bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proposal for practical multi-kingdom classification of eukaryotes based on monophyly and comparable divergence time criteria
Authors: Tedersoo Leho 
Published: December 2017

SummaryMuch of the ecological, taxonomic and biodiversity research relies on understanding of phylogenetic relationships among organisms. There are multiple available classification systems that all suffer from differences in naming, incompleteness, presence of multiple non-monophyletic entities and poor correspondence of divergence times. These issues render taxonomic comparisons across the main groups of eukaryotes and all life in general difficult at best. By using the monophyly criterion, roughly comparable time of divergence and information from multiple phylogenetic reconstructions, I propose an alternative classification system for the domain Eukarya to improve hierarchical taxonomical comparability for animals, plants, fungi and multiple protist groups. Following this rationale, I propose 32 kingdoms of eukaryotes that are treated in 10 subdomains. These kingdoms are further separated into 43, 115, 140 and 353 taxa at the level of subkingdom, phylum, subphylum and class, respectively (http://dx.doi.org/10.15156/BIO/587483). Most of the names have been used previously or these were deduced from those of the type taxa to be able to unambiguously link genera to higher taxonomic levels. In the era of phylogenomics, understanding about the phylogenetic relationships among organisms is rapidly increasing. Classifications systems must keep pace with this race to serve the research community by consistent improvements in precision in terms of taxonomic resolution and maintaining monophyly of the ingredient taxa.
Dot2dot: Accurate Whole-Genome Tandem Repeats Discovery
Authors: Genovese Loredana M. , Mosca Marco M. , Pellegrini Marco , Geraci Filippo 
Published: December 2017

AbstractThe advent of sequencing technologies and the consequent computational analysis of genomes has confirmed the evidence that DNA sequences contain a relevant amount of repetitions. A particularly important category of repeating sequences is that of tandem repeats (TRs). TRs are short, almost identical sequences that lie adjacent to each other. The abundance of TRs in eukaryotic genomes has suggested that they play a role in many cellular processes and, indeed, are also involved in the onset and progress of several genetic disorders.Building upon the idea that similar sequences can be easily displayed using graphical methods, we formalized the structure that TRs induce in dot plot matrices where a sequence is compared with itself. We further observed that a compact representation of these matrices can be built and searched in linear time in the size of the input sequence. Exploiting this observation, we developed an algorithm fast enough to be suitable for whole-genome discovery of tandem repeats.We compared our algorithm with seven state of the art methods using as a gold standard five collections of tandem repeats: pathology-linked, forensic, for population analysis, genealogic-oriented, and variable TRs in regulatory regions. In addition, we run our algorithm on seven reference genomes to test the suitability of our approach for whole-genome analysis. Experiments show that our method: is always more accurate than the other methods, and completes the analysis of the biggest available reference genome in about one day running at a rate of 0.98Gbp/h on a standard workstation.
Differential effects of learned associations with words and pseudowords on event-related brain potentials
Authors: Kulke Louisa , Bayer Mareike , Grimm Anna-Maria , Schacht Annekathrin 
Published: December 2017

Associated stimulus valence affects neural responses at an early processing stage. However, in the field of written language processing, it is unclear whether semantics of a word or low-level visual features affect early neural processing advantages. The current study aimed to investigate the role of semantic content on reward and loss associations. Participants completed a learning session to associate either words (Experiment 1, N=24) or pseudowords (Experiment 2, N=24) with different monetary outcomes (gain-associated, neutral or loss-associated). Gain-associated stimuli were learned fastest. Behavioural and neural response changes based on the associated outcome were further investigated in separate test sessions. Responses were faster towards gain- and loss-associated than neutral stimuli if they were words, but not pseudowords. Early P1 effects of associated outcome occurred for both pseudowords and words. Specifically, loss-association resulted in increased P1 amplitudes to pseudowords, compared to decreased amplitudes to words. Although visual features are likely to explain P1 effects for pseudowords, the inversed effect for words suggests that semantic content affects associative learning, potentially leading to stronger associations.Highlights- Neural mechanisms of gain/loss association to pseudowords and words were investigated- Loss effects can be observed for the P1 component- Words and pseudowords differ in the direction of loss effects- Semantic content may play a role during word association- Low-level visual features may play a role during pseudoword association
Can net diversification rates account for spatial patterns of species richness?
Authors: Sanín Camilo , Jiménez Iván , Fjeldså Jon , Rahbek Carsten , Cadena Carlos Daniel 
Published: December 2017

ABSTRACTThe diversification rate hypothesis (DRH) proposes that spatial patterns of species richness result from spatial variation in net diversification rates. We developed an approach using a time-calibrated phylogeny and distributional data to estimate the maximum explanatory power of the DRH, over a given time period, to current species richness in an area. We used this approach to study species richness patterns of a large family of suboscine birds across South America. The maximum explanatory power of the DRH increased with the duration of the time period considered and grain size; it ranged from 13 – 37 fold local increases in species richness for T = 33 Ma to less than 2-fold increases for T ≤ 10 Ma. For large grain sizes (≤ 8° × 8°) diversification rate over the last 10 Ma could account for all the spatial variance in species richness, but for smaller grain sizes commonly used in biogeographical studies (1° × 1°), it could only explain < 16% of this variance. Thus, diversification since the Late Miocene, often thought to be a major determinant of Neotropical diversity, had a limited imprint on spatial richness patterns at small grain sizes. Further application of our approach will help determine the role of the DRH in explaining current spatial patterns of species richness.Note to readersThis manuscript has been seen by a few researchers, some of whom suggested that before publishing our work in a peer-reviewed journal we should conduct simulations to demonstrate that our methods properly estimate the contribution of variance in diversification rates to spatial variation in species richness. Although we believe that our approach derives logically from theory and statistics and is therefore valid, we understand that it is rather unique and see why some readers would think that an independent validation is necessary. Unable to complete such validation in the near future, however, we decided to make this manuscript available as a preprint to share our ideas and hopefully stimulate discussion on what we believe is a most interesting topic. We also hope to receive feedback that may enable us to improve our work for publication in a journal at a later date.
Murine polyomavirus microRNAs promote viruria during the acute phase of infection
Authors: Burke James M. , Bass Clovis R. , Ulug Emin T. , Sullivan Christopher S. 
Published: December 2017

AbstractPolyomaviruses (PyVs) can cause serious disease in immunosuppressed hosts. Several pathogenic PyVs encode microRNAs (miRNAs), small RNAs that regulate gene expression via RNA silencing. Despite recent advances in understanding the activities of PyV miRNAs, the biological functions of PyV miRNAs duringin vivoinfections are mostly unknown. Studies presented here use murine polyomavirus (MuPyV) as a model to assess the roles of the PyV miRNAs in a natural host. This analysis reveals that a MuPyV mutant that is unable to express miRNAs has enhanced viral DNA loads in select tissues at late times after infection, indicating that during infection of a natural host, PyV miRNAs function to reduce viral replication during the persistent phase of infection. Additionally, MuPyV miRNAs promote viruria during the acute phase of infection as evidenced by a defect in shedding during infection with the miRNA mutant virus. The viruria defect of the miRNA mutant virus could be rescued by infecting Rag2-/-mice. These findings implicate miRNA activity in both the persistent and acute phases of infection and suggest a role for MuPyV miRNA in evading the adaptive immune response.ImportanceMicroRNAs are expressed by diverse viruses, but for only a few is there any understanding of theirin vivofunction. PyVs can cause serious disease in immunocompromised hosts. Therefore, increased knowledge of how these viruses interact with the immune response is of possible clinical relevance. Here we show a novel activity for a viral miRNA in promoting virus shedding. This work indicates that in addition to any role for the PyV miRNA in long-term persistence, that it also has biological activity during the acute phase. As this mutant phenotype is alleviated by infection of mice lacking an effective adaptive immune response, our work also connects thein vivoactivity of a PyV miRNA to the immune response. Given that PyV-associated disease is associated with alterations in the immune response, our findings may help to better understand how the balance between PyV and the immune response becomes altered in pathogenic states.
Bacterial Community Shift in Marine Tar Balls following Low Salinity Exposure
Authors: Tran Mai Hoang , Park Joong-Wook 
Published: December 2017

AbstractThe persistence and recurrence of tar balls causes detrimental effects on coastal wildlife, tourism, and fisheries. Previously, the human pathogen Vibrio vulnificus was detected in marine tar balls in the Gulf of Mexico. Marine tar balls also migrate to low-salt water bodies near the shore. The bacterial communities in tar balls from these environments, however, have not been fully characterized. Herein we describe our studies on the effect of reduced salinity on bacterial communities in marine tar balls. Tar balls collected from the Gulf of Mexico were incubated in deionized water for six months, and their microbial fingerprints were visualized using denaturing gradient gel electrophoresis. Our data show that the indigenous bacterial communities in marine tar balls shifted after being exposed to low-salinity condition. Dominant genera in the tar balls at low salinity were Aquisalimonas and Parvibaculum, neither of which includes known human pathogens.
MYC-driven epigenetic reprogramming favors the onset of tumorigensis by inducing a stem cell-like state
Authors: Poli Vittoria , Fagnocchi Luca , Fasciani Alessandra , Cherubini Alessandro , Mazzoleni Stefania , Ferrillo Sara , Miluzio Annarita , Gaudioso Gabriella , Vaira Valentina , Turdo Alice , Giaggianesi Miriam , Chinnici Aurora , Lipari Elisa , Bicciato Silvio , Bosari Silvano , Todaro Matilde , Zippo Alessio 
Published: December 2017

AbstractBreast cancer consists of highly heterogeneous tumors, whose cell of origin and driver oncogenes resulted difficult to be uniquely defined. Here we report that MYC acts as tumor reprogramming factor in mammary epithelial cells by inducing an alternative epigenetic program, which triggers loss of cell identity and activation of oncogenic pathways. Over-expression of MYC induces transcriptional repression of lineage-specifying transcription factors, causing decommissioning of luminal-specific enhancers. MYC-driven dedifferentiation supports the onset of a stem cell-like state by inducing the activation of de novo enhancers, which drive the transcriptional activation of oncogenic pathways. Furthermore, we demonstrate that the MYC-driven epigenetic reprogramming favors the formation and maintenance of tumor initiating cells endowed with metastatic capacity. This study supports the notion that MYC-driven tumor initiation relies on cell reprogramming, which is mediated by the activation of MYC-dependent oncogenic enhancers, thus establishing a therapeutic rational for treating basal-like breast cancers.
Changes in levels of major yolk protein in the coelomic fluid and gonad during the reproductive cycle in wild sea urchins,Mesocentrotus nudus
Authors: Ura Kazuhiro , Takei Narumi , Higuchi Ichiro , Yuhi Tomoharu , Nishimiya Osamu , Takagi Yasuaki 
Published: December 2017

AbstractBoth female and male sea urchins accumulate the major yolk protein (MYP) in the nutritive phagocytes of immature gonads before gametogenesis, and MYP is the most abundant protein in the coelomic fluid of both sexes. In females, MYP in the coelomic fluid is taken up by the nutritive phagocytes and transported to the growing oocytes. This study examined quantitative changes of MYP in the coelomic fluid of both sexes during the reproductive cycle of wild sea urchins,Mesocentrotus nudus. Levels of MYP in the coelomic fluid of females increased and reached a peak at the histological pre-mature stage of gonad activity (i.e. Stage 3), and positive correlation between the MYP level and the gonadosomatic index (GSI) was observed. In male sea urchins the level of MYP in the coelomic fluid increased at the pre-mature stage, though positive correlation between the MYP level and GSI was not observed. These results indicate that MYP in the coelomic fluid is suitable as a biomarker of the onset and progression of sexual maturity in female sea urchins.
Novel psychoactive substance use by mental health service consumers: an online survey of inpatient health professionals’ views and experiences
Authors: Hughes Elizabeth , Bressington Dan , Sharratt Kathryn , Gray Richard 
Published: December 2017

Purpose
There is evidence that novel psychoactive substances (NPS) are commonly used by people with severe mental illness. The purpose of this paper is to undertake a scoping survey to explore the inpatient mental health workers’ perceptions of NPS use by consumers.

Design/methodology/approach
A cross-sectional online survey of mental health professionals is used in the study. The participants were opportunistically recruited through social media and professional networks.

Findings
A total of 98 participants (of 175 who started the survey) were included in the analysis. All reported that some patients had used NPS prior to admission. Over 90 per cent of participants reported observing at least one adverse event relating to NPS use in the previous month. The majority of participants reported that patients had used NPS during their inpatient admission. Three quarters were not clear if their workplace had a policy about NPS. Most wanted access to specific NPS information and training. The participants reported that they lacked the necessary knowledge and skills to manage NPS use in the patients they worked with.

Research limitations/implications
Whilst the authors are cautious about the generalisability (due to methodological limitations), the findings provide useful insight into the perceptions of inpatient staff regarding the extent and impact of NPS use including concerns regarding the impact on mental and physical health, as well as ease of availability and a need for specific training and guidance.

Practical implications
Mental health professionals require access to reliable and up-to-date information on changing trends in substance use. Local policies need to include guidance on the safe clinical management of substance use and ensure that NPS information is included.

Originality/value
To the best of the authors’ knowledge, this is the first survey of the perceptions of mental health staff working in inpatient mental health settings regarding NPS. The findings suggest that NPS is a common phenomenon in inpatient mental health settings, and there is a need for more research on the impact of NPS on people with mental health problems.
Harm reduction in a Norwegian housing first project: a qualitative study of the treatment providers’ practice
Authors: Andvig Ellen Sofie , Sælør Knut Tore , Ogundipe Esther 
Published: December 2017

PurposeLittle is known about how harm reduction is practiced in Norwegian housing first (HF) projects. The purpose of this paper is to explore, describe, and interpret how providers apply a harm reduction approach within a housing project focused on individuals who are homeless with co-morbid substance use and mental health problems.Design/methodology/approachThis qualitative study was part of a larger evaluation study of a three-year HF project in a Norwegian municipality. Data were collected using four multi-stage focus groups with five providers working in the HF project. Focus group interviews were transcribed verbatim and analyzed using thematic analysis.FindingsAnalysis resulted in three main themes: “Letting the service user sit in the driver’s seat,” “We don’t follow service provision contracts, we do everything,” and “Collaborating with the local community.”Research limitations/implicationsThere is a need to develop increased knowledge about service users’ experiences within the harm reduction approach.Practical implicationsTo practice effective harm reduction, treatment providers must have open authorizations and the opportunity to exercise professional judgment. Harm reduction practice must also focus on social, political, and economic factors influencing users’ everyday lives.Originality/valueThe paper contributes to the knowledge base on harm reduction within HF practice that differs from a traditional model wherein clients are expected to abstain from substance use. It highlights important preconditions for challenges practitioners might encounter at both individual and service system levels.
3PL provider selection by AHP and TOPSIS methodology
Authors: Bianchini Augusto 
Published: January 2018

Purpose
The purpose of this paper is to provide a two-phase analytical hierarchy process (AHP) and the technique for order preference by similarity to ideal solution (TOPSIS) approach that is a multi-criteria decision-making methodology (MCDM) in the evaluation of third-party logistics (3PL) providers.

Design/methodology/approach
After the description of the selection criteria of 3PL providers that are determined by company management, the weights of criteria are calculated by applying the AHP method. The TOPSIS method is then employed to achieve the final ranking results. A sensitivity analysis is developed for a deeper comprehension of results reliability.

Findings
The paper shows the complexity of a real 3PL provider change. At the same time, a simple MCDM methodology is provided to assure the success of this activity in which many other companies have failed.

Research limitations/implications
The proposed MCDM methodology represents a very good compromise between a reliable solution and reasonable computational and human effort. 3PL provider selection or change is an extremely complex decision that could be investigated in greater detail with other more complex methodology, with a consequently higher investment, that is not so affordable for all budgets.

Originality/value
It is the first time that a two-phase AHP and TOPSIS methodology is applied to an Italian biscuit company for a 3PL provider change together with the analysis of logistics performance after two years. The paper shows a detailed methodology application that could be very useful for managers for their specific application.
Stakeholder responses toward fast food chains’ CSR
Authors: Kim Yeonsoo , Zapata Ramos Mari Luz 
Published: January 2018

Purpose
The purpose of this paper is to examine how stakeholders perceive the motives behind fast food companies’ public health-related corporate social responsibility (CSR) and general social issue-related CSR initiatives, and their responses toward CSR in terms of supportive communication intent, investment intent, and purchase intent. The authors further examine the impact of perceived CSR motives on intent and whether a healthier chain image has an effect on stakeholder responses.

Design/methodology/approach
An online experiment was conducted. This study employed a randomized 2 (CSR type: health-related CSR vs generic social issue-related CSR)×2 (chain image: healthier chain vs general fast-food chain) full factorial design using general stakeholder samples.

Findings
For an ordinary fast food restaurant, generic social issue-related CSR programs elicited significantly more positive perceptions of CSR motives, supportive communication intent and investment intent, than public-health related CSR. When a company has a healthier image, stakeholders do not distinguish between CSR types. Stakeholders perceive both CSR types as stemming from mutually beneficial motives and show neutral to slightly positive reactions to both CSR. A positively perceived CSR motive plays a determinant role in anticipating communication, investment, and purchase intents.

Originality/value
This is the first study that examines stakeholder perception of motives behind and responses toward fast food chains’ health-related vs generic social issue-related CSR initiatives, in light of corporate image. The study findings help public relations practitioners, public health professionals, parent groups, and legislators understand stakeholders’ reactions toward CSR initiatives in the fast food industry and help them monitor practices for improvements.
The methodological quality of systematic reviews indexed in the MEDLINE database
Authors: Martín-Rodero Helena , Sanz-Valero Javier , Galindo-Villardón Purificación 
Published: December 2017

Purpose
The purpose of this paper is to describe and analyse the methodology quality of the literature search protocols of systematic reviews and to assess the relevance of the search filter that applies PubMed for retrieving this type of publication of the MEDLINE database.

Design/methodology/approach
For the selection of the document type, a literature search about nutritional and metabolic diseases was carried out in MEDLINE and the PubMed filter was used for retrieving “Systematic Reviews”, selecting “Nutritional and Metabolic Diseases” from the Medical Subject Headings (MeSH) database as Major Topic to determine the area of knowledge. Data analysis was carried out using “External Logistic Biplot”, a novel multivariate statistical technique in the field of medical documentation.

Findings
The results highlight the large variability of the methodology used in the literature search protocols of the systematic reviews analysed and confirm the low precision of the filter used by PubMed for the recovery of systematic reviews.

Originality/value
The Logistic Biplot used in this research allows an optimal categorization of the different documentary typologies and classifies the documents by their methodological quality, demonstrating its usefulness for the future development of the bibliometric analysis.