined. This modifier equation which can describe both activation and inhibition is compared to standard inhibitory equations with the development of global data fitting templates in Excel, and via the global fitting of these equations to previously reported enzyme kinetic data. This equation and the template developed in this article should prove to be useful tools in the study of enzyme inhibition and activation.
Ancient mitogenomes of Argentine Patagonia (6070-310 YBP) reveal the early contribution of lineages not previously found in South America
Authors: Parolin Maria Laura , Fregel Lorenzo Rosa Irene , Bravi Claudio Marcelo , Mendez Fernando Luis , Dahinten Silvia Lucrecia , Gómez-Otero Julieta , Shapiro Beth , Green Richard Edward , Tamburrini Camila , Basso Nestor Guillermo , Bustamante Carlos
Published: January 2018

Patagonia, a cul-de-sac for the continental dispersal of Homo sapiens into the Americas, has been extensively analyzed by archaeologists and bioanthropologists. Despite its deep and rich archaeological record, the genetic make up of its pre-contact inhabitants is barely known. We present the analysis of 19 mitogenomes recovered by NGS from archaeological sites in Central Patagonia (Chubut, Argentina). 15 are pre-contact samples, (6,010-770YBP), and four are samples from historical times (550-310YBP). Preservation of the samples was extraordinary, with endogenous DNA values up to 68%. Preliminary analysis indicates that mtDNA genomes. Central Patagonia belong to haplogroups B2 (21%), C1b (21%), C1c (5%), D1 (47%) and D4h3a (5%). This is surprising when compared with a database of 19,000 control region sequences and >2,100 mitogenomes of Native American origin: 1) While modern indigenous populations from Northern and Central Patagonia of Argentina and Chile derive 41-54% of their maternal lineages from clades B2i2 and C1b13, none of these are present in our dataset; 2) 75% of our B2 and C1b lineages share derived polymorphism with lineages so far known to be present only in modern Central-Western Argentina; and 3) although modern Patagonians carry the highest continental frequencies of D1g, the ancient set is enriched mostly in D1g5, a lineage widely distributed from South-Central Andes to Tierra del Fuego (including two samples with private motifs not described before). The upcoming analysis of the nuclear portion of these samples will help us better understand migratory and admixture processes in the Patagonian region.
Tolerance: the forgotten child of plant resistance
Authors: Peterson Robert K , Varella Andrea C , Higley Leon G
Published: January 2018

Plant resistance against insect herbivory has greatly focused on antibiosis, whereby the plant has a deleterious effect on the herbivore, and antixenosis, whereby the plant is able to direct the herbivore away from it. Although these two types of resistance may reduce injury and yield loss, they can produce selection pressures on insect herbivores that lead to resistance. Tolerance, on the other hand, is a more sustainable pest management strategy because it involves only a plant response and therefore does not cause evolution of resistance in target pest populations. Despite its attractive attributes, tolerance has been poorly studied and understood. In this critical, interpretive review, we discuss tolerance to insect herbivory and the biological and socioeconomic factors that have limited its use in plant resistance and integrated pest management. First, tolerance is difficult to identify, and the mechanisms conferring it are poorly understood. Second, the genetics of tolerance are mostly unknown. Third, several obstacles hinder the establishment of high-throughput phenotyping methods for large-scale screening of tolerance. Fourth, tolerance has received little attention from entomologists because, for most, their primary interest, research training, and funding opportunities are in mechanisms which affect pest biology, not plant biology. Fifth, the efforts of plant resistance are directed at controlling pest populations rather than managing plant stress. We conclude this paper by discussing future research and development activities.
Sci-Hub provides access to nearly all scholarly literature
Authors: Himmelstein Daniel S , Romero Ariel R , McLaughlin Stephen R , Greshake Tzovaras Bastian , Greene Casey S
Published: January 2018

The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent of Sci-Hub's coverage was unclear. As of March 2017, we find that Sci-Hub's database contains 68.9% of all 81.6 million scholarly articles, which rises to 85.2% for those published in closed access journals. Furthermore, Sci-Hub contains 77.0% of the 5.2 million articles published by inactive journals. Coverage varies by discipline, with 92.8% coverage of articles in chemistry journals compared to 76.3% for computer science. Coverage also varies by publisher, with the coverage of the largest publisher, Elsevier, at 97.3%. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. Finally, we estimate that over a six-month period in 2015–2016, Sci-Hub provided access for 99.3% of valid incoming requests. Hence, the scope of this resource suggests the subscription publishing model is becoming unsustainable. For the first time, the overwhelming majority of scholarly literature is available gratis to anyone with an Internet connection.
Sci-Hub provides access to nearly all scholarly literature
Authors: Himmelstein Daniel S , Romero Ariel R , McLaughlin Stephen R , Greshake Tzovaras Bastian , Greene Casey S
Published: January 2018

The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent of Sci-Hub’s coverage was unclear. As of March 2017, we find that Sci-Hub’s database contains 68.9% of all 81.6 million scholarly articles, which rises to 85.2% for those published in toll access journals. Coverage varies by discipline, with 92.8% coverage of articles in chemistry journals compared to 76.3% for computer science. Coverage also varies by publisher, with the coverage of the largest publisher, Elsevier, at 97.3%. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. We find Sci-Hub preferentially covers popular, paywalled content, containing 96.2% of citations to toll access journals since 2015. For recently requested articles by Unpaywall users, oaDOI provided access to 48.8% whereas Sci-Hub contained 81.5%. Together, oaDOI and Sci-Hub covered 94.1%, demonstrating that gaps in Sci-Hub’s coverage, especially for open access articles, can be filled using licit services. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection. Sci-Hub’s scope suggests the subscription publishing model is becoming unsustainable.
RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages
Authors: Morozov Sergey Y. , Lazareva Ekaterina A. , Solovyev Andrey G.
Published: January 2018

Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional domains and an additional helicase domain, were found to be preserved in many families during the evolution of the order Lepidoptera. In the present paper, in species of orders Hemiptera and Orthoptera, we found helicase domain-encoding sequences integrated into ORF1 of retrotransposons of the Jockey family. RNA helicases encoded by transposons of TRAS and Jockey families represented separate brunches in a phylogenetic tree of helicase domains and thus could be considered as independently originated in the evolution of insect transposons. Transcriptome database analyses revealed that both TRAS and Jockey transposons encoding the helicase domain represented transcribed genome sequences. Moreover, the transposon-encoded helicases were found to contain the full set of conserved motifs essential for their enzymatic activities. Taking into account the previously reported ability of RNA helicase encoded by TRAS ORF2 to suppress post-transcriptional RNA silencing, we propose possible scenarios of evolutionary fixation of actively expressed functional helicases of viral origin in insect retrotransposons as genetic elements advantageous for both transposons and their insect hosts.
The data and analysis underlying NIH’s decision to cap research support lacked rigor and transparency: a commentary
Authors: Janssens A Cecile JW , Miller Gary W , Narayan K Venkat
Published: January 2018

The US National Institutes of Health (NIH) recently announced that they would limit the number of grants per scientist and redistribute their funds across a larger group of researchers. The policy was withdrawn a month later after criticism from the scientific community. Even so, the basis of this defunct policy was flawed and it merits further examination. The amount of grant support would have been quantified using a new metric, the Grant Support Index (GSI), and limited to a maximum of 21 points, the equivalent of three R01 grants. This threshold was decided based upon analysis of a new metric of scientific output, the annual weighted Relative Citation Ratio, which showed a pattern of diminishing returns at higher values of the GSI. In this commentary, we discuss several concerns about the validity of the two metrics and the quality of the data that the NIH had used to set the grant threshold. These concerns would have warranted a re-analysis of new data to confirm the legitimacy of the GSI threshold. Data-driven policies that affect the careers of scientists should be justified by nothing less than a rigorous analysis of high-quality data.
A Mixed Graph Framework to evaluate the complementarity of communication Tools
Authors: Carvalho Leonardo , Bezerra Eduardo , Guedes Gustavo , Assis Laura , Lima Leonardo , Barbastefano Rafael , Ziviani Artur , Porto Fabio , Ogasawara Eduardo
Published: January 2018

Due to the constant innovations in communications tools, several organizations are constantly evaluating the adoption of new communication tools (NCT) with respect to current ones. Especially, many organizations are interested in checking if NCT is really bringing benefits in their production process. We can state an important problem that tackles this interest as for how to identify when NCT is providing a significantly different complementary communication flow with respect to the current communication tools (CCT). This paper presents the Mixed Graph Framework (MGF) to address the problem of measuring the complementarity of a NCT in the scenario where some CCT is already established. We evaluated MGF using synthetic data that represents an enterprise social network (ESN) in the context of well-established e-mail communication tool. Our experiments observed that the MGF was able to identify whether a NCT produces significant changes in the overall communications according to some centrality measures.
A novel animal model for neuroinflammation and white matter degeneration
Authors: Ji Baohu , Higa Kerin , Soontornniyomkij Virawudh , Miyanohara Atsushi , Zhou Xianjin
Published: January 2018

Small interference RNA has been widely used to suppress gene expression. Three different short-hairpin RNAs (shRNAs) against dopamine D1 receptor (Drd1), driven by mouse U6 promoter in self-complementary AAV8 vector (scAAV8), were used to silence mouse striatal Drd1 expression. Transduction of mouse striatum with all 3 scAAV8-D1shRNA virus, but not the control scAAV8 virus, causes extensive neuroinflammation, demyelination, and axon degeneration. RNA interference is known to be coupled to the innate immune system as a host cell defense against virus infection. Activation of the innate immune system may play a causal role in the development of neuroinflammation and white matter degeneration, providing a novel animal model for multiple sclerosis (MS) and other neuroinflammatory diseases.
Seasonality of cellulitis: evidence from Google Trends
Authors: Zhang Xin , Dang Shuangsuo , Ji Fanpu , Bao Xiongxiong , Wang Wenjun
Published: January 2018

According to our clinical experience, cellulitis is common in summer; however, very few studies have mentioned this trend. Using Google Trends, we analyzed the monthly data of Google searches for ‘cellulitis’ from 31 countries on six continents. Seasonality explained 34%-92% of the variability in search volume, with peaks occurring in summer months. The analyses offered new insights into the epidemiology of cellulitis on national and international scales. Clinical data are needed to validate the Internet search data.
Effects of perceptual similarity but not semantic association on false recognition in aging
Authors: Burnside Kayleigh , Hope Caroline , Gill Emma , Morcom Alexa M
Published: January 2018

This study investigated semantic and perceptual influences on false recognition in older and young adults in a variant on the Deese-Roediger-McDermott paradigm. In two experiments, participants encoded intermixed sets of semantically associated words, and sets of unrelated words. Each set was presented in a shared distinctive font. Older adults were no more likely to falsely recognize semantically associated lure words compared to unrelated lures also presented in studied fonts. However, they showed an increase in false recognition of lures which were related to studied items only by a shared font. The data show that older adults do not always rely more on prior knowledge in episodic memory tasks. They converge with other findings suggesting that older adults may also be more prone to perceptually-driven errors.
Geraniales Phylogeny Poster (GPP)
Authors: Jeiter Julius , Cole Theodor C H , Hilger Hartmut H
Published: January 2018

The Geraniales Phylogeny Poster (GPP) depicts the phylogenetic relationships between the five families of the order recognized here: Geraniaceae, Hypseocharitaceae, Vivianiaceae, Francoaceae, and Melianthaceae – down to the genus level – based on past and most recent research results. Unifying apomorphic, plesiomorphic, diagnostic, and nondiagnostic traits are mapped on the according nodes of the branches of the tree. All relevant morphological features are listed in a table to provide a clear overview and comparison between the genera. The purpose of the poster is to serve as a free, openly available educational tool and data resource for students, advanced scholars, researchers, and teachers.
A Simple Encryption Algorithm
Authors: St. Pierre Joseph Keenan
Published: January 2018

In this paper I present a Simple Encryption Algorithm (SEAL), by which 128-bit long blocks can be quickly encrypted/decrypted. The algorithm is designed to run efficiently in software without any specialized hardware while still guaranteeing a strong degree of confidentiality. The cipher is composed entirely of simple bit-wise operations, such as the exclusive-or and circular shift, in addition to modular addition, thereby making it exceedingly easy to implement in most programming languages as well as efficient in terms of performance.
The role of the submentalis muscle in the feeding biomechanics of the marine toad, Rhinella marina
Authors: Puljan Dan , Anderson Curt
Published: January 2018

It is well documented that coordination of feeding behavior in anuran amphibians requires precise coordination of the jaw levators and depressors with the timing of the protraction of the tongue. (for review, see Nishikawa, 2000). However, the neuronal mechanism initiating and synchronizing this coordination is not well understood. In addition to the intermandibularis muscle and tongue musculature in the lower jaw, there is a small, transverse muscle at the tip of the jaw, the m. submentalis. Previous anatomical work has demonstrated the presence of muscle spindles in the submentalis, leading to the hypothesis that the activation of this muscle may provide proprioceptive information to aid in coordinating the feeding biomechanics in Rhinella marina. Here, we demonstrate that the submentalis likely acts as a ‘trigger’ to initiate the hypoglossal nerve to activate the tongue, and without feedback information from the muscle spindles of the submentalis, tongue protraction is compromised.
Positive association of supersaturation effects in the human airways with influenza activity in subtropical climate: influenza seasons in Okinawa (2007-2012) – New method for analyzing and forecasting (first preliminary results)
Authors: Ishmatov Aleksandr N
Published: January 2018

There are many theories of the seasonality of influenza for different climatic zones. But none of the known theories provides a clear explanation, especially for the tropical and subtropical climate.

Here we have originally analyzed the association/connection of activity of seasonal influenza in Okinawa (subtropical zone) with the probability of occurring of supersaturation in the human airways when inhaling environmental air under specific weather conditions.

We have shown for the first time that the effects of supersaturation in the human airways may be associated with main representative peaks of intensity/activity of influenza in Okinawa in the period of observation from Jan 2007 until Dec 2012 including 2009 pandemic.

Our observation is the first one which clearly shows in the practice that the effect of supersaturation in the airways can be used for understanding and forecast the influenza activity in subtropical and tropical zones. Because the effect of supersaturation may lead to an additional risk of acidification of epithelial lining fluid in the local areas of the respiratory tract and to additional risk of deposition of infectious agents from inhaled air in the upper airways.
Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic data: The BOLD_NCBI _Merger
Authors: Macher Jan-Niklas , Macher Till-Hendrik , Leese Florian
Published: January 2018

Metabarcoding and metagenomic approaches are becoming routine techniques in biodiversity assessment and ecological studies. The assignment of taxonomic information to sequences is challenging, as many reference libraries are lacking information on certain taxonomic groups and can contain erroneous sequences. Combining different reference databases is therefore a promising approach for maximizing taxonomic coverage and reliability of results. This tutorial shows how to use the “BOLD_NCBI_Merger” script to combine sequence data obtained from the National Center for Biotechnology Information (NCBI) GenBank and the Barcode of Life Database (BOLD) and prepare it for taxonomic assignment with the software MEGAN.
A unique exceptionally well-preserved pterosaur skull from the Crato Formation of Brazil
Authors: Campos Hebert Bruno Nascimento , Cincotta Aude , Frey Eberhard , Godefroit Pascoal , Yans Johan
Published: January 2018

The posterior part of a skull from a tapejarid pterosaur was studied for the exceptional preservation of its soft-tissues. The specimen comes from the Early Cretaceous (Aptian) Crato Formation of northeastern Brazil. It shows a peculiar soft sagittal crest that gives new information about the anatomy and the diversity of tapejarids. The specimen lies on five limestone slabs. The bony part comprised the posterior part of the skull, with the braincase and one complex of three dorsally oriented and associated bony crests. The crest consists of a huge and elongated parietal crest, a trabecular frontal crest, and an occipital spine. The specimen preserves the posterior parts of the nasoantorbital fenestra and orbit. The soft cranial crest is characterized by a multilinear dorsal crest with almost parallel fibres, which curve posteriorly. Pigment organelles – melanosomes – were observed in the crest as well as ‘hair-like’ fibres (pycnofibres). They present diverse shapes and sizes, suggesting diverse colorations for the soft tissues. The new tapejarid shares certain features with the tapejarids Tupandactylus imperator and “Huaxiapterus” benxiensis, which include an elongated parieto-occipital crest. Nonetheless, it differs from Tupandactylus imperator and Ingridia navigans by the following characteristics: absence of a suprapremaxillary spine, very dorsally oriented posterior crests, as well as a specific morphology for the soft crest. Our specimen can therefore be assigned to a new taxon of Tapejaridae, a group previously reported from the Crato Formation.
Genetic evaluation and core collection construction of crape myrtle accessions using newly developed EST-SSR markers
Authors: Ye Yuanjun , Feng Lu , Ju Yiqian , Cai Ming , Cheng Tangren , Wang Jia , Zhang Qixiang , Pan Huitang
Published: January 2018

Crape myrtle is an important ornamental woody plant, due to its long-lasting mid summer bloom and rich color . However, limited molecular markers on this species hinder the breeding and genetic studies. In this work, 8,652 EST-SSRs were identified from crape myrtle transcriptome data. Di-nucleotide repeats (57.1%) were the most abundant type followed by tri-, tetra-, penta-, hexa-nucleotide repeats, with the AG/CT motif occurring most frequently. Of the 1200 synthesized primer pairs, 761 EST-SSRs (63.4%) were successfully amplified and 245 EST-SSRs (20.4%) showed polymorphic. High cross-species transferabilities of these markers were observed except in L. speciosa (26.7%). The polymorphic information content (PIC) for each locus ranged from 0.210 to 0.813 with a mean of 0.589, suggesting a high level of informativeness. Using 30 polymorphic EST-SSRs, structure and cluster analyses roughly divided the 73 accessions into three major groups with some admixtures. Based on the SSR data and clustering analysis, a final core collection (20 accessions) was identified, which captured Na, Ne, I, and PIC value with a retention rate of 92.8%, 113.6%, 110.6% and 109.7%, respectively. Thus, this work contributes to the better understanding of the genetic diversity and germplasm resources conservation in Lagerstroemia species.
Upper Karoo vertebrate assemblages (Late Triassic/Early Jurassic) of the Late Kariba region, Zimbabwe
Authors: Barrett Paul M , Broderick Tim , Chapelle Kimberley , Choiniere Jonah , Edwards Steve , Munyikwa Darlington , Viglietti Pia , Zondo Michel
Published: January 2018

Southern Africa provides critical information on Late Triassic–Early Jurassic terrestrial tetrapod faunas. Most of the localities in this region are in South Africa and Lesotho, but preliminary work in Zimbabwe has revealed significant potential. Early Jurassic Zimbabwean localities have yielded the basal sauropodomorph Massospondylus, the early sauropod Vulcanodon and theropod material. Late Triassic localities are also known, but have yielded only fragmentary specimens thus far.

In early 2017, a joint South African-Zimbabwean-UK team conducted fieldwork in the upper Karoo-aged deposits along the shores of Lake Kariba, northern Zimbabwe (Mid-Zambesi Basin). We relocated the Vulcanodon type locality on Island 126/127 and found that, contrary to previous reports suggesting a Toarcian age, the quarry was in a horizon pre-dating the onset of Drakensburg volcanism (= Batoka Basalts). It is situated instead within the earlier Lower Jurassic Forest Sandstone. This indicates that Vulcanodon is 10–15 million years older than thought previously, recalibrating several nodes within Sauropoda and indicating extensive overlap between true sauropods and 'prosauropods'.

Other new vertebrate localities show that sauropodomorphs are present in the Forest Sandstone and upper Tashinga (Late Triassic) formations, but a grey mudstone facies within the Pebbly Arkose Member of the latter unit yields a more aquatic fauna, including lungfish and phytosaurs, but lacking sauropodomorphs. The phytosaur occurrence is the first in Africa south of the Sahara. Faunal and sedimentological evidence indicates that the Late Triassic and Early Jurassic sites in this region were deposited under more mesic environments than their lateral equivalents in South Africa.
Increasing cyclic electron flow mediated by NDH is related to heat tolerance under low light in grape leaves
Authors: Sun Yongjiang , Hao Guimei , Gao Yulu , Du Yuanpeng , Yang Xinhong , Zhai Heng
Published: January 2018

Examination of the effects of high temperature (42 °C) on the photoinhibition of photosystem II (PSII) in grape leaves revealed that the extent of photoinhibition of PSII was lower in the light (200 μmol m-2 s-1) than in the dark. Heat stress in the dark induced severe injury in the grapevines, as determined by the critical temperature (Tc). The maximal efficiency of PSII photochemistry (Fv/Fm) decreased significantly in the dark, but it decreased much less in the light. In addition, there was a lower level of degradation of the D1 protein in the light than in the dark. Furthermore, the NAD(P)H dehydrogenase (NDH)-dependent cyclic electron ﬂow (CEF) was remarkably enhanced in the light, but it was suppressed in the dark. The half-time of P700+ re-reduction (t1/2) was reduced moer in in the light than in the dark during heat stress. Compared to the control leaves, the antimycin A (AA)-treated leaves showed much less of a decrease in Fv/Fm in the light than in the dark during heat stress; however, this increase seemed to disappear in methyl viologen (MV)-treated leaves. Based on these results, we propose a significant physiological function of the NDH-dependent CEF pathway under low light is the protection of PSII against heat-induced photoinhibition.
Lymph node inspired computing: towards holistic immune system inspired algorithms for human-engineered complex systems
Authors: Banerjee Soumya
Published: January 2018

The immune system is a distributed decentralized system that functions without any centralized control. The immune system has millions of cells that function somewhat independently and can detect and respond to pathogens with considerable speed and efficiency. Lymph nodes are physical anatomical structures that allow the immune system to rapidly detect pathogens and mobilize cells to respond to it. Lymph nodes function as: 1) information processing centers, and 2) a distributed detection and response network. We introduce biologically inspired computing that uses lymph nodes as inspiration. We outline applications to diverse domains like mobile robots, distributed computing clusters, peer-to-peer networks and online social networks. We argue that lymph node inspired computing systems provide powerful metaphors for distributed computing and complement existing artificial immune systems. We view our work as a first step towards holistic simulations of the immune system that would capture all the complexities and the power of a complex adaptive system like the immune system. Ultimately this would lead to holistic immune system inspired computing that captures all the complexities and power of the immune system in human-engineered complex systems.
Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods
Authors: Santamaria Carlos A , Bluemel Joanna K , Bunbury Nancy , Curran Melinda
Published: January 2018

Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.
The many forms of beta diversity: a comment on McGill et al. and some notational suggestions
Authors: Jeppsson Tobias
Published: January 2018

Fundamentally, beta diversity is a measure of species turnover across time or space. In practice, it is sometimes unclear exactly what aspect of beta diversity that is implied in studies. For instance, a trend in ’spatial beta diversity’ can be used to refer to both differences in spatial beta diversity between sites, as well as a temporal trend in spatial beta diversity (at the same site). In a recent review, McGill et al. [1] provide a useful and much needed overview of different aspects of biodiversity change, and show areas where we lack knowledge. Even so, McGill et al. ignore some aspects of beta diversity and sometimes pool different types of beta diversity under the same heading. However, their review mainly focused on temporal trends in diversity, while I here want to highlight spatial patterns in temporal β -diversity (species turnover) as an important but somewhat overlooked component of biodiversity change. Furthermore, I propose a slightly modified classification and nomenclature of metrics of biodiversity change, with the aim of complementing their review. The notation used here can hopefully be useful to other authors as well.
Extensive transcriptional variation poses a challenge to thermal stress biomarker development for endangered corals
Authors: Parkinson John E , Bartels Erich , Devlin-Durante Meghann K , Lustic Caitlin , Nedimyer Ken , Schopmeyer Stephanie , Lirman Diego , LaJeunesse Todd C , Baums Iliana B
Published: January 2018

As climate changes, sea surface temperature anomalies that negatively impact coral reef organisms continue to increase in frequency and intensity. Yet, despite widespread coral mortality, genetic diversity remains high even in those coral species listed as threatened. While this is good news in many ways it presents a challenge for the development of biomarkers that can identify resilient or vulnerable genotypes. Taking advantage of three coral restoration nurseries in Florida that serve as long-term common garden experiments, we exposed over thirty genetically distinct Acropora cervicornis colonies to hot and cold temperature shocks seasonally and measured pooled gene expression responses using RNAseq. Targeting a subset of twenty genes, we designed a high-throughput qPCR array to quantify expression in all individuals separately under each treatment with the goal of identifying thermal stress biomarkers. We observed extensive transcriptional variation in the population, suggesting abundant raw material is available for adaptation via natural selection. However, this high variation made it difficult to correlate gene expression changes with colony performance metrics such as growth, mortality, and bleaching susceptibility. Nevertheless, we identified several promising biomarkers for acute thermal stress that may improve coral restoration and climate change mitigation efforts in the future.
Excuse me, do you have a moment to talk about version control?
Authors: Bryan Jennifer
Published: January 2018

Data analysis, statistical research, and teaching statistics have at least one thing in common: these activities all produce many files! There are data files, source code, figures, tables, prepared reports, and much more. Most of these files evolve over the course of a project and often need to be shared with others, for reading or edits, as a project unfolds. Without explicit and structured management, project organization can easily descend into chaos, taking time away from the primary work and reducing the quality of the final product. This unhappy result can be avoided by repurposing tools and workflows from the software development world, namely, distributed version control. This article describes the use of the version control system Git and and the hosting site GitHub for statistical and data scientific workflows. Special attention is given to projects that use the statistical language R and, optionally, R Markdown documents. Supplementary materials include an annotated set of links to step-by-step tutorials, real world examples, and other useful learning resources.
Lessons from between the white lines for isolated data scientists
Authors: Baumer Benjamin S
Published: January 2018

Many current and future data scientists will be "isolated"---working alone or in small teams within a larger organization. This isolation brings certain challenges as well as freedoms. Drawing on my considerable experience both working in the professional sports industry and teaching in academia, I discuss troubled waters likely to be encountered by newly-minted data scientists, and offer advice about how to navigate them. Neither the issues raised nor the advice given are particular to sports, and should be applicable to a wide range of knowledge domains.
Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter
Authors: Zeng Quanchao , Liu Yang , An Shaoshan
Published: January 2018

The forest ecosystem is the main component of terrestrial ecosystems. The global climate and the functions and processes of soil microbes in the ecosystem are all influenced by litter decomposition. The effects of litter decomposition on the abundance of soil microorganisms remain unknown. Here, we analyzed soil bacterial communities during the litter decomposition process in an incubation experiment under treatment with different litter quantities based on annual litterfall data (normal quantity, 200 g/(m2/yr); double quantity, 400 g/(m2/yr) and control, no litter). The results showed that litter quantity had significant effects on soil carbon fractions, nitrogen fractions, and bacterial community compositions, but significant differences were not found in the soil bacterial diversity. The normal litter quantity enhanced the relative abundance of Actinobacteria and Firmicutes and reduced the relative abundance of Bacteroidetes, Plantctomycets and Nitrospiare. The Beta-, Gamma-, and Deltaproteobacteria were significantly less abundant in the normal quantity litter addition treatment, and were subsequently more abundant in the double quantity litter addition treatment. The bacterial communities transitioned from Proteobacteria-dominant (Beta-, Gamma-, and Delta) to Actinobacteria-dominant during the decomposition of the normal quantity of litter. A cluster analysis showed that the double litter treatment and the control had similar bacterial community compositions. These results suggested that the double quantity litter limited the shift of the soil bacterial community. Our results indicate that litter decomposition alters bacterial dynamics under the accumulation of litter during the vegetation restoration process, which provides important significant guidelines for the management of forest ecosystems.