bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catchments catch all in South African coastal lowlands: multilocus phylogeography and distribution modelling of Nymania capensis (Meliaceae) reveal topographic and palaeoclimatic connectivity constraints
Authors: Potts Alastair J 
Published: January 2018

Background. This study investigates orbitally-forced range dynamics at a regional scale by exploring the evolutionary history of Nymania capensis (Meliaceae) across the deeply incised landscapes of the subescarpment coastal lowlands of South Africa; a region home to three biodiversity hotspots (Succulent Karoo, Fynbos, and Maputaland-Pondoland-Albany hotspots).
Methods. A range of methods are used including: multilocus phylogeography (chloroplast and high- and low-copy nuclear DNA), molecular dating and species distribution modelling (SDM).
Results. The results support an ‘evolutionarily distinct catchment’ hypothesis where: 1) diﬀerent catchments contain genetically distinct lineages, 2) limited genetic structuring was detected within basins whilst high structuring was detected between basins, and 3) within primary catchment populations display a high degree of genealogical lineage sorting. In addition, the results support a glacial refugia hypothesis as: a) the timing of chloroplast lineage diversiﬁcation is restricted to the Pleistocene in a landscape that has been relatively unchanged since the late Pliocene, and b) the projected LGM distribution of suitable climate for N. capensis suggest fragmentation into refugia that correspond to the current phylogeographic populations.
Discussion. This study highlights the interaction of topography and subtle Pleistocene climate variations as drivers affecting both seed and pollen flow along these lowlands. This lends support to the region’s large-scale conservation planning efforts, which used catchments as foundational units for conservation as these are likely to be evolutionary significant units.
Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles
Authors: Peroni Silvio , Osborne Francesco , Di Iorio Angelo , Nuzzolese Andrea Giovanni , Poggi Francesco , Vitali Fabio , Motta Enrico 
Published: January 2018

Purpose: this paper introduces the Research Articles in Simplified HTML (or RASH ), which is a Web-first format for writing HTML-based scholarly papers; it is accompanied by the RASH Framework , i.e. a set tools for interacting with RASH-based articles. The paper also presents an evaluation that involved authors and reviewers of RASH articles, submitted to the SAVE-SD 2015 and SAVE-SD 2016 workshops.
Design: RASH has been developed in order to: be easy to learn and use; share scholarly documents (and embedded semantic annotations) through the Web; support its adoption within the existing publishing workflow
Findings : the evaluation study confirmed that RASH can already be adopted in workshops, conferences and journals and can be quickly learnt by researchers who are familiar with HTML.
Research limitations: the evaluation study also highlighted some issues in the adoption of RASH, and in general of HTML formats, especially by less technical savvy users. Moreover, additional tools are needed, e.g. for enabling additional conversion from/to existing formats such as OpenXML.
Practical implications: RASH (and its Framework) is another step towards enabling the definition of formal representations of the meaning of the content of an article, facilitate its automatic discovery, enable its linking to semantically related articles, provide access to data within the article in actionable form, and allow integration of data between papers.
Social implications: RASH addresses the intrinsic needs related to the various users of a scholarly article: researchers (focussing on its content), readers (experiencing new ways for browsing it), citizen scientists (reusing available data formally defined within it through semantic annotations), publishers (using the advantages of new technologies as envisioned by the Semantic Publishing movement).
Value: RASH focuses strictly on writing the content of the paper (i.e., organisation of text + semantic annotations) and leaves all the issues about it validation, visualisation, conversion, and semantic data extraction to the various tools developed within its Framework.
Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles
Authors: Peroni Silvio , Osborne Francesco , Di Iorio Angelo , Nuzzolese Andrea Giovanni , Poggi Francesco , Vitali Fabio , Motta Enrico 
Published: January 2018

Purpose: this paper introduces the Research Articles in Simplified HTML (or RASH ), which is a Web-first format for writing HTML-based scholarly papers; it is accompanied by the RASH Framework , a set of tools for interacting with RASH-based articles. The paper also presents an evaluation that involved authors and reviewers of RASH articles submitted to the SAVE-SD 2015 and SAVE-SD 2016 workshops.
Design: RASH has been developed aiming to: be easy to learn and use; share scholarly documents (and embedded semantic annotations) through the Web; support its adoption within the existing publishing workflow
Findings : the evaluation study confirmed that RASH is ready to be be adopted in workshops, conferences, and journals and can be quickly learnt by researchers who are familiar with HTML.
Research limitations: the evaluation study also highlighted some issues in the adoption of RASH, and in general of HTML formats, especially by less technically savvy users. Moreover, additional tools are needed, e.g. for enabling additional conversions from/to existing formats such as OpenXML.
Practical implications: RASH (and its Framework) is another step towards enabling the definition of formal representations of the meaning of the content of an article, facilitating its automatic discovery, enabling its linking to semantically related articles, providing access to data within the article in actionable form, and allowing integration of data between papers.
Social implications: RASH addresses the intrinsic needs related to the various users of a scholarly article: researchers (focussing on its content), readers (experiencing new ways for browsing it), citizen scientists (reusing available data formally defined within it through semantic annotations), publishers (using the advantages of new technologies as envisioned by the Semantic Publishing movement).
Value: RASH helps authors to focus on the organisation of their texts, supports them in the task of semantically enriching the content of articles, and leaves all the issues about validation, visualisation, conversion, and semantic data extraction to the various tools developed within its Framework.
Congregating behavior and response to resource distribution of the Green House Millipede, Oxidus gracilis
Authors: Bulpitt Gregory 
Published: January 2018

Background. Congregating behaviors, though common among many animal species, are little studied among millipedes. It is also unclear to what extent abiotic factors influence the distribution and behavior of millipedes. The species Oxidus gracilis was surveyed around several streams on the island of Mo’orea along with soil moisture, leaf litter cover, and rock cover. Experiments were designed in order to determine how an innate congregating behavior may affect their distributions.
Methods. Fifteen transects were performed in the field, recording O. gracilis abundances and the three environmental factors every 1 m. Forty trials were performed using covered bins filled with soil and five fruits of the Tahitian chestnut tree (Inocarpus fagifer). Ten millipedes were placed in the box and left for an hour, after which the number of individuals per fruit was recorded.
Results. It was found that while none of the three environmental factors were strong indicators of the distribution of O. gracilis , individuals did in fact demonstrate a tendency to congregate in the experimental trials.
Discussion. The lack of significant relationships with the three environmental parameters suggests a generalist behavior of this millipede species, potentially benefitting its invasive nature. The congregating behavior could potentially be for the purposes of mating or defense. Although not studied in this paper, it is possible that conspecific chemical cues are responsible.
Sponge physiology: the effects of temperature on the regeneration and reaggregation of sponges (Haliclona reniera)
Authors: Runzel Charlotte C 
Published: January 2018

Background. Increases in oceanic temperatures are expected to affect the cellular function of ecologically important organisms, such as sponges. Sponges are important to biodiversity, coral reef systems, benthic and spongiverous organisms, and the biomedical industry. Sponges can repair wounds (regeneration) and rebuild their body from separated cells (reaggregation). The rates of regeneration and reaggregation can serve as a proxy for cellular functions. These processes are important to sponge physiology, growth and competition in reef systems. This study will examine how temperature affects the regeneration and reaggregation of Haliclona reniera.
Methods. This study considered the effects of temperature on growth and reaggregation. Percent of reaggregation was measured in a range of temperatures (4-34˚C) for 15 minutes and analyzed using imageJ software. Regeneration rates of wounded sponges were measured in fluctuating (28-32˚C & 28-34˚C) and non-fluctuating (28˚C and 32˚C) oceanic temperatures. The depth and size of H. reniera was measured with transects.
Results. Through observing growth and aggregation rates in a variety of temperatures, this study showed that sponges exposed to average fluctuations at 1m (28-32˚C) had higher regeneration rates than those exposed to high fluctuations (28-34˚C) at 0.5m. Wounded sponges regenerated faster in higher temperatures (32˚C) than in lower temperatures (28˚C). Aggregation cells fit a temperature performance curve with a peak at 29.5˚C, or just above average oceanic temperatures (29˚C). H. reniera was most commonly found at depths of 1m.
Discussion. Although coral and other organisms may be greatly affected by oceanic warming, sponges may persist, depending on how oceanic temperature will fluctuate in the future. H. reniera repaired wounds faster in average temperature with normally occurring fluctuations and aggregated most frequently at temperatures slightly above average (29.5˚C). With IPCC predictions of increased oceanic temperatures and fluctuations, H. reniera may not have ideal oceanic conditions, but will still endure these conditions. With coral reefs affected by climate change conditions, many organisms may die off, perhaps transitioning coral reefs into sponge reefs.
Understanding of the activity of a protein involved in DNA repair by biochemical, structural and in silico approaches
Authors: Morrone Castrese , Miggiano Riccardo , Serpe Mario , Massarotti Alberto , Valenti Anna , Del Monaco Giovanni , Rossi Mosé , Rossi Franca , Rizzi Menico , Ciaramella Maria , Perugino Giuseppe 
Published: January 2018

The repair of DNA from alkylation damage is generally performed by evolutionary conserved protein complexes. However, specific repair of O6-alkylated-guanines is a task of a small class of proteins called AGTs (alkylated DNA-protein alkyl-transferases): by using a single-step reaction mechanism, the alkylic group is irreversibly transferred to a catalytic cysteine in the active site, inducing the in vitro and in vivo inactivation and destabilization of the protein. Although some conformational changes after the alkylation are supposed, a complete picture of structural rearrangements occurring during the reaction cycle is missing. The complete knowledge of these structural movements is a great challenge and a fundamental task for the development of new inhibitors of the human AGT, whose overexpression leads to a resistance in several types of tumor cells to the chemoterapic alkylating agents-based treatment. We used the Sulfolobus solfataricus thermostable ortholog (SsOGT) as a model for AGTs [1], by performing biochemical, structural, molecular dynamics and in silico analysis of ligand-free, DNA-bound and alkylated version of the protein. With this protein, we were able to highlight conformational changes and perturbations of intramolecular interaction occurring during lesion recognition and catalysis, confirming our previous hypothesis that coordination between the N- and C-terminal domains of SsOGT is important for protein activity and stability [2]. All the data allowed us to propose a general model of structural rearrangements occurring during the reaction cycle of AGTs [3], and proposing it as a starting point to design strategies to modulate AGT activity in therapeutic settings.
[1] G. Perugino, A. Vettone, G. Illiano, A. Valenti, M.C. Ferrara, M. Rossi, M. Ciaramella (2012) Activity and regulation of archaeal DNA alkyltransferase: conserved protein involved in repair of DNA alkylation damage. J. Biol. Chem., 287, 4222-4231.
[2] G.Perugino, R.Miggiano, M.Serpe, A.Vettone, A.Valenti, S.Lahiri, F.Rossi, M.Rossi, M. Rizzi, M. Ciaramella (2015) Structure-function relationships governing activity and stability of a DNA alkylation damage repair thermostable protein. Nucleic Acids Res., 43, 8801-8816.
[3] C. Morrone, R. Miggiano, M. Serpe, A. Massarotti, A. Valenti, G. del Monaco, M. Rossi, F. Rossi, M. Rizzi, G. Perugino, M. Ciaramella (2017) Interdomain interactions rearrangements control the reaction steps of a thermostable DNA alkyltransferase. BBA-Gen. Sub., 1861, 2, 86-96.
Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model
Authors: Dang Yalong , Waxman Susannah , Wang Chao , Jensen Adrianna , Loewen Ralitsa T , Bilonick Richard , Loewen Nils A 
Published: January 2018

Objective: Trabecular meshwork (TM) is the primary substrate of outflow resistance in glaucomatous eyes. Repopulating diseased TM with fresh, functional TM cells might represent a novel therapeutic breakthrough. Various decellularized TM scaffolds were developed by ablating existing cells with suicide gene therapy or saponin, but always with incomplete cell removal or dissolve the extracellular matrix. We hypothesized that a chemical-free, freeze-thaw method would be able to produce a fully decellularized TM scaffold for cell transplantation.
Materials and Methods: We obtained 24 porcine eyes from a local abattoir, dissected and mounted them in an anterior segment perfusion and pressure transduction system within two hours of sacrifice. After they stabilized for 72 hours, eight eyes each were assigned to freeze-thaw (F) ablation (-80°C×2), to 0.02% saponin (S) treatment, or the control group (C), respectively. The trabecular meshwork was transduced with an eGFP expressing feline immunodeficiency viral (FIV) vector and tracked via fluorescent microscopy to confirm ablation. Following treatment, the eyes were perfused with standard tissue culture medium for 180 hours. We assessed histological changes by hematoxylin and eosin staining. TM cell viability was evaluated with a calcein AM/propidium iodide (PI) assay. We measured IOP and modeled it with a linear mixed effects model using a B-spline function of time with 5 degrees of freedom.
Results: F and S experienced a similar IOP reduction by 30% from baseline (P=0.64). IOP reduction of about 30% occurred in F within 24 hours and in S within 48 hours. Live visualization of eGFP demonstrated that F conferred a complete ablation of all TM cells and only a partial ablation in S. Histological analysis confirmed that no TM cells survived in F while the extracellular matrix remained. The viability assay showed very low PI and no calcein staining in F in contrast to numerous PI-labeled dead TM cells and calcein-labeled viable TM cells in S.
Conclusion: We developed a rapid TM ablation method that uses cyclic freezing that is free of biological or chemical agents and able to produce a decellularized TM scaffold with preserved TM excellular matrix in an organotypic perfusion culture.
Assessing strengths and weaknesses of DNA metabarcoding based macroinvertebrate identification for routine stream monitoring
Authors: Elbrecht Vasco , Vamos Edith , Meissner Kristian , Aroviita Jukka , Leese Florian 
Published: January 2018

1) DNA metabarcoding holds great promise for the assessment of macroinvertebrates in stream ecosystems. However, few large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification.
2) We performed metabarcoding using four primer sets on macroinvertebrate samples from 18 stream sites across Finland. The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. Specimens were morphologically classified, following standardised protocols, to the lowest taxonomic level for which identification was feasible in the routine national monitoring.
3) DNA metabarcoding identified more than twice the number of taxa than the morphology-based protocol, and also yielded a higher taxonomic resolution. For each sample, we detected more taxa by metabarcoding than by the morphological method, and all four primer sets exhibited comparably good performance. Sequence read abundance and the number of specimens per taxon (a proxy for biomass) were significantly correlated in each sample, although the adjusted R2 were low. With a few exceptions, the ecological status assessment metrics calculated from morphological and DNA metabarcoding datasets were similar. Given the recent reduction in sequencing costs, metabarcoding is currently approximately as expensive as morphology-based identification.
4) Using samples obtained in the field, we demonstrated that DNA metabarcoding can achieve comparable assessment results to current protocols relying on morphological identification. Thus, metabarcoding represents a feasible and reliable method to identify macroinvertebrates in stream bioassessment, and offers powerful advantage over morphological identification in providing identification for taxonomic groups that are unfeasible to identify in routine protocols. To unlock the full potential of DNA metabarcoding for ecosystem assessment, however, it will be necessary to address key problems with current laboratory protocols and reference databases.
High definition video loggers provide new insights into behaviour, physiology, and the oceanic habitat of marine top predators
Authors: Mattern Thomas , McPherson Michael D , Ellenberg Ursula , van Heezik Yolanda , Seddon Philipp J 
Published: January 2018

1. Camera loggers are increasingly used to examine behavioural aspects of free-ranging animals. However, often video loggers are deployed with a focus on specific behavioural traits utilizing small cameras with a limited field of view, poor light performance and video quality. Yet rapid developments in consumer electronics provide new devices with much improved visual data allowing a wider scope for studies employing this novel methodology.
2. We developed a camera logger that records full HD video through a wide-angle lens, providing high resolution footage with a greater field of view than other camera loggers. Main goal was the analysis of foraging behaviour of a marine top-predator, the Yellow-eyed penguin in New Zealand, in the context habitat characteristics. Frame-by-frame analysis allowed accurate timing of prey pursuits and time spent over certain seafloor types. Similarly, it was possible to time breathing intervals between dives and quantify exhalation events during prey events, a previously undescribed behaviour. Screen overlays facilitate analysis of flipper angles and beat frequencies throughout various stages of the dive cycle.
3. The recorded video footage showed that prey species were associated with certain seafloor types, revealed different predator evasion strategies by benthic fishes, and highlighted varying energetic consequences for penguins pursuing certain types of prey. Flipper movement analysis confirmed decreasing effort during descent phases as the bird gained depth, and that ascent was principally passive. Breathing episodes between dives were short (<1 s) while the majority of the time was devoted to subsurface scanning with a submerged head.
4. Video data recorded on free-ranging animals not only provides a wealth of information recorded from a single deployment but also necessitates new approaches with regards to analysis of visual data. Here, we demonstrate the diversity of information that can be gleaned from video logger data, if devices with high video resolution and wide field of view are utilized
USMI Galaxy Demonstrator (UGD): a collection of tools to integrate microorganisms information
Authors: Colobraro Daniele Pierpaolo , Romano Paolo 
Published: January 2018

Due to the fragmentation of microbial information and the several branch of human activities encompassed by microorganism applications, a comprehensive approach for merging information on microbes is needed. Although on line service providers collect several data on microorganisms and provide services for microbial Biological Resource Centres (mBRCs), such services are still limited both in contents and aims. The USMI Galaxy Demonstrator (UGD), an implementation of the Galaxy framework exploiting the XML-based Microbiological Common Language (MCL), is meant to support researchers to make an integrated access to enriched information from microbial catalogues, as well as to help mBRC curators in validating and enriching the contents of their catalogues. Researchers and mBRC curators may exploit the UGD to avoid manual, potentially long, searches on the web and to identify and select microorganisms of interest.
UGD tools are written in Python, version 2.7. They allow to enrich the basic information provided by catalogues with related taxonomy, literature, sequence and chemical compound data retrieved from some of the main databases on the basis of the strain number, i.e. the unique identifier for a given culture, and the species names. The data is retrieved by querying database Web Services using either the Simple Object Access Protocol (SOAP) or the Representational State Transfer (REST) access protocols. The MCL format provides a versatile way to archive and exchange data among mBRCs.
Galaxy is a well-known, open, web-based platform which offers many tools to retrieve, manage and analyze different kind of information arising from any life science domain. By exploiting Galaxy flexibility,UGD implements some tools and workflows that can be used to find and integrate several information on microorganisms. UGD tools integrate basic information which may support mBRC staff in the insertion of all fundamental strain information in a proper format allowing integration and interoperability with external databases. They also extend the output by adding information on source materials, including species and strain numbers, and retrieve associated microorganisms which use a compound or an enzyme in whatever metabolic pathway by returning the accession number, synonyms, links to external databases, taxon name, and strain number of the requested molecule.