bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post-graduate scholars can publish Compended-Guides to the literature of their field using Knowledge-Step-Forums
Authors: Jewett Don L 
Published: January 2018

"Publication forms the core structure supporting the development and transmission of scientific knowledge" (Galbraith2015). Yet, with the WorldWideWeb a dominant part of current scientific publication and information-dissemination, internet "publication" is still paper-based in its style and methods, even when it uses a digital medium. Such a paper-based publishing "model" is not adequate for a Web-based world.
In 2006, an estimated 3,700 peer-reviewed scientific articles were published per day (Bjork2009)! This totals about 1.35 million articles per year. A similar estimate for 2011 was 1.8 million (Outsell2013), which is almost 5,000 per day. The total number of English-language scholarly documents accessible on the Web was estimated in 2014 to be at least 114 million (Khabsa2014). The methods and features described here are clearly needed now, and will be absolutely necessary in the future, when even more articles are published and available.
In this context of an overload of information from scientific articles, described here is the idea of Knowledge-Step Forums as the basis for creating new peer-reviewed, compended "Literature-Guides", each on a very narrow topic and in a MultiLevel Format (Knowledge-Step Compendia). A multitude of Forum-Compendors, who need not be a senior faculty member (as is the case in traditional literature-reviews), but can be pre-docs, post-docs, and senior medical/surgical residents, will be aided by their mentors and online experts to create these Knowledge-Step Compendia. All participants (students and faculty) will be motivated by their own self-interest and thus each gains from the activity, it being a means to self-organize groups of like-minded scholars that can be the basis for reviews of new data, discovering new ideas, and finding jobs.
The Software for Knowledge-Step Forums will also be useful to speed publication on the Web because it will easily support Publication Preprints with online peer-review.
Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates
Authors: Marjanović David , Laurin Michel 
Published: January 2018

The largest published data matrix for phylogenetic analysis of Paleozoic limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) supported variously controversial hypotheses; e.g., it recovered Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH) – though only, as we show, by one step.
We report thousands of suboptimal scores due to typographic and similar errors and to questionable coding decisions: logically linked (redundant) characters, others with only one described state, even characters for which most taxa were scored after presumed relatives. Even continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded.
After these issues are improved – we document and justify all changes to the matrix –, but no characters are removed or added, we find (Analysis R1) much longer trees with e.g. monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega rootward of Acanthostega; Anthracosauria rootward of Temnospondyli which includes Caerorhachis; the LH is 9 steps shorter than the TH (R2; constrained) and 12 steps shorter the “polyphyly hypothesis” (PH – R3; constrained).
We then added 48 OTUs to the original 102. This destabilizes some parts of the tree, e.g. the positions of Anthracosauria, Temnospondyli and Caerorhachis. Yet, many added taxa have well-resolved positions, ranging from the well known Chroniosaurus (Chroniosuchia), which lies just crownward of Temnospondyli and Gephyrostegidae, to isolated lower jaws. Even though Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4) and TH (R5) rises to 12 steps, that between LH and PH (R6) to 17 steps; the TH also requires several more regains of lost bones than the LH. Brachydectes (Lysorophia) is not found next to Lissamphibia.
We duplicated all analyses after coding losses of bones as irreversible. The impact on the results is modest. Anthracosauria is always rootward of Temnospondyli. With 102 OTUs, the LH (R7) is 10 steps shorter than the TH (R8) and 11 steps shorter than the PH (R9); with 150, the LH (R10) is 14 steps shorter than the TH (R12) – and 13 steps shorter than the PH (R11).
Bootstrap values are mostly low, and plummet when taxa are added. Statistically, the TH (R2, R5, R8, R12) is not distinguishable from the LH or the PH, but the LH (R1, R4, R7, 53 R10) and the PH (R3, R6, R9, R11) may be distinguishable from each other under both taxon samples and both reversibility settings. A reliable test is not available.
We discuss the relationships of certain taxa, approaches to coding, some character complexes, and prospects for further improvement of this matrix.
To transmit genes without becoming mother: An evolutionary conflict behind denial of pregnancy
Authors: Sandoz Patrick 
Published: January 2018

Aim: The etiology of pregnancy denial remains poorly understood. Neither necessary nor sufficient conditions can be synthesized from the risk factors identified from psychological analyses. In accordance with clinical observations, we aim to explain denial of pregnancy from an evolutionary conflict perspective.
Methods: Authors investigate evolutionary biology aspects and emphasize on the transition from solitary animal species to social species. The possibility of conflicts between primitive species-perpetuation forces and subjective social-identity forces are explored.
Results: As members of a social species, human beings have a dual, contradictory character of independent organisms but interdependent people. This results in evolutionary inherited conflicts that, with respect to women's reproduction, distinguish between primitive and social-identity issues: i) to transmit genes by giving birth and ii) to become mother. Authors explain denial of pregnancy as a standby-in-tension response to a conflicting attempt to transmit genes without becoming mother. It may thus be considered as temporarily adaptive response by postponing conflict resolution. This model, based on subjective internal appraisals, is compatible with a huge diversity of causative events as expected from the specificity of each woman's life course.
Conclusions: The proposed etiology is consistent with clinical observations and brings prior models into agreement. From a clinical practice perspective, the ability to explain denial of pregnancy rationally may favor understanding and acceptation by concerned women. Health professionals' information may also be facilitated and psychotherapeutic follow up may gain in efficiency with reduced recidivism.
More generally, this evolutionary conflict approach provides a supplementary perspective to explore psychosomatic dysfunctions.
A primer for managing international collaboration and legal compliance in biobank based genomics
Authors: Klingström Tomas , Bongcam-Rudloff Erik , Reichel Jane 
Published: January 2018

Resolving ethical and legal concerns is a time consuming but rarely insurmountable task when obtaining samples from biobanks. The BBMRI-LPC project has throughout its lifetime resolved numerous such issues and intense communication between involved researchers and experts have been necessary to resolve various issues. To facilitate efficient communication it is useful for non-experts to have an at least basic understanding on how the regulatory system for managing biological samples is constructed to balance the sometimes conflicting needs of privacy, trust and scientific progress.
Although laws regulating research oversight have been implemented differently in every country, there is a similarity of core principles founded on international charters. These core principles are based on the concept of consent and actions taken by the biobank in regards to sample usage rely on either an explicit or presumed consent. In interview studies among donors chief concerns among donors are focused on privacy, efficient sample utilization and if donors are given access to information generated from their samples. Despite a lack of clear evidence regarding which concern takes precedent among donors, scientific as well as public discourse has largely focused on privacy concerns and the right of donors to control the usage of their samples.
As a result biobank governance has taken a largely negative approach to uncertainties in sample utilization. This mean that sample usage is likely to be restricted if there is any uncertainty if the intended usage is in line with donor expectations. To help biobank professionals avoid making unnecessary mistakes we have developed this basic primer covering the relationship between ethics and law, the concept of informed consent and consideration for returning findings to donors.
Multivariate statistical approaches for uncovering spatio-temporal and treatment-derived differences in the molecular physiology of a model coral-dinoflagellate mutualism: a meta-analysis
Authors: Mayfield Anderson B , Chen Chii-Shiarng 
Published: January 2018

Background: Multivariate statistical approaches (MSA), such as principal components analysis and multidimensional scaling, seek to uncover meaningful patterns within datasets by considering multiple response variables in a concerted fashion. Although these techniques are readily used by ecologists to visualize and explain differences between study sites, they could theoretically be employed to differentiate organisms within an experimental framework while simultaneously identifying response variables that drive documented experimental differences.
Methods: A meta-analysis employing various MSA was conducted to re-analyze data from two studies that sought to understand the response of the common, Indo-Pacific reef coral Seriatopora hystrix to temperature changes.
Results: Gene expression and physiological data partitioned experimental specimens by time of sampling, treatment temperature, and site of origin upon employing MSA.
Discussion: These findings 1) signify that S. hystrix and its dinoflagellate endosymbionts display physiological and molecular signatures that are characteristic of sampling time, site of colony origin, and/or temperature regime and 2) promote the utility of MSA for documenting biologically meaningful shifts in the physiological and/or sub-cellular response of marine invertebrates exposed to environmental change.
Natural compounds as potential PI3K-AKT1 signaling pathway inhibitors by means of pharmacophore modeling
Authors: Dotolo Serena , Gaeta Angelo , Facchiano Angelo 
Published: January 2018

AKT1, a modulator of PI3K-AKT1 pathway, is dysregulated in several human diseases, and understanding deeper its role in the complexity of biological systems remains an important goal. The research has been focused on development and study of potential synthetic-natural allosteric inhibitors for AKT1, and recent studies have shown how some natural compounds may play this role (1). We are interested in a screening of small bioactive molecules, in order to identify the potential “lead compounds”, for next experimental assays, searching those potentially able to inhibit AKT1 and its signaling mechanisms, trying to re-establish the normal balance and safeguarding of human health. The workflow executed is the following: 1) search in PDB database of a model structure for AKT1 (comparing different structures and choosing the most suitable for our purposes), through algorithm BLAST. 2) pharmacophore modeling by means of ZINCpharmer web-server, to investigate all purchasable compounds of the ZINC database, using the Pharmer as efficient and exact pharmacophore search technology (2). 3) screening of possible natural AKT1 inhibitors, using the pharmacophore generated by ZINCpharmer, choosing only the best candidates for next steps. 4) molecular validation of selected compounds, to analyze the ligand-protein interactions. 5) study of physical-chemical properties of selected compounds to trace their origin. 6)prediction of their biosynthetic pathways and Pharmacokinetics/Pharmacodynamics models, by means of ADMET/toxicity predictor server in order to direct the design of next experimental assays. Our attention is focused on the study of natural compounds that can show many health benefits, through the realization and analysis of “pharmacophore modeling”, essential step in drug discovery (3). We selected the PDB structure 3O96 as the reference complex (protein-ligand), and we analyzed it by means of ZINCpharmer, to generate three different “pharmacophore models” with three different list of natural compounds. It is performed a thorough screening of compounds applying other filters, to find some good candidates as possible natural AKT1 allosteric inhibitors. The compounds that match a well-defined pharmacophore have been analyzed through direct molecular docking, for selecting only the best candidates and studying the protein-ligand interactions. Selected compounds have been investigated in more details, to trace their origin, by their chemical-physical properties. This information can help us to predict some plausible enzyme-catalyzed reaction pathways, investigated with PathPred server and KEGG compound database, in order to highlight the most important reactions for biosynthesis of compounds and obtain PharmacoKinetics/PharmacoDynamics (PK/PD) models through ADME predictor server and to realize of next experimental assays.
(Abstract truncated at 3,000 characters - the full version is available in the pdf file)
A cellular automata to simulate the growth and death of a cell culture
Authors: Guerrisi Giuseppe , Giordano Deborah , Marabotti Anna , Raiconi Giancarlo , Tagliaferri Roberto 
Published: January 2018

Motivation: The term “cell culture” is generally referred to the process by which some cells, often derived from multicellular organisms or tissues, or tumoral cell lines, are grown under controlled conditions outside of their natural environment. This system is very useful for different applications, for example to study physiological phenomena, or for the production of some useful molecules, or for testing the toxicity of some compounds. The life of the cells in culture is conditioned by many elements. Apart from physical factors such as pH and temperature, the growth of a cell culture is conditioned by its density: cells compete for the nutrients and growth factors available and die when they are exhausted. Moreover, dead cells release in the medium some toxic factors that, in their turn, can lead the surrounding cells to death. Additionally, the presence of exogenous toxic factors in the medium can induce cell death We present a cellular automata developed in order to reproduce the growth of a cell culture of a particular human cell line, Caco-2, derived from human colorectal adenocarcinoma cells. The cellular automata has been developed in order to reproduce the phenotype of Caco-2 cells, their cell cycle with all phases, and the influence of 4-nonylphenol (4-NP), an environmental pollutant, on this model system.
Methods: The cellular automata developed is a grid whose dimensions reproduce a cell counting Burker chamber. Two matrices have been used to take into account, respectively, the global duration of the cellular growth and the phase of the cell cycle for each cell. Two vectors are also introduced to take into account the length of each phase and their variability range. A shuffling algorithm is used to distribute the starting cells on the chamber, then the algorithm starts by assigning a variable lag phase before reproducing the start of the cell cycle with the entering of the cells in G1 phase. All the following phases of the cell cycle are characterized by a fixed length (in minutes) + 10% variability. The cell death is described by a logarithmic function that is influenced by different factors: culture density, cellular senescence, presence of dead cells in the environment of each cell, introduction of a toxic substance. The application was developed in a stand-alone manner and has been written in Java using the OpenGL library integrated in Java.
Results The application is made by an intuitive GUI to set several parameters useful for the simulation (see Figure, panel A). In order to highlight the different cell cycle phases, different colors were attributed to each phase. The cellular automata is evolving in the space and in the time reproducing the four steps of the cell cycle (G1, S, G2, M). The evolution of the simulated cell growth reproduces the phenomena present in a real Caco-2 cell culture. (Abstract truncated at 3,000 characters - the full version is available in the pdf file)
Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi
Authors: Ishengoma Edson , Agaba Morris , Cavener Douglas R 
Published: January 2018

Background. The capacity of species to respond and perceive visual signal is integral to their evolutionary success. Giraffe is closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with most of them. To what extent giraffe unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood.
Methods. The recent availability of giraffe and okapi genome provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site test of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and their corresponding orthologous sequences from other mammals obtained from public gene banks.
Results. Signatures of selection was identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW in giraffe. Significant selection divergence was identified in SAG while positive selection was detected in LUM when okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants.
Discussion. By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and okapi vision adaptation. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and okapi habitat. Moreover, requirement for long distance vision associated with predation likely played an important role in the adaptive pressure on giraffe vision genes.
Atropos: specific, sensitive, and speedy trimming of sequencing reads
Authors: Didion John P , Martin Marcel , Collins Francis S 
Published: January 2018

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves a four-fold increase in trimming accuracy and a decrease in execution time of ~50% (using 16 parallel execution threads). Furthermore, Atropos maintains high accuracy even when trimming simulated data with a high rate of error. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of most current-generation sequencing data sets.
Atropos is open source and free software written in Python and available at https://github.com/jdidion/atropos.
The psychometric properties of a Scale for Achievement Motive in Rehabilitation, and the effects of achievement motive on self-efficacy, hopelessness, and economic poverty for community-dwelling elderly people using rehabilitation services
Authors: Sano Nobuyuki , Kyougoku Makoto 
Published: January 2018

Background: Achievement motive is expected to prevent lack of self-efficacy and hope, which negatively impact rehabilitation support, health, and psychological well-being. It has been indicated that the factor structure of the Scale for Achievement Motive in Rehabilitation (SAMR), which was developed to evaluate the state of achievement motive in clients, is affected by gender, age, and type of disorder; however, the item responses for the SAMR have not been fully elucidated.
Purpose: This study demonstrates the effects of achievement motive on self-efficacy, hopelessness, and economic poverty. The secondary purpose was to test the psychometric properties for the robustness of factor analysis and the item responses for the SAMR.
Methods: A cross-sectional study was conducted to assess achievement motive, self-efficacy, hopelessness, and economic poverty in 581 community-dwelling elderly people. Data from a self-administered questionnaire were analyzed for structural relationship, using a structural equation modeling approach, multi-group confirmatory factor analysis, and multidimensional item response theory.
Results: For structural relationship, the modified model indicated an adequate model fit level {Comparative Fit Index (CFI) = 0.914, Tucker Lewis Index (TLI) = 0.906, Root Mean Square Error of Approximation (RMSEA) = 0.062, 90% Confidence Interval (CI) [0.058, 0.066]}, with significant effects among achievement motive, self-efficacy, and hopelessness; i.e., the direct and indirect effects of achievement motive on self-efficacy and hopelessness were accepted. For multi-group confirmatory factor analysis, the SAMR factor structure displayed strong measurement invariance across the group for gender, care level, and age. For multidimensional item response theory, the results showed enough item discrimination and difficulty intensity for each SAMR item.
Discussion: This study suggests that achievement motive is important to prevent clients from missing and giving up their goals and to execute support in rehabilitation smoothly. In addition, we suggest that SAMR is a structurally valid scale to measure two-factor structures across different groups, and the item characteristics and total score enable proper understanding of achievement motive.