bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental correlates of internal coloration in frogs vary throughout space and lineages
Authors: Franco-Belussi Lilian , Provete Diogo Borges , de Oliveira Classius 
Published: March 2017

SummaryInternal organs of ectotherms have melanin-containing cells. Several studies analyzed their developmental origin, role in immunity, and hormonal regulation. However, little is known about how environmental variables influence the distribution and quantity of organ coloration. Here, we addressed how environmental variables (temperature, UV, and photoperiod) influence the internal coloration of amphibians after controlling for spatial and phylogenetic autocorrelations. Coloration in all organs was correlated with phylogeny. However, the coloration of the heart, kidneys, and rectum of hylids,R. schneideri,someLeptodactylus,andProceratophryswere influenced by temperature and photoperiod, whereas that of the testicle, lumbar parietal peritoneum, lungs, and mesenterium of Leiuperinae, Hylodidae,Adenomera,mostLeptodactyluswere influenced by UVB and temperature variation. Therefore, the amount of internal melanin seems to be a key trait influencing species distribution of frogs throughout space, since it can protect internal organs against the deleterious effect of high UV-B, temperature variation, and photoperiod.SignificanceThe functions of internal coloration in fishes and frogs are little known. Internal pigmentation is commonly altered in fish and the degree of response is correlated with body transparency levels, suggesting possible adaptive functions. Here, we assume that internal melanin has protective functions against UV-B, temperature variation, and photoperiod. Thus it could influence frogs species distribution throughout space. The melanin coloration of each organ was influenced by distinct environmental variables depending on the lineages of species. Our results could direct further studies about the functions of internal coloration.
First landscape of binding to chromosomes for a domesticated mariner transposase in the human genome: diversity of genomic targets of SETMAR isoforms in two colorectal cell lines
Authors: Antoine-Lorquin Aymeric , Arnaoty Ahmed , Asgari Sassan , Batailler Martine , Beauclair Linda , Belleannée Catherine , Bire Solenne , Buisine Nicolas , Coustham Vincent , Girault Alban , Guyetant Serge , Lecomte Thierry , Piégu Benoît , Pitard Bruno , Stévant Isabelle , Bigot Yves 
Published: March 2017

ABSTRACTSetmaris a 3-exons gene coding a SET domain fused to aHsmar1transposase. Its different transcripts theoretically encode 8 isoforms with SET moieties differently spliced.In vitro,the largest isoform binds specifically toHsmar1DNA ends and with no specificity to DNA when it is associated with hPso4. In colon cell lines, we found they bind specifically to two chromosomal targets depending probably on the isoform,Hsmar1ends and sites with no conserved motifs. We also discovered that the isoforms profile was different between cell lines and patient tissues, suggesting the isoforms encoded by this gene in healthy cells and their functions are currently not investigated.
Clinically Useful Brain Imaging for Neuropsychiatry: How Can We Get There?
Authors: Milham Michael P. , Craddock R. Cameron , Klein Arno 
Published: March 2017

AbstractDespite decades of research, visions of transforming neuropsychiatry through the development of brain imaging-based ‘growth charts’ or ‘lab tests’ have remained out of reach. In recent years, there is renewed enthusiasm about the prospect of achieving clinically useful tools capable of aiding the diagnosis and management of neuropsychiatric disorders. The present work explores the basis for this enthusiasm. We assert that there is no single advance that currently has the potential to drive the field of clinical brain imaging forward. Instead, there has been a constellation of advances that, if combined, could lead to the identification of objective brain imaging-based markers of illness. In particular, we focus on advances that are helping to: 1) elucidate the research agenda for biological psychiatry (e.g., neuroscience focus, precision medicine), 2) shift research models for clinical brain imaging (e.g., big data exploration, standardization), 3) break down research silos (e.g., open science, calls for reproducibility and transparency), and 4) improve imaging technologies and methods. While an arduous road remains ahead, these advances are repositioning the brain imaging community for long-term success.
Managed woodlot revealed a trade-off between edible leaves and timber production inVitex donianaSweet (Lamiaceae)
Authors: N’Danikou Sognigbé , Tchokponhoué Dèdéou A. , Houdégbé Aristide C. , Agossou Aboègnonhou O.C. , Achigan-Dako Enoch G. , Assogba Komlan Françoise , Vodouhè Raymond S. , Ahanchédé Adam 
Published: March 2017

AbstractVitex donianaSweet is a major wild-harvested tree resource for food in Benin. However, the species is under threats characterised by increasing human pressure on remnant populations. This study represents the first to explore species’ response to biotic stress. We tested the response ofV. donianato coppicing and fertilization. Two stump heights (20 and 40 cm) in combination with three organic manure rates (0.5; 1 and 1.5 kg per seedling), with eight replicates were tested in a randomised complete block design. We used mixed effect models with pseudoreplication, and the maximum likelihood method to compare effects of fixed factors on sprouting vigour, sprout growth and biomass yield in the short (12 months) and medium (5 years) terms. Results indicated that stump height significantly affected sprouting and all growth parameters, in the short and medium terms. However, there seemed a delayed effect of manure. We found initial seedling growth also an important factor. The hidden effect of stump height on biomass yield is discussed. Findings clearly indicate a trade-off between edible leaves and timber production by managed woodlot. Implications of findings for further investigation of above and below ground biomass dynamics and resources allocation in treated trees are discussed.HighlightsA clear trade-off between edible leaves and timber production is observed in managedVitex donianaSweet woodlot. Coppicing as a biotic stress induced important physiological changes that merit further investigations.
Learning to See Again: Biological Constraints on Cortical Plasticity and the Implications for Sight Restoration Technologies
Authors: Beyeler Michael , Rokem Ariel , Boynton Geoffrey M. , Fine Ione 
Published: March 2017

1. ABSTRACTThe “bionic eye” – so long a dream of the future – is finally becoming a reality with retinal prostheses available to patients in both the US and Europe. However, clinical experience with these implants has made it apparent that the vision provided by these devices differs substantially from normal sight. Consequently, the ability to learn to make use of this abnormal retinal input plays a critical role in whether or not some functional vision is successfully regained. The goal of the present review is to summarize the vast basic science literature on developmental and adult cortical plasticity with an emphasis on how this literature might relate to the field of prosthetic vision. We begin with describing the distortion and information loss likely to be experienced by visual prosthesis users. We then define cortical plasticity and perceptual learning, and describe what is known, and what is unknown, about visual plasticity across the hierarchy of brain regions involved in visual processing, and across different stages of life. We close by discussing what is known about brain plasticity in sight restoration patients and discuss biological mechanisms that might eventually be harnessed to improve visual learning in these patients.
Beyond Reward Prediction Errors: Human Striatum Updates Rule Values During Learning
Authors: Ballard Ian , Miller Eric M. , Piantadosi Steven T. , Goodman Noah , McClure Samuel M. 
Published: March 2017

ABSTRACTHumans naturally group the world into coherent categories defined by membership rules. Rules can be learned implicitly by building stimulus-response associations using reinforcement learning (RL) or by using explicit reasoning. We tested if the striatum, in which activation reliably scales with reward prediction error, would track prediction errors in a task that required explicit rule generation. Using functional magnetic resonance imaging during a categorization task, we show that striatal responses to feedback scale with a “surprise” signal derived from a Bayesian rule-learning model and are inconsistent with RL prediction error. We also find that striatum and caudal inferior frontal sulcus (cIFS) are involved in updating the likelihood of discriminative rules. We conclude that the striatum, in cooperation with the cIFS, is involved in updating the values assigned to categorization rules when people learn using explicit reasoning.
Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks
Authors: Beretta Stefano , Castelli Mauro , Gonçalves Ivo , Merelli Ivan , Ramazzotti Daniele 
Published: March 2017

AbstractGene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental data through computational analysis. However, this task is typically complicated by the enormously large scale of the unknowns in a rather small sample size. Furthermore, when the goal is to study causal relationships within the network, tools capable of overcoming the limitations of correlation networks are required. In this work, we make use of Bayesian Graphical Models to attach this problem and, specifically, we perform a comparative study of different state-of-the-art heuristics, analyzing their performance in inferring the structure of the Bayesian Network from breast cancer data.
A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content inOryza sativa
Authors: Bowman Megan J. , Pulman Jane A. , Liu Tiffany L. , Childs Kevin L. 
Published: March 2017

AbstractAccurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent the variation found within a genome. One aspect of gene variation is GC content, which differs across species and is bimodal in grass genomes. We find that gene prediction programs trained on genes with random GC content do not completely predict all grass genes with extreme GC content. We present a new GC-specific MAKER annotation protocol to predict new and improved gene models and assess the biological significance of this method inOryza sativa.
Is the 25-year hepatitis C marathon coming to an end to declare victory?
Authors: Ahmed Khulood , Almashhrawi Ashraf , Ibdah Jamal A. , Tahan Veysel 
Published: March 2017

ABSTRACTHepatitis C virus (HCV) which was originally recognized as posttransfusion non-A, non-B hepatitis has been a major global health problem affecting 3% of the world population. Interferon/peginterferon and ribavirin combination therapy was the backbone of chronic HCV therapy for two decades of the journey. However, the interferon based treatment success rate was around 50% with many side effects. Many chronic HCV patients with psychiatric diseases, or even cytopenias, were ineligible for HCV treatment. Now, we no longer need any injectable medicine. New direct-acting antiviral agents against HCV allowed the advance of interferon-free and ribavirin-free oral regimens with high rates of response and tolerability. The cost of the medications should not be a barrier to their access in certain parts of the world. While we are getting closer, we should still focus on preventing the spread of the disease, screening and delivering the cure globally to those in need. In the near future, development of an effective vaccine against HCV would make it possible to eradicate HCV infection worldwide completely.
Segregation lift: A general mechanism for the maintenance of polygenic variation under seasonally fluctuating selection
Authors: Wittmann Meike J. , Bergland Alan O. , Feldman Marcus W. , Schmidt Paul S. , Petrov Dmitri A. 
Published: March 2017

AbstractMost natural populations are affected by seasonal changes in temperature, rainfall, or resource availability. Seasonally fluctuating selection could potentially make a large contribution to maintaining genetic polymorphism in populations. However, previous theory suggests that the conditions for multi-locus polymorphism are restrictive. Here we explore a more general class of models with multi-locus seasonally fluctuating selection in diploids. In these models, loci first contribute additively to a seasonal score, with a dominance parameter determining the relative contributions of heterozygous and homozygous loci. The seasonal score is then mapped to fitness via a monotonically increasing function, thereby accounting for epistasis. Using mathematical analysis and individual-based simulations, we show that stable polymorphism at many loci is possible if currently favored alleles are sufficiently dominant with respect to the additive seasonal score (but not necessarily with respect to fitness itself). This general mechanism, which we call “segregation lift”, operates for various genotype-to-fitness maps and includes the previously known mechanism of multiplicative selection with marginal overdominance as a special case. We show that segregation lift may arise naturally in situations with antagonistic pleiotropy and seasonal changes in the relative importance of traits for fitness. Segregation lift is not affected by problems of genetic load and is robust to differences in parameters across loci and seasons. Under segregation lift, loci can exhibit conspicuous seasonal allele-frequency fluctuations, but often fluctuations may also be small and hard to detect. Via segregation lift, seasonally fluctuating selection might contribute substantially to maintaining genetic variation in natural populations.
Population-specific imputation of gene expression improves prediction of pharmacogenomic traits for African Americans
Authors: Gottlieb Assaf , Daneshjou Roxana , DeGorter Marianne , Montgomery Stephen B. , Altman Russ B. 
Published: March 2017

ABSTRACTGenome-wide association studies (GWAS) are useful for discovering genotype-phenotype associations but are limited because they require large cohorts to identify a signal, which can be population-specific. Mapping genetic variation to genes improves power, and allows the effects of both protein coding variation as well as variation in expression to be combined into “gene level” effects.Previous work has shown that warfarin dose can be predicted using information from genetic variation that affects protein coding regions. Here, we introduce a method that improves the predicted dose by integrating tissue-specific gene expression. In particular, we use drug pathways and expression quantitative trait loci knowledge to impute gene expression—on the assumption that differential expression of key pathway genes may impact dose requirement. We focus on 116 genes from the pharmacokinetic (PK) and pharmacodynamic (PD) pathways of warfarin within training and validation sets comprising both European and African-descent individuals. We build gene-tissue signatures associated with warfarin dose, and identify a signature of eleven gene-tissue pairs that significantly augment the International Warfarin Pharmacogenetics Consortium dosage-prediction algorithm in both populations. Our results demonstrate that imputed expression can improve dose prediction, in a population-specific manner.
The mutational decay of male and hermaphrodite competitive fitness in the androdioecious nematodeC. elegans, in which males are naturally rare
Authors: Yeh Shu-Dan , Saxena Ayush , Crombie Timothy , Feistel Dorian , Johnson Lindsay M. , Lam Isabel , Lam Jennifer , Saber Sayran , Baer Charles F. 
Published: March 2017

AbstractAndrodioecious Caenorhabditis have a high frequency of self-compatible hermaphrodites and a low frequency of males. The effects of mutations on male fitness are of interest for two reasons. First, when males are rare, selection on male-specific mutations is less efficient than in hermaphrodites. Second, males may present a larger mutational target than hermaphrodites because of the different ways in which fitness accrues in the two sexes.We report the first estimates of male-specific mutational effects in an androdioecious organism. The rate of male-specific inviable or sterile mutations is ≤ 5 x 10−4/generation, below the rate at which males would be lost solely due to those kinds of mutations. The rate of mutational decay of male competitive fitness is ~0.17%/generation; that of hermaphrodite competitive fitness is ~0.11%/generation. The point estimate of ~1.5X faster rate of mutational decay of male fitness is nearly identical to the same ratio in Drosophila. Estimates of mutational variance (VM) for male mating success and competitive fitness are not significantly different from zero, whereas VM for hermaphrodite competitive fitness is similar to that of non-competitive fitness. The discrepancy between the two sexes is probably due to the greater inherent variability of mating relative to internal self-fertilization.
Changes in PUB22 Ubiquitination Modes Triggered by MITOGEN-ACTIVATED PROTEIN KINASE3 Dampen the Immune Response
Authors: Furlan Giulia , Nakagami Hirofumi , Eschen-Lippold Lennart , Jiang Xiyuan , Majovsky Petra , Kowarschik Kathrin , Hoehenwarter Wolfgang , Lee Justin , Trujillo Marco 
Published: March 2017

Abstract
Crosstalk between posttranslational modifications, such as ubiquitination and phosphorylation, play key roles in controlling the duration and intensity of signaling events to ensure cellular homeostasis. However, the molecular mechanisms underlying the regulation of negative feedback loops remain poorly understood. Here, we uncover a pathway in Arabidopsis thaliana by which a negative feedback loop involving the E3 ubiquitin ligase PUB22 that dampens the immune response is triggered by MITOGEN-ACTIVATED PROTEIN KINASE3 (MPK3), best known for its function in the activation of signaling. PUB22's stability is controlled by MPK3-mediated phosphorylation of residues localized in and adjacent to the E2 docking domain. We show that phosphorylation is critical for stabilization by inhibiting PUB22 oligomerization and, thus, autoubiquitination. The activity switch allows PUB22 to dampen the immune response. This regulatory mechanism also suggests that autoubiquitination, which is inherent to most single unit E3s in vitro, can function as a self-regulatory mechanism in vivo.
How and what teachers learn from collaborative professional development
Authors: Wood Keith , Jaidin Halida , Jawawi Rosmawijah , Perera J.S.H.Q. , Salleh Sallimah , Shahrill Masitah , Sithamparam Saratha 
Published: March 2017

Purpose
The purpose of this paper is to report on a study of teacher learning through participation in sustained collaborative subject-based professional development groups supported by a facilitator, using a model of teachers’ conceptions of teaching developed from phenomenography to identify what are the critical features of teaching that must be present if teachers are to learn, and using a variation theory of learning to explain how they learn.

Design/methodology/approach
The groups engaged in cycles of lesson study action research to improve the learning outcomes of their students. The authors intended to engage the teachers in an exploration of their own and their students’ experiences to understand the relationship between the enactment of the research lesson(s) and the educational outcome. The authors collected over 157 hours of video recorded teachers’ meetings involving 15 groups, 47 hours of follow-up interviews and 97 hours of lessons. In this paper the authors report on the progress of one of those groups. The authors analysed the transcripts to see what, if any, dimensions of variation were opened in discussion, affording the opportunity for learning. The authors sought the simultaneous juxtaposition, the bringing together, of threads that have entered the discussion that have the potential to open dimensions of variation – to add critical features to the “what” and “how” dimensions of teaching.

Findings
The authors identified necessary conditions for teacher learning through collaborative subject-based professional development groups. Any member of the group might bring this about. The facilitator or coach might be expected to perform this role in the group, and to sustain the group’s attention on the critical features of the object of learning.

Practical implications
The paper provides valuable insights into strategies to change teacher perspectives from a transmission oriented to a construction oriented view of teaching in the face of new and challenging curriculum demands.

Originality/value
In the work reported here the authors have used variation theory to design lesson study. This is rather different from a learning study where the teachers engaged in the study use variation theory to design their research lesson(s). It is a learning study of teachers’ professional development.
Two tenses are better than one
Authors: Lindström Clare 
Published: March 2017

PurposeThe purpose of this paper is to present findings from a learning study (Lindström, 2015) with Swedish sixth grade pupils on the English grammatical structure, the progressive aspect (PROG). The focus is on how the lesson design and the treatment of the subject content, informed by variation theory, affected the learning of the PROG.Design/methodology/approachFour teachers of English as a foreign language, including the teacher researcher, collaborated to plan, teach, evaluate and analyse a series of six research lessons. The theoretical framework was the variation theory of learning which was used both to design the lessons and analyse teaching and learning. A basic assumption is that learning is a function of discernment, and discernment is conditional upon experiencing variaion. Empirical data consisted of interview transcripts, pre- and post-lesson assessments, and video recordings of the lessons.FindingsThe use of the present tense when teaching the PROG was insufficient. When the past tense was introduced, along with particularly powerful examples, pupils’ understanding of the PROG improved. Furthermore, reversing the conventional order by instead beginning the lesson with examples in the past tense, helped the pupils to generalise the meanings of the PROG. Improved pupil learning outcomes were observed when the PROG was treated from the perspective of wholeness, simultaneity and complexity.Originality/valueThe findings challenge conventional ways of teaching the PROG and thus have value for instruction of English as a foreign language.
Organization studies as symmetrical ethnology
Authors: Czarniawska Barbara 
Published: March 2017

Purpose
The purpose of this paper is to challenge some of the taken for granted assumptions of contemporary ethnographic practice by exploring reasons for fieldwork and the debt that is owed to those in the field.

Design/methodology/approach
Exploring traditional and contemporary reasons for fieldwork and comparing ostensive and performative styles of reporting organization studies.

Findings
The argument is that traditional ethnographic approaches do not fit contemporary organizing practices. In their place, a “symmetrical ethnology” is proposed.

Research limitations/implications
More reflective use of labels and terms.

Practical implications
Better communication with practitioners.

Social implications
Better dialogue with wider circles.

Originality/value
An important and timely critique of ethnography together with a reformulation and a number of suggestions for future practice.