bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social learning through associative processes: A computational theory
Authors: Lind Johan , Ghirlanda Stefano , Enquist Magnus 
Published: October 2018

AbstractSocial transmission of information is a key phenomenon in the evolution of behavior and in the establishment of traditions and culture. The diversity of social learning phenomena has engendered a diverse terminology and numerous ideas about underlying learning mechanisms, at the same time that some researchers have called for a unitary analysis of social learning in terms of associative processes. Leveraging previous attempts and a recent computational formulation of associative learning, we analyze the following learning scenarios in some generality: learning responses to social stimuli, including learning to imitate; learning responses to non-social stimuli; learning sequences of actions; learning to avoid danger. We conceptualize social learning as situations in which stimuli that arise from other individuals have an important role in learning. This role is supported by genetic predispositions that either cause responses to social stimuli or enable social stimuli to reinforce specific responses. Our explorations show that, when guided by such predispositions, associative processes can give rise to a wide variety of social learning phenomena, such as stimulus and local enhancement, contextual imitation and simple production imitation, observational conditioning, and social and response facilitation. In addition, we clarify how associative mechanisms can result in transfer of information and behavior from experienced to naïve individuals.
Evolution of empathetic moral evaluation
Authors: Radzvilavicius Arunas L. , Stewart Alexander J. , Plotkin Joshua B. 
Published: October 2018

AbstractSocial norms can promote cooperation in human societies by assigning reputations to individuals based on their past actions. A good reputation indicates that an individual is worthy of help and is likely to reciprocate. A large body of research has established the norms of moral assessment that promote cooperation and maximize social welfare, assuming reputations are objective. But if there is no centralized institution to provide objective moral evaluation, then opinions about an individual’s reputation may differ across a population. Here we use evolutionary game theory to study the effects of empathy – the capacity to make moral evaluations from the perspective of another person. We find that empathetic moral evaluation tends to foster cooperation by reducing the rate of unjustified defection. The norms of moral evaluation previously considered most socially beneficial depend on high levels of empathy, whereas different norms are required to maximize social welfare in populations unwilling or incapable of empathy. We demonstrate that empathy itself can evolve through social contagion and attain evolutionary stability under most social norms. We conclude that a capacity for empathetic moral evaluation represents a key component to sustaining cooperation in human societies: cooperation requires getting into the mindset of others whose views differ from our own.
A network module for the Perseus software for computational proteomics facilitates proteome interaction graph analysis
Authors: Rudolph Jan , Jürgen Cox 
Published: October 2018

ABSTRACTProteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e.g. with affinity purification experiments, but networks are also used to explore proteomics data. PerseusNet supports the biomedical researcher for both modes of data analysis with a multitude of activities. For affinity purification, a volcano plot-based statistical analysis method for network generation is featured which is scalable to large numbers of baits. For posttranslational modifications of proteins, such as phosphorylation, a collection of dedicated network analysis tools helps elucidating cellular signaling events. Co-expression network analysis of proteomics data adopts established tools from transcriptome co-expression analysis. PerseusNet is extensible through a plug-in architecture in a multi-lingual way, integrating analyses in C#, Python and R and is freely available at http://www.perseus-framework.org.
Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis
Authors: Võsa Urmo , Claringbould Annique , Westra Harm-Jan , Bonder Marc Jan , Deelen Patrick , Zeng Biao , Kirsten Holger , Saha Ashis , Kreuzhuber Roman , Kasela Silva , Pervjakova Natalia , Alvaes Isabel , Fave Marie-Julie , Agbessi Mawusse , Christiansen Mark , Jansen Rick , Seppälä Ilkka , Tong Lin , Teumer Alexander , Schramm Katharina , Hemani Gibran , Verlouw Joost , Yaghootkar Hanieh , Sönmez Reyhan , Brown Andrew , Kukushkina Viktorija , Kalnapenkis Anette , Rüeger Sina , Porcu Eleonora , Kronberg-Guzman Jaanika , Kettunen Johannes , Powell Joseph , Lee Bernett , Zhang Futao , Arindrarto Wibowo , Beutner Frank ,   BIOS Consortium, Brugge Harm ,   i2QTL Consortium, Dmitreva Julia , Elansary Mahmoud , Fairfax Benjamin P. , Georges Michel , Heijmans Bastiaan T. , Kähönen Mika , Kim Yungil , Knight Julian C. , Kovacs Peter , Krohn Knut , Li Shuang , Loeffler Markus , Marigorta Urko M. , Mei Hailang , Momozawa Yukihide , Müller-Nurasyid Martina , Nauck Matthias , Nivard Michel , Penninx Brenda , Pritchard Jonathan , Raitakari Olli , Rotzchke Olaf , Slagboom Eline P. , Stehouwer Coen D.A. , Stumvoll Michael , Sullivan Patrick , Hoen Peter A.C. ‘t , Thiery Joachim , Tönjes Anke , van Dongen Jenny , van Iterson Maarten , Veldink Jan , Völker Uwe , Wijmenga Cisca , Swertz Morris , Andiappan Anand , Montgomery Grant W. , Ripatti Samuli , Perola Markus , Kutalik Zoltan , Dermitzakis Emmanouil , Bergmann Sven , Frayling Timothy , van Meurs Joyce , Prokisch Holger , Ahsan Habibul , Pierce Brandon , Lehtimäki Terho , Boomsma Dorret , Psaty Bruce M. , Gharib Sina A. , Awadalla Philip , Milani Lili , Ouwehand Willem , Downes Kate , Stegle Oliver , Battle Alexis , Yang Jian , Visscher Peter M. , Scholz Markus , Gibson Gregory , Esko Tõnu , Franke Lude 
Published: October 2018

SummaryWhile many disease-associated variants have been identified through genome-wide association studies, their downstream molecular consequences remain unclear.To identify these effects, we performedcis-andtrans-expressionquantitative trait locus (eQTL) analysis in blood from 31,684 individuals through the eQTLGen Consortium.We observed thatcis-eQTLs can be detected for 88% of the studied genes, but that they have a different genetic architecture compared to disease-associated variants, limiting our ability to usecis-eQTLs to pinpoint causal genes within susceptibility loci.In contrast, trans-eQTLs (detected for 37% of 10,317 studied trait-associated variants) were more informative. Multiple unlinked variants, associated to the same complex trait, often converged on trans-genes that are known to play central roles in disease etiology.We observed the same when ascertaining the effect of polygenic scores calculated for 1,263 genome-wide association study (GWAS) traits. Expression levels of 13% of the studied genes correlated with polygenic scores, and many resulting genes are known to drive these traits.
The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K
Authors: Bushell Simon R. , Pike Ashley C.W. , Falzone Maria E. , Rorsman Nils J. G. , Ta Chau M , Corey Robin A. , Newport Thomas D. , Shintre Chitra A. , Tessitore Annamaria , Chu Amy , Wang Qinrui , Shrestha Leela , Mukhopadhyay Shubhashish M.M. , Love James D. , Burgess-Brown Nicola A. , Sitsapesan Rebecca , Stansfeld Phillip J. , Huiskonen Juha T. , Tammaro Paolo , Accardi Alessio , Carpenter Elisabeth P. 
Published: October 2018

AbstractMembranes in cells have defined distributions of lipids in each leaflet, controlled by lipid scramblases and flip/floppases. However, for some intracellular membranes such as the endoplasmic reticulum the scramblases have not been identified. Members of the TMEM16 family have either lipid scramblase and ion channel activity, or specific chloride channel activity. Although TMEM16K is widely distributed and associated with the neurological disorder autosomal recessive spinocerebellar ataxia type 10 (SCAR10), its location in cells, function and structure are largely uncharacterised. Here we show that TMEM16K is an ER-resident calcium-regulated lipid scramblase. Our crystal structures of TMEM16K show a scramblase fold, with an open lipid transporting groove. Additional structures solved by cryo-EM reveal extensive conformational changes extending from the cytoplasmic to the ER side of the membrane, giving a state with a closed lipid permeation pathway. Molecular dynamics simulations showed that the open-groove conformation is necessary for scramblase activity. Our results suggest mechanisms by which missense variants of TMEM16K could cause SCAR10 ataxia, providing new hypotheses to explore for therapy.
MEK/mTOR-dependent D1 dopamine receptor activation induces local protein synthesis via eEF2 dephosphorylation in neurons
Authors: David Orit , Barrera Iliana , Koltun Bella , Ironi Sivan , Gal-Ben-Ari Shunit , Rosenblum Kobi 
Published: October 2018

AbstractNeuromodulators in general, and dopamine in particular, define brain and neuronal states in different ways including regulation of global and local mRNA translation. Yet, the signaling pathways underlying the effects of dopamine on mRNA translation are not clear. Here, using genetic, pharmacologic, biochemical, and imaging methods, we tested the hypothesis that dopamine regulates phosphorylation of the eukaryotic elongation factor 2 (eEF2). We found that activation of dopamine receptor D1 but not D2 leads to rapid dephosphorylation of eEF2 at Thr56 in cortical primary neuronal culture and in vivo in a time-dependent manner. Additionally, NMDA receptor, mTOR, and ERK pathways are upstream to the D1 receptor-dependent eEF2 dephosphorylation and essential for it. Furthermore, D1 receptor activation resulted in a major reduction in dendritic eEF2 phosphorylation levels together with a correlative increase in local mRNA translation. These results reveal the role of eEF2 in dopamine regulation of local mRNA translation in neurons.One-sentence summaryD1 receptor activation increases protein synthesis in dendrites by inactivating eEF2K in an ERK2/mTOR-dependent manner.
Biochemical and physiological investigations on adenosine 5’ monophosphate deaminase from Plasmodium spp.
Authors: Nagappa Lakshmeesha Kempaiah , Balaram Hemalatha 
Published: October 2018

Abbreviations:HGXPRT - Hypoxanthine-guanine-xanthine phosphoribosyltransferase, ADSS - Adenylosuccinate synthetase, ASL - Adenylosuccinate lyase, GMPS - Guonosine monophosphate synthetase, IMPDH - Inosine monophosphate dehydrogenase, ISN1 - Inosine monophosphate specific nucleotidase, PNP - Purine nucleoside phosphorylaseSummaryInterplay between ATP generating and utilizing pathways in a cell is responsible for maintaining cellular ATP/energy homeostasis that is reflected by Adenylate Energy Charge (AEC) ratio. Adenylate kinase (AK), that catalyzes inter-conversion of ADP, ATP and AMP, plays a major role in maintaining AEC, and is regulated by cellular AMP levels. Hence, the enzymes AMP deaminase (AMPD) and nucleotidases, which catabolize AMP, indirectly regulate AK activity and in-turn affect AEC. Here, we present the first report on AMPD fromPlasmodium, the causative agent of malaria. The recombinant enzyme expressed inSaccharomyces cerevisiaewas studied using functional complementation assay and residues vital for enzyme activity have been identified. Similarities and differences betweenPlasmodium falciparumAMPD (PfAMPD) and its homologs from yeast,Arabidopsisand humans are also discussed. The AMPD gene was deleted in the murine malaria parasiteP. bergheiand was found to be non-essential for intra-erythrocytic growth of the knockout parasites. However, when episomal expression was attempted, viable parasites were not obtained, suggesting that perturbing AMP homeostasis by over-expressing AMPD might be lethal. As AMPD is known to be allosterically modulated by ATP, GTP and phosphate, allosteric activators of PfAMPD could be developed as anti-parasitic agents.
Genomic architecture of parallel ecological divergence: beyond a single environmental contrast
Authors: Morales Hernán E. , Faria Rui , Johannesson Kerstin , Larsson Tomas , Panova Marina , Westram Anja M. , Butlin Roger K. 
Published: October 2018

AbstractThe genetic basis of parallel ecological divergence provides important clues to the operation of natural selection and the predictability of evolution. Many examples exist where binary environmental contrasts seem to drive parallel divergence. However, this simplified view can conceal important components of parallel divergence because environmental variation is often more complex. Here, we disentangle the genetic basis of parallel divergence across two axes of environmental differentiation (crab-predation vs. wave-action and low-shore vs. high-shore habitat contrasts) in the marine snail Littorina saxatilis, a well established natural system of parallel ecological divergence. We used whole-genome resequencing across multiple instances of these two environmental axes, at local and regional scales from Spain to Sweden. Overall, sharing of genetic differentiation is generally low but it is highly heterogeneous across the genome and increases at smaller spatial scales. We identified genomic regions, both overlapping and non-overlapping with recently described candidate chromosomal inversions, that are differentially involved in adaptation to each of the environmental axis. Thus, the evolution of parallel divergence in L. saxatilis is largely determined by the joint action of geography, history, genomic architecture and congruence between environmental axes. We argue that the maintenance of standing variation, perhaps as balanced polymorphism, and/or the re-distribution of adaptive variants via gene flow can facilitate parallel divergence in multiple directions as an adaptive response to heterogeneous environments.
A Systematic Approach to Identify Recycling Endocytic Cargo Depending on the GARP Complex
Authors: Eising Sebastian , Thiele Lisa , Fröhlich Florian 
Published: October 2018

AbstractProteins and lipids of the plasma membrane underlie constant remodeling via a combination of the secretory- and the endocytic pathway. In the yeast endocytic pathway, cargo is sorted for recycling to the plasma membrane or degradation in vacuoles. In a previous paper we have shown a role for the GARP complex in sphingolipid sorting and homeostasis (Fröhlich et al. 2015). However, the majority of cargo sorted in a GARP dependent process remain largely unknown. Here we use auxin induced degradation of GARP combined with mass spectrometry based vacuolar proteomics and lipidomics to show that recycling of two specific groups of proteins, the amino-phospholipid flippases and cell wall synthesis proteins depends on a functional GARP complex. Our results suggest that mis-sorting of flippases and remodeling of the lipid composition are the first occurring defects in GARP mutants. Our assay can be adapted to systematically map cargo of the entire endocytic pathway.
On the prevalence of uninformative parameters in statistical models applying model selection in applied ecology
Authors: Leroux Shawn J. 
Published: October 2018

AbstractResearch in applied ecology provides scientific evidence to guide conservation policy and management. Applied ecology is becoming increasingly quantitative and model selection via information criteria has become a common statistical modeling approach. Unfortunately, parameters that contain little to no useful information are commonly presented and interpreted as important in applied ecology. I review the concept of an uninformative parameter in model selection using information criteria and perform a literature review to measure the prevalence of uninformative parameters in model selection studies applying Akaike’s Information Criterion (AIC) in 2014 in four of the top journals in applied ecology(Biological Conservation,Conservation Biology,Ecological Applications,Journal of Applied Ecology).Twenty-one percent of studies I reviewed applied AIC metrics. Many (31.5 %) of the studies applying AIC metrics in the four applied ecology journals I reviewed had or were very likely to have uninformative parameters in a model set. In addition, more than 40 % of studies reviewed had insufficient information to assess the presence or absence of uninformative parameters in a model set. Given the prevalence of studies likely to have uninformative parameters or with insufficient information to assess parameter status (71.5 %), I surmise that much of the policy recommendations based on applied ecology research may not be supported by the data analysis. I provide warning signals and a decision tree to help reduce the prevalence of uninformative parameters in studies applying model selection with information criteria. The four warning signals and decision tree should assist authors, reviewers, and editors to screen for uninformative parameters in studies applying model selection with information criteria. In the end, careful thinking at every step of the scientific process and greater reporting standards are required to detect uninformative parameters in studies adopting an information criteria approach.
Determination of biophysical parameters for enhancement of human osteoblast proliferation by mechanical vibration in the infrasonic frequency range
Authors: Nahum Rosenberg , Jacob Halevi Politch , Orit Rosenberg , Haim Abramovich 
Published: October 2018

AbstractExperimental methods for studying an enhancement of osteoblast proliferation in vitro provide tools for the research of biochemical processes involved in bone turnover in vivo. Some of the current methods used for this purpose are based on the ability of the osteoblasts to enhance proliferation by mechanical stimulation. We describe an experimental approach of biomechanical stimulation of cultured human osteoblast-like cells by vibration. This method is based on the specially designed controlled vibration setup that consists of an electric actuator, with horizontally mounted well plate containing cell cultures. Previously this method found to be effective to enhance cell proliferation, but the exact mechanical parameters of effective vibration were elusive. The current low friction system for mechanical stimulation of osteoblast-like cells in vitro provides recording of narrow range mechanical parameters in the infrasonic spectrum.We exposed human osteoblast-like cells in explant monolayer culture to mechanical vibration in the 10-70Hz range of frequencies and found that 50-70 Hz of vibration frequency is optimal for inducing osteoblast proliferation that was deduced from interrelation between unchanged cell number in culture samples with significant decrease in cell death rate (decreased LDH activity in culture media, p<.05) and with parallel decrease of their maturation level (p<.01).In this report we determined the optimal mechanical parameters and excitation protocol for induction of osteoblast proliferation in vitro by using a tunable and versatile mechanical platform, which can be used in the research of cell mechanotransduction.
Heat Shock in C. elegans Induces Downstream of Gene Transcription andAccumulation of Double-Stranded RNA
Authors: Melnick Marko , Gonzales Patrick , Cabral Joseph , Allen Mary A. , Dowell Robin D. , Link Christopher D. 
Published: October 2018

AbstractWe observed that heat shock of Caenorhabditis elegans leads to the formation of nuclear double-stranded RNA (dsRNA) foci, detectable with a dsRNA-specific monoclonal antibody. These foci significantly overlap with nuclear HSF-1 granules. To investigate the molecular mechanism(s) underlying dsRNA foci formation, we used RNA-seq to globally characterize total RNA and immunoprecipitated dsRNA from control and heat shocked worms. We find antisense transcripts are generally increased after heat shock, and a subset of both sense and antisense transcripts enriched in the dsRNA pool by heat shock overlap with dsRNA transcripts enriched by deletion of tdp-1, which encodes the C. elegans ortholog of TDP-43. Interestingly, transcripts involved in translation are over-represented in the dsRNAs induced by either heat shock or deletion of tdp-1. Also enriched in the dsRNA transcripts are sequences downstream of annotated genes (DoGs), which we globally quantified with a new algorithm. To validate these observations, we used fluorescence in situ hybridization (FISH) to confirm both antisense and downstream of gene transcription for eif-3.B, one of the affected loci we identified.
Stressed mothers, tolerant daughters: a case studyabout the physiological responses and growth of sugarcane plants under water deficit
Authors: Marcos Fernanda C. C. , Silveira Neidiquele M. , Marchiori Paulo E. R. , Machado Eduardo C. , Souza Gustavo M. , Landell Marcos G. A. , Ribeiro Rafael V. 
Published: October 2018

AbstractDrought stress can imprint marks in plants after a previous exposure, leading to a permissive state that facilitates a more effective response to subsequent stress events. Such stress imprints would benefit plants obtained from progenitors previously exposed to drought. Herein, our hypothesis was that daughter plants obtained from mother plants previously exposed to water deficit will perform better under water deficit as compared to those obtained from mothers that did not face stressful conditions. Sugarcane mother plants were grown under well-hydrated conditions or subjected to three cycles of water deficit by water withholding. Then, daughter plants produced through vegetative propagation were subjected to water deficit. Leaf gas exchange was reduced under water deficit and daughters from mothers that experienced water deficit presented a faster recovery of CO2 assimilation and higher instantaneous carboxylation efficiency after rehydration as compared to daughters from mothers that did not face water deficit. Plants obtained from mother plants that faced water deficit showed the highest leaf proline concentration under water deficit as well as higher leaf H2O 2 concentration and leaf ascorbate peroxidase activity regardless of water regime. Under well-watered conditions, daughters from mothers that faced stressful conditions presented higher root H2O2 concentration and root catalase activity than ones from mothers that did not experience water shortage. Such physiological changes were associated with improvements in leaf area and shoot and root dry matter accumulation in daughters from stressed mothers. Our results suggest that root H2O2 concentration is a chemical signal associated with stress memory and improved sugarcane growth. Such findings bring a new perspective to sugarcane production systems, in which stress memory can be explored for improving drought tolerance in rainfed areas.