bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring policy analytical capacity for the environment: A case for engaging new actors
Authors: Angel Hsu 
Published: October 2015

Abstract
This paper discusses how varied policy analytical capacity can be evaluated at the systemic level through observed gaps in environmental data monitoring and reporting among countries. Such analytical capacity at the knowledge system level facilitates transparency and credibility needed for nation-states to cooperate on issues requiring global coordination, including “super-wicked” environmental issues like climate change. So far there has been relatively sparse attention paid to whether countries will have the ability — or policy analytical capacity — to report the necessary data and indicators required for the next round of global Sustainable Development Goals (SDGs) being proposed. In this paper, I argue that the varied policy analytical capacity within the global environmental knowledge system necessitates the participation of new institutions and actors. Identifying gaps in data availability at a global, systemic scale, this paper presents a proxy measure of policy analytical capacity based on publicly-reported national statistics of air and water quality performance. Such discrepancies evaluated at a systemic level make a case for channels by which citizen scientists, independent watchdogs, private sector companies and third-party organizations can participate to enhance the policy analytical capacity of governments.
Beyond Animals and Plants: Dynamic Maternal Effects in the FungusNeurospora crassa
Authors: Zimmerman Kolea C. K. , Levitis Daniel A. , Pringle Anne 
Published: October 2015

ABSTRACTMaternal effects are widely documented in animals and plants, but not in fungi or other eukaryotes. A principal cause of maternal effects is asymmetrical parental investment in a zygote, creating greater maternal versus paternal influence on offspring phenotypes. Asymmetrical investments are not limited to animals and plants, but are also prevalent in fungi and groups including apicocomplexans, dinoflagellates, and red algae. Evidence suggesting maternal effects among fungi is sparse and anecdotal. In an experiment designed to test for maternal effects across sexual reproduction in the model fungusNeurospora crassa, we measured offspring phenotypes from crosses of all possible pairs of 22 individuals. Crosses encompassed reciprocals of 11 mating-type “A” and 11 mating-type “a” wild strains. After controlling for the genetic and geographic distances between strains in any individual cross, we found strong evidence for maternal control of sporocarp production, as well as maternal effects on spore numbers and spore germination. However, both parents exert equal influence on the percentage of spores that are pigmented, and size of pigmented spores. We propose a model linking the stage-specific presence or absence of maternal effects to cellular developmental processes: effects appear to be mediated primarily through the maternal cytoplasm, and, after spore cell walls form, maternal influence on spore development is limited. Maternal effects in fungi, thus far largely ignored, are likely to shape species’ evolution and ecology. The association of anisogamy and maternal effects in a fungus suggests maternal effects may also influence the biology of other anisogamous eukaryotes.
in silicoWhole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis ofde novogenome sequencing studies
Authors: Zhou Xiaofan , Peris David , Kominek Jacek , Kurtzman Cletus P , Hittinger Chris Todd , Rokas Antonis 
Published: October 2015

AbstractThe availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled thede novodecoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, andde novoassembly algorithms have augmented the complexity ofde novogenome sequencing projects in non-model organisms. To reduce the costs and challenges inde novogenome sequencing projects and streamline their experimental design and analysis, we developed iWGS (in silicoWholeGenomeSequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of ade novogenome sequencing project: data generation (through simulation), data quality control,de novoassembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design ofde novogenome sequencing projects and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available athttps://github.com/zhouxiaofan1983/iWGS.
Comparing cancer cell lines and tumor samples by genomic profiles
Authors: Sinha Rileen , Schultz Nikolaus , Sander Chris 
Published: October 2015

AbstractCancer cell lines are often used in laboratory experiments as models of tumors, although they can have substantially different genetic and epigenetic profiles compared to tumors. We have developed a general computational method – TumorComparer - to systematically quantify similarities and differences between tumor material when detailed genetic and molecular profiles are available. The comparisons can be flexibly tailored to a particular biological question by placing a higher weight on functional alterations of interest (‘weighted similarity’). In a first pan-cancer application, we have compared 260 cell lines from the Cancer Cell Line Encyclopaedia (CCLE) and 1914 tumors of six different cancer types from The Cancer Genome Atlas (TCGA), using weights to emphasize genomic alterations that frequently recur in tumors. We report the potential suitability of particular cell lines as tumor models and identify apparently unsuitable outlier cell lines, some of which are in wide use, for each of the six cancer types. In future, this weighted similarity method may be generalized for use in a clinical setting to compare patient profiles consisting of genomic patterns combined with clinical attributes, such as diagnosis, treatment and response to therapy.
Deep learning for population genetic inference
Authors: Sheehan Sara , Song Yun S. 
Published: October 2015

AbstractGiven genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce here a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. In contrast to Approximate Bayesian Computation, another likelihood-free approach widely used in population genetics and other fields, deep learning does not require a distance function on summary statistics or a rejection step, and it is robust to the addition of uninformative statistics. To demonstrate that deep learning can be effectively employed to estimate population genetic parameters and learn informative features of data, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated byDrosophila,where pervasive selection confounds demographic analysis. We apply our method to 197 AfricanDrosophila melanogastergenomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for AfricanDrosophila melanogasterare too extreme, likely due in part to the unaccounted impact of selection.
New aspects of the clinicopathological features and treatment of mycosis fungoides and Sézary syndrome
Authors: Furue Masutaka , Kadono Takafumi 
Published: October 2015

AbstractMycosis fungoides and Sézary syndrome are T‐helper (Th)2‐skewed cutaneous lymphomas. The clinical course of mycosis fungoides is classically indolent, manifesting as patches, plaques and tumors. Along with their progression, Th2 dominance tends to be accelerated. In this review, we discuss the epidemiology, clinicopathogenetic features and therapeutic approaches in mycosis fungoides and Sézary syndrome.
Tackling extremes: challenges for ecological and evolutionary research on extreme climatic events
Authors: Bailey Liam D. , van de Pol Martijn 
Published: October 2015

Summary

Extreme climatic events (ECEs) are predicted to become more frequent as the climate changes. A rapidly increasing number of studies – though few on animals – suggest that the biological consequences of ECEs can be severe.

However, ecological research on the impacts of ECEs has been limited by a lack of cohesiveness and structure. ECEs are often poorly defined and have often been confusingly equated with climatic variability, making comparison between studies difficult. In addition, a focus on short‐term studies has provided us with little information on the long‐term implications of ECEs, and the descriptive and anecdotal nature of many studies has meant it is still unclear what the key research questions are.

Synthesizing the current state of work is essential to identify ways to make progress. We conduct a synthesis of the literature and discuss conceptual and practical challenges faced by research on ECEs.

We consider three steps to advance research. First, we discuss the importance of choosing an ECE definition and identify the pros and cons of ‘climatological’ and ‘biological’ definitions of ECEs. Secondly, we advocate research beyond short‐term descriptive studies to address questions concerning the long‐term implications of ECEs, focussing on selective pressures and phenotypically plastic responses and how they might differ from responses to a changing climatic mean. Finally, we encourage a greater focus on multi‐event studies that help us understand the implications of changing patterns of ECEs, through the combined use of modelling, experimental and observational field studies.

This study aims to open a discussion on the definitions, questions and methods currently used to study ECEs, which will lead to a more cohesive approach to future ECE research.
Within‐ and trans‐generational effects of herbivores and detritivores on plant performance and reproduction
Authors: González‐Megías Adela 
Published: October 2015

SummaryMutualistic and antagonistic above‐ground and below‐ground species have the potential to be involved in strong interactions that can either weaken or strengthen their individual impacts on plants. Their impacts can also have delayed effects on a plant's progeny by altering offspring traits and survival. Few studies have explored the effect of herbivore and detritivore interactions with parent plants on offspring vital life‐cycle processes, such as seedling emergence rate, seedling establishment and offspring survival.In the field, I experimentally studied the combined effects of floral herbivores (FH), root herbivores (RH) and detritivores on plant growth and reproduction ofMoricandia moricandioides(Brassicaceae). In particular, I analysed the trans‐generational effects of herbivores and detritivores on seed and juvenile production as well as on vital life‐cycle processes (i.e. seedling emergence rates, survival).Floral herbivores strongly reduced the number of flowers, fruits, seeds and juveniles. Detritivores had an impact on plant success by increasing seed quality (% N and N : C ratio), although the effect was altered by the presence of floral and RH.I found maternal effects (trans‐generational effects) of FH, RH and detritivores. Floral herbivores reduced seedling emergence and establishment. Floral and RH in combination reduced seedling emergence timing, but the effect was counteracted by detritivores. Detritivores also reduced the negative effect of FH on offspring mortality rate.This study shows that the impact of above‐ground and below‐ground organisms onM. moricandioidesplants go beyond seed production and were evident in the probability of establishment and survival of the following generation. Trans‐generational effects were induced by all three groups of interacting organisms and the net consequences for plant offspring depended on the organisms interacting with the plant.
The advantage of the extremes: tree seedlings at intermediate abundance in a tropical forest have the highest richness of above‐ground enemies and suffer the most damage
Authors: Bachelot Benedicte , Uríarte María , Thompson Jill , Zimmerman Jess K. 
Published: October 2015

Summary

Tropical forest tree diversity has been hypothesized to be maintained via the attraction of density responsive and species‐specific enemies. Tests of this hypothesis usually assume a linear relationship between enemy pressure (amount of damage and enemy richness) and seedling or tree density. However, enemy pressure is likely to change nonlinearly with local seedling abundance and community scale tree abundance if enemies are characterized by nonlinear functional responses.

We examined the abiotic and biotic factors associated with richness of above‐ground enemies and foliar damage found in tree seedlings in a tropical forest in Puerto Rico. Rather than identify specific enemies targeting these seedlings, we used damage morphotypes, a paleo‐ecological method, to derive a proxy for enemy species richness.

We found that the relationships between local and (conspecific seedling density) community scale (conspecific basal area of adult trees) abundance and both richness of above‐ground enemies and foliar damage were hump‐shaped. Seedlings of tree species existing at intermediate levels of abundance, at both local and community scales, suffered more damage and experienced pressure from a greater diversity of enemies than those existing at high or low densities.

We hypothesized that greater damage at intermediate abundance level could arise from a rich mixture of generalist and specialist enemies targeting seedlings of intermediate abundance tree species. Consistent with this hypothesis, we found that generalist enemies were more diverse on species at rare or intermediate abundance relative to common tree species. However, specialist enemies showed no significant trend across tree species abundance at either the local or community scales.

Synthesis. Our results suggest that interspecific variation in tree species abundance leads to differences in the magnitude and type of damage tropical tree seedlings suffer. This variation leads to a nonlinear, hump‐shaped relationship between species abundance and enemy damage, highlighting fruitful directions for further development of species coexistence theory.
Differentiating the bipolar disorders from borderline personality disorder
Authors: Bayes A. J. , McClure G. , Fletcher K. , Román Ruiz del Moral Y. E. , Hadzi‐Pavlovic D. , Stevenson J. L. , Manicavasagar V. L. , Parker G. B. 
Published: October 2015

ObjectiveTo identify features differentiating bipolar disorder (BP) from borderline personality disorder (BPD) and with each condition variably defined.MethodParticipants were assigned a BP or BPD diagnosis on the basis of DSM criteria and, separately, by clinical judgment, and undertook a diagnostic interview and completed self‐report measures.ResultsPredictors of BPD status varied according to diagnostic decisions, but with the most consistent items being childhood sexual abuse, childhood depersonalization, personality variables relating to relationship difficulties and sensitivity to criticism, and the absence of any BP family history. Across diagnostic groups, personality measure items alone predicted diagnostic allocation with an accuracy of 81–84%, the refined study variables other than hypo/manic features improved the classification rates to 88%, and when the presence or absence of hypo/manic features was added, classification rates increased to 92–95%.ConclusionStudy findings indicate that BPD can be differentiated from BP with a high degree of accuracy.
Australia's Individualised Disability Funding Packages: When Do They Provide Greater Choice and Opportunity?
Authors: Laragy Carmel , Fisher Karen R. , Purcal Christiane , Jenkinson Samantha 
Published: October 2015

Australia's new National Disability Insurance Scheme (NDIS) uses individualised funding packages instead of traditional block‐funded disability services to support people with disability. The NDIS works with the person and their family to assess the person's needs and develop a plan that determines their funding allocation. Funding can be used to purchase support from a disability service or from the open market. People can purchase support that suits their cultural and personal preferences. This paper examined whether individual funding packages met their aims in Western Australia, where they had been the primary mechanism of disability support for over 25 years. An exploratory case study was conducted consisting of face‐to‐face, in‐depth interviews with 11 key participants: people with disability, senior government administrators, service provider managers, and a support worker. Complex systems theory was used to review the data and findings showed that individualised funding packages did not automatically result in more choice and greater opportunities. People needed information to make informed decisions; supportive and creative support from social workers and other professionals; and welcoming communities. The findings can inform policies and assist social workers facilitate maximum choice and opportunities for people with disability and their families.
Biochemical and Histological Effects of Thiamine Pyrophosphate against Acetaminophen‐Induced Hepatotoxicity
Authors: Uysal Hilal Bektas , Dağlı Bekir , Yılmaz Mustafa , Kahyaoğlu Fadime , Gökçimen Alparslan , Ömürlü İmran Kurt , Demirci Buket 
Published: October 2015

AbstractThe aim of this study was to investigate whether thiamine pyrophosphate (TPP) has biochemical and histological preventive effects on oxidative liver damage induced by paracetamol (APAP). Rats were divided into the following groups: healthy control (HG), APAP (AG, 1500 mg/kg, orally), thiamine pyrophosphate (TPPG, 100 mg/kg, intraperitoneally), APAP+NAC (ANAC, 100 mg/kg, intraperitoneally), APAP+TPP (ATPG) and APAP+NAC+TPP (ANTG). Oxidant, antioxidant parameters, liver function tests and histological assessment were performed between groups. Malondialdehyde levels in the AG, HG, TPPG, ANAC, ATPG and ANTG groups were 0.470 ± 0.210, 0.213 ± 0.004, 0.194 ± 0.001, 0.197 ± 0.06, 0.199 ± 0.008 and 0.173 ± 0.010 μmol/g protein, respectively. Total glutathione levels were 7.787 ± 0.395, 14.925 ± 0.932, 13.200 ± 0.984, 13.162 ± 0.486, 13.287 ± 0.787 and 13.500 ± 0.891 μm/g protein, respectively. In the AG group, marked liver damage occurred with the elevation of liver function tests and oxidative stress markers, such as malondialdehyde, myeloperoxidase and nitric oxide (p < 0.05). Biochemical results were congruent with the histological changes of oxidative damage. Compared to the AG group (p < 0.05), TPP significantly reduced oxidant parameter levels in the ATPG group and simultaneously increased the antioxidant parameter levels of catalase and glutathione. The histological changes were improved to almost normal hepatic structure. Moreover, TPP had nearly the same hepatoprotective effect as NAC, and there was statistically no additional benefit with NAC co‐treatment. There was no statistically significant difference (p > 0.05) among the ANAC, ANTG and ATPG groups in terms of oxidant/antioxidant levels. TPP proved to be as efficacious as standard therapy and may be beneficial in APAP‐induced hepatotoxicity.
Large-Scale Signal Detection: A Unified Perspective
Authors: Mukhopadhyay Subhadeep 
Published: October 2015

SummaryThere is an overwhelmingly large literature and algorithms already available on “large-scale inference problems” based on different modeling techniques and cultures. Our primary goal in this article is not to add one more new methodology to the existing toolbox but instead (i) to clarify the mystery how these different simultaneous inference methods are connected, (ii) to provide an alternative more intuitive derivation of the formulas that leads to simpler expressions in order (iii) to develop a unified algorithm for practitioners. A detailed discussion on representation, estimation, inference, and model selection is given. Applications to a variety of real and simulated datasets show promise. We end with several future research directions.
Hemisynthesis, Antitumoral Effect, and Molecular Docking Studies of Ferutinin and Its Analogues
Authors: Safi Rémi , Rodriguez Fréderic , Hilal Georges , Diab‐Assaf Mona , Diab Youssef , El‐Sabban Marwan , Najjar Fadia , Delfourne Evelyne 
Published: October 2015

The natural product ferutinin was shown to act as an agonist to estrogen receptor ERα and agonist/antagonist to ERβ featuring a weak antiproliferative activity toward breast cancer cells. To enhance this activity, ferutinin analogues were synthesized by esterification of jaeschkenadiol with different acids. These compounds were assayed for their in vitro antiproliferative activity against estrogen‐dependent (MCF‐7) and estrogen‐independent (MDA‐MB‐231) breast cancer cell lines. Among the compounds, 3c’ exhibited a potent inhibitory selective activity against MCF‐7 with IC50 value of 1 μm. Docking simulation of 3c’ in the ligand binding domain of the ERs indicated a potential antagonism interaction with both ER subtypes. Functional assay showed that 3c’ binds as an antagonist to ERα protein while ferutinin acts as an agonist.