bluuebunny/crossref_metadata_2025 huggingface dataset:
Ontogeny of familiarity with foraging landscape and foraging abilities in the tropical social waspRopalidia marginata
Authors: Mandal Souvik , Brahma Anindita , Gadagkar Raghavendra
Published: March 2018

Possessing spatial familiarity with their foraging landscape may enable animals to reduce foraging effort without compromising on foraging benefits. For animals inhabiting feature-rich landscapes, spatial familiarity can increase with increasing age/experience. To check whether this holds for individually foraging tropical social waspRopalidia marginata, we recorded the number and duration of all foraging trips, the identity of the materials brought to the nest (building material, water or food) and the directions of outbound and inbound flights (respective to their nests) of known-age foragers from three natural colonies, each for three consecutive days. The average trip duration and time spent daily in foraging increased rapidly until about first four weeks of their life, during which they rarely brought food to their nest, although many of them brought building material and water. Thereafter, their average as well as per day duration of foraging trip started decreasing gradually. Nevertheless, their foraging efficiency and success for food kept on increasing monotonically with age. These results suggest that older wasps were more efficient in foraging despite spending less time doing so. With increasing age, wasps developed individual preferences for the direction of their outbound flights, increased directionality of their inbound trips as well as the angular difference between their outbound and subsequent inbound flights, indicating development of spatial memory. We conclude that wasps acquire familiarity with their foraging landscape in their initial foraging phase and gradually develop robust memory for rewarding sites and routes to those sites, which enables them to increase their foraging capabilities.

SUMMARY STATEMENT

Contrary to insects inhabiting less-featured landscapes, tropical social wasps invest weeks to get familiar with foraging landscapes during their early foraging lives. This eventually enables them to increase foraging gain with reduced effort.
Post-decision wagering after perceptual judgments reveals bi-directional certainty readouts
Authors: Moreira Caio M. , Rollwage Max , Kaduk Kristin , Wilke Melanie , Kagan Igor
Published: March 2018

Humans and other animals constantly evaluate their decisions in order to learn and behave adaptively. Experimentally, such evaluation processes are accessed using metacognitive reports made after decisions, typically using verbally formulated confidence scales. When subjects report high confidence, it reflects a high certainty of being correct, but a low confidence might signify either low certainty about the outcome, or a high certainty of being incorrect. Hence, metacognitive reports might reflect not only different levels of decision certainty, but also two certainty directions (certainty of being correct and certainty of being incorrect). It is important to test if such bi-directional processing can be measured because, for decision-making under uncertainty, information about being incorrect is as important as information about being correct for guidance of subsequent behavior. We were able to capture implicit bi-directional certainty readouts by asking subjects to bet money on their perceptual decision accuracy using a six-grade wager scale (post-decision wagering, PDW). To isolate trial-specific aspects of metacognitive judgments, we used pre-decision wagering (wagering before the perceptual decision) to subtract, from PDW trials, influences resulting from non-trial-specific assessment of expected difficulty and psychological biases. This novel design allowed independent quantification of certainty of being correct and certainty of being incorrect, showing that subjects were able to read out certainty in a bi-directional manner. Certainty readouts about being incorrect were particularly associated with metacognitive sensitivity exceeding perceptual sensitivity (i.e. meta-d′ > d′), suggesting that such enhanced metacognitive efficiency is driven by information about incorrect decisions. Readouts of certainty in both directions increased on easier trials, and both certainty directions were also associated with faster metacognitive reaction times, indicating that certainty of being incorrect was not confounded with low certainty. Finally, both readouts influenced the amount of money subjects earned through PDW, suggesting that bi-directional readouts are important for planning future actions when feedback about previous decisions is unavailable.
A projection specific logic to sampling visual inputs in mouse superior colliculus
Authors: Reinhard Katja , Li Chen , Do Quan , Burke Emily , Heynderickx Steven , Farrow Karl
Published: March 2018

Using sensory information to trigger different behaviours relies on circuits that pass-through brain regions. However, the rules by which parallel inputs are routed to different downstream targets is poorly understood. The superior colliculus mediates a set of innate behaviours, receiving input from ~30 retinal ganglion cell types and projecting to behaviourally important targets including the pulvinar and parabigeminal nucleus. Combining transsynaptic circuit tracing with in-vivo and ex-vivo electrophysiological recordings we observed a projection specific logic where each collicular output pathway sampled a distinct set of retinal inputs. Neurons projecting to the pulvinar or parabigeminal nucleus uniquely sampled 4 and 7 cell types, respectively. Four others innervated both pathways. The visual response properties of retinal ganglion cells correlated well with those of their disynaptic targets. These findings suggest that projection specific sampling of retinal inputs forms a mechanistic basis for the selective triggering of visually guided behaviours by the superior colliculus.
Genetic recombination of poliovirus facilitates subversion of host barriers to infection
Authors: Acevedo Ashley , Woodman Andrew , Arnold Jamie J. , Yeh Ming Te , Evans David , Cameron Craig E. , Andino Raul
Published: March 2018

The contribution of RNA recombination to viral fitness and pathogenesis is poorly defined. Here, we isolate a recombination-deficient, poliovirus variant and find that, while recombination is detrimental to virus replication in tissue culture, recombination is important for pathogenesis in infected animals. Notably, recombination-defective virus exhibits severe attenuation following intravenous inoculation that is associated with a significant reduction in population size during intra-host spread. Because the impact of high mutational loads manifests most strongly at small population sizes, our data suggest that the repair of mutagenized genomes is an essential function of recombination and that this function may drive the long-term maintenance of recombination in viral species despite its associated fitness costs.

Significance Statement

RNA recombination is a widespread but poorly understood feature of RNA virus replication. For poliovirus, recombination is involved in the emergence of neurovirulent circulating vaccine-derived poliovirus, which has hampered global poliovirus eradication efforts. This emergence illustrates the power of recombination to drive major adaptive change; however, it remains unclear if these adaptive events represent the primary role of recombination in virus survival. Here, we identify a viral mutant with a reduced rate of recombination and find that recombination also plays a central role in the spread of virus within animal hosts. These results highlight a novel approach for improving the safety of live attenuated vaccines and further our understanding of the role of recombination in virus pathogenesis and evolution.
Femtomolar and selective dopamine detection by a gold nanoparticle enhanced surface plasmon resonance aptasensor
Authors: Cao Yong , McDermott Mark T.
Published: March 2018

Ultrasensitive and selective detection and quantification of dopamine (DA) plays a key role in monitoring neurodegenerative diseases. However, the detection limit reported for DA detection is typically in the lower nM range. Pushing the detection limit to pM or lower for this particular target to cover the physiological levels (< 130 pM) is significant. Herein, DA DNA aptamer (DAAPT) gold nanoparticle (AuNP) conjugate is utilized to enhance the surface plasmon resonance (SPR) signal, which enables to detect and quantify DA in the femtomolar (200 fM) to picomolar range. To the best of our knowledge, this is the lowest detection limit achieved for SPR sensing of dopamine. The as-prepared 10 nm DAAPT-AuNP conjugate demonstrates strong binding affinity (Kd = 3.1 ± 1.4 nM) to the complementary DNA (cDNA) probe on gold chip. The cDNA probe is immobilized to the chip via polydopamine surface chemistry, which allows the Michael addition of any primary amine-terminated biomolecules. By adjusting the concentration of the DAAPT-AuNP conjugate, two calibration curves are generated with dynamic ranges from 100 µM to 2 mM, and from 200 fM to 20 nM, respectively. Both calibration curves have negative slopes, showing good agreement to a dose-response curve in an enzyme inhibition assay. In addition, the sensing strategy is evaluated to be specific for DA detection using a series of DA analogs and other metabolites as potential interferences.
Discordant attributes of structural and functional connectivity in a two-layer multiplex network
Authors: Lim Sol , Radicchi Filippo , van den Heuvel Martijn P , Sporns Olaf
Published: March 2018

Several studies have suggested that functional connectivity (FC) is constrained by the underlying structural connectivity (SC) and mutually correlated. However, not many studies have focused on differences in the network organization of SC and FC, and on how these differences may inform us about their mutual interaction. To explore this issue, we adopt a multi-layer framework, with SC and FC, constructed using Magnetic Resonance Imaging (MRI) data from the Human Connectome Project, forming a two-layer multiplex network. In particular, we examine whether node strength assortativity within and between the SC and FC layer may confer increased robustness against structural failure. We find that, in general, SC is organized assortatively, indicating brain regions are on average connected to other brain regions with similar node strengths. On the other hand, FC shows disassortative mixing. This discrepancy is apparent also among individual resting-state networks within SC and FC. In addition, these patterns show lateralization, with disassortative mixing within FC subnetworks mainly driven from the left hemisphere. We discuss our findings in the context of robustness to structural failure, and we suggest that discordant and lateralized patterns of associativity in SC and FC may explain laterality of some neurological dysfunctions and recovery.
Ancestral diet leads to dynamic transgenerational plasticity for five generations in Drosophila melanogaster
Authors: Emborski Carmen , Mikheyev Alexander S
Published: March 2018

Ancestral exposures can influence phenotypic expression in subsequent generations, which influence diverse biological processes ranging from phenotypic plasticity to obesity. Currently, most transgenerational studies work under the assumption of transgenerational response stability and reproducibility through time and across exposure differences, relying on short-term (i.e. 2-3 generations) single-exposure experiments. Yet, little evidence exists in the literature to validate this assumption, leaving the consistency and reliability of interpretations in question. Additionally, as most studies have focused on proximal mechanistic (‘how’) rather than ultimate evolutionary (‘why’) questions, the interpretations of observed responses and broader evolutionary implications remain unclear. In the current study, we begin to address these gaps by analyzing the transgenerational effects of three dietary sugar concentrations (i.e. no, low, and high) relative to controls on body composition (i.e. whole body fat and sugar concentrations) and reproduction (i.e. lifetime fitness) over five generations in both males and females. We found that the changes in ancestral diet led to complex transgenerational body composition and fitness fluctuations relative to control offspring responses, despite the conformity of the treatments to a control diet in the F1-F5 generations. Interestingly, the direction of response frequently changed from generation to generation, and as a function of ancestral exposures and sex. These fluctuating response findings have not been documented previously, and were broadly consistent in both our pilot and main experiments. Our results highlight the dynamic and multifaceted nature of transgenerational plasticity, and provide some of the first evidence that transgenerational response stability may not be universally valid.

Summary Statement

Alterations in ancestral dietary sugar transgenerationally influences body composition and fitness in Drosophila melanogaster, leading to fluctuating responses relative to controls over five generations following exposure.
Blimp-1 mediates tracheal lumen maturation in Drosophila melanogaster
Authors: Öztürk-Çolak Arzu , Stephan-Otto Attolini Camille , Casanova Jordi , Araújo Sofia J.
Published: March 2018

The specification of tissue identity during embryonic development requires precise spatiotemporal coordination of gene expression. Many transcription factors required for the development of organs have been identified and their expression patterns are known; however, the mechanisms through which they coordinate gene expression in time remain poorly understood. Here we show that hormone-induced transcription factor Blimp-1 participates in the temporal coordination of tubulogenesis in Drosophila melanogaster by regulating the expression of many genes involved in tube maturation. In particular, we demonstrate that Blimp-1 regulates the expression of genes involved in chitin deposition and F-actin organization. We show that Blimp-1 is involved in the temporal control of lumen maturation by regulating the beginning of chitin deposition. We also report that Blimp-1 represses a variety of genes involved in tracheal maturation. Finally, we reveal that the kinase Btk29A serves as a link between Blimp-1 transcriptional repression and apical extra-cellular matrix organization.
The Mathematics of Descriptions in Descriptive Epidemiology
Authors: Ozonoff David , Pogel Alex
Published: March 2018

Identifying patterns of disease distribution in a population is the task of descriptive epidemiology, where the patterns are descriptions of how the disease is distributed in the population. In everyday public health practice it is descriptive epidemiology that is hard at work when we inform the public about health problems, monitor its health status, gather information for planning and administrative purposes, or generate hypotheses to be tested by further analytic investigations. In this paper we pursue a formalization of the population descriptions that are the heart of descriptive epidemiology. We call attention to a fact, so far unrecognized by epidemiologists, that the set of (complete) population descriptions, suitably defined, has an associated relational and algebraic structure. This formalization allows us to access mathematical properties of this structure of an epidemiologic dataset with methods developed over the past 30 years.
A Sentence Supramodal Areas Atlas (Sensaas) Based on Multiple Task-Induced Activation Mapping and Graph Analysis of Intrinsic Connectivity in 144 Healthy Right-Handers
Authors: Labache L , Joliot M , Saracco J , Jobard G , Hesling I , Zago L , Mellet E , Petit L , Crivello F , Mazoyer B , Tzourio-Mazoyer N
Published: March 2018

We herein propose an atlas of 32 sentence-related areas based on a 3-step method combining the analysis of activation and asymmetry during multiple language tasks with hierarchical clustering of resting-state connectivity and graph analyses. 144 healthy right-handers performed fMRI runs based on language production, reading and listening, both with sentences and lists of over-learned words. Sentence minus word-list BOLD contrast and left-minus-right BOLD asymmetry for each task were computed in pairs of homotopic regions of interest (hROIs) from the AICHA atlas. Thirty-two hROIs were identified that were conjointly activated and leftward asymmetrical in each of the 3 language contrasts. Analysis of resting- state temporal correlations of BOLD variations between these 32 hROIs allowed the segregation of a core network, SENT_CORE including 18 hROIs. Resting-state graph analysis applied to SENT_CORE hROIs revealed that the pars triangularis of the inferior frontal gyrus and the superior temporal sulcus were hubs based on their degree centrality, betweenness, and participation values, corresponding to epicentres of sentence processing. Positive correlations between DC and BOLD activation values for SENT_CORE hROIs were observed across individuals and across regions regardless of the task: the more a SENT_CORE area is connected at rest the stronger it is activated during sentence processing. DC measurements in SENT_CORE may thus be a valuable index for the evaluation of inter-individual variations in language areas functional activity in relation to anatomical or clinical patterns in large populations. SENSAAS (SENtence Supramodal Areas AtlaS), comprising the 32 supramodal sentence areas, including SENT-CORE network, can be downloaded at http://www.gin.cnrs.fr/en/tools/.
MicroRNAs as potential therapeutics to enhance chemosensitivity in advanced prostate cancer
Authors: Lin Hui-Ming , Nikolic Iva , Yang Jessica , Castillo Lesley , Deng Niantao , Chan Chia-Ling , Yeung Nicole K. , Dodson Eoin , Elsworth Benjamin , Spielman Calan , Lee Brian Y. , Boyer Zoe , Simpson Kaylene J. , Daly Roger J. , Horvath Lisa G. , Swarbrick Alexander
Published: March 2018

Docetaxel and cabazitaxel are taxane chemotherapy treatments for metastatic castration-resistant prostate cancer (CRPC). However, therapeutic resistance remains a major issue. MicroRNAs are short non-coding RNAs that can silence multiple genes, regulating several signalling pathways simultaneously. Therefore, synthetic microRNAs may have therapeutic potential in CRPC by regulating genes involved in taxane response and minimise compensatory mechanisms that cause taxane resistance. To identify microRNAs that can improve the efficacy of taxanes in CRPC, we performed a genome-wide screen of 1280 microRNAs in the CRPC cell lines PC3 and DU145 in combination with docetaxel or cabazitaxel treatment. Mimics of miR-217 and miR-181b-5p enhanced apoptosis significantly in PC3 cells in the presence of these taxanes. These mimics downregulated at least a thousand different transcripts, which were enriched for genes with cell proliferation and focal adhesion functions. Individual knockdown of a selection of 46 genes representing these transcripts resulted in toxic or taxane sensitisation effects, indicating that these genes may be mediating the effects of the microRNA mimics. A range of these genes are expressed in CRPC metastases, suggesting that these microRNA mimics may be functional in CRPC. With further development, these microRNA mimics may have therapeutic potential to improve taxane response in CRPC patients.
Dazl regulates germ cell survival through a network of polyA-proximal mRNA interactions
Authors: Zagore Leah L. , Sweet Thomas J. , Hannigan Molly M. , Weyn-Vanhentenryck Sebastien M. , Jobava Raul , Hatzoglou Maria , Zhang Chaolin , Licatalosi Donny D.
Published: March 2018

The RNA binding protein Dazl is essential for gametogenesis, but its direct in vivo functions, RNA targets, and the molecular basis for germ cell loss in DAZL null mice are unknown. Here, we mapped transcriptome-wide Dazl-RNA interactions in vivo, revealing Dazl binding to thousands of mRNAs via polyA-proximal 3’UTR interactions. In parallel, fluorescence activated cell sorting and RNA-Seq identified mRNAs sensitive to Dazl deletion in male germ cells. Despite binding a broad set of mRNAs, integrative analyses indicate that Dazl post-transcriptionally controls only a subset of its mRNA targets, namely those corresponding to a network of genes critical for germ cell proliferation and survival. Additionally, we provide evidence that polyA sequences have key roles in specifying Dazl-RNA interactions across the transcriptome. Altogether, our results reveal a mechanism for Dazl-RNA binding, and illustrate that Dazl functions as a master regulator of a post-transcriptional mRNA program essential for germ cell survival.
Transcription factor TAp73 and microRNA-449 complement each other to support multiciliogenesis
Authors: Wildung Merit , Esser Tilman Uli , Grausam Katie Baker , Wiedwald Cornelia , Volceanov-Hahn Larisa , Riedel Dietmar , Beuermann Sabine , Li Li , Zylla Jessica , Guenther Ann-Kathrin , Wienken Magdalena , Ercetin Evrim , Han Zhiyuan , Bremmer Felix , Shomroni Orr , Andreas Stefan , Zhao Haotian , Lizé Muriel
Published: March 2018

Motile cilia serve vital functions in development, homeostasis and regeneration. We recently demonstrated that TAp73 is an essential transcriptional regulator of respiratory multiciliogenesis. Here, we show that TAp73 is expressed in multiciliated cells (MCCs) of diverse tissues. Analysis of TAp73 mutant animals revealed that TAp73 regulates Foxj1, Rfx2, Rfx3, axonemal dyneins Dnali1 and Dnai1, plays a pivotal role in the generation of MCCs in male and female reproductive ducts, and contributes to fertility. However, the function of MCCs in the brain appears to be preserved despite the loss of TAp73, and robust activity of cilia-related networks is maintained in the absence of TAp73. Notably, TAp73 loss leads to distinct changes in ciliogenic microRNAs: miR34bc expression is reduced, whereas the miR449 cluster is induced in diverse multiciliated epithelia. Among different MCCs, choroid plexus (CP) epithelial cells in the brain display prominent miR449 expression, whereas brain ventricles exhibit significant increase in miR449 levels along with an increase in the activity of ciliogenic E2F4/MCIDAS circuit in TAp73 mutant animals. Conversely, E2F4 induces robust transcriptional response from miR449 genomic regions. To address whether increased miR449 levels in the brain maintain the multiciliogenesis program in the absence of TAp73, we deleted both TAp73 and miR449 in mice. Although loss of miR449 alone led to a mild ciliary defect in the CP, more pronounced ciliary defects and hydrocephalus were observed in the brain lacking both TAp73 and miR449. In contrast, miR449 loss in other MCCs failed to enhance ciliary defects associated with TAp73 loss. Together, our study shows that, in addition to the airways, TAp73 is essential for generation of MCCs in male and female reproductive ducts, whereas miR449 and TAp73 complement each other to support multiciliogenesis and CP development in the brain.
A Comprehensive Mathematical Model of Surface Electromyography and Force Generation
Authors: Petersen Eike , Rostalski Philipp
Published: March 2018

The purpose of this article is to provide a unified description of a comprehensive mathematical model of surface electromyographic (EMG) measurements and the corresponding force signal in skeletal muscles. The model comprises motor unit pool organization, recruitment and rate coding, intracellular action potential generation and the resulting EMG measurements, as well as the generated muscular force during voluntary isometric contractions. It consolidates and extends the results of several previous publications that proposed mathematical models for the individual model components. A parameterization of the electrical and mechanical components of the model is proposed that ensures a physiologically meaningful EMG-force relation in the simulated signals. Moreover, a novel nonlinear transformation of the excitation model input is proposed, which ensures that the model force output equals the desired target force. Finally, an alternative analytical formulation of the EMG model is proposed, which renders the physiological meaning of the model more clear and facilitates a mathematical proof that muscle fibers in this model at no point in time represent a net current source or sink.

Neuromuscular physiology is a vibrant research field that has recently seen exciting advances. Many previous publications have focused on thorough analyses of particular aspects of neuromuscular physiology, yet an integration of the various novel findings into a single, comprehensive model is missing. A consistent description of a complete physiological model as presented here, including thorough justification of model component choices, will facilitate the use of these advanced models in future research. Results of a numerical simulation highlight the model’s capability to reproduce many physiological effects observed in experimental measurements, and to produce realistic synthetic data that are useful for the validation of signal processing algorithms. The model is based on recent advances in the understanding of muscular physiology and hence also applicable for analyzing the influence of various physiological and measurement setup parameters on the measured force and EMG signals.
DoesBorrelia burgdorferisensu lato facilitate the colonisation of marginal habitats byIxodes ricinus? A correlative study in the Swiss Alps
Authors: Lemoine Mélissa , Cornetti Luca , Tschirren Barbara
Published: March 2018

Parasites can alter host and vector phenotype and thereby affect ecological processes in natural populations. Laboratory studies have shown thatBorrelia burgdorferisensu lato, the causative agent of human Lyme borreliosis, induces physiological alterations in its main tick vector in Europe,Ixodes ricinus, which increase its survival under challenging conditions. We hypothesise that these phenotypic alterations may allowI. ricinusto colonise marginal habitats, thereby fuelling the ongoing range expansion ofI. ricinustowards higher elevations and latitudes induced by climate change. To explore the potential for such an effect under natural conditions, we studied the prevalence ofB. burgdorferis.l. in questingI. ricinusand its variation with elevation in the Swiss Alps. We screened forB. burgdorferis.l. infection in questing nymphs ofI. ricinus(N = 411) from 15 sites between 528 and 1774 m.a.s.l to test ifB. burgdorferis.l. prevalence is higher at high elevations (i.e. in marginal habitats). We found thatB. burgdorferis.l. prevalence inI. ricinusnymphs decreased linearly with increasing elevation and that it was 12.6% lower inI. ricinusnymphs collected at high elevations compared to nymphs in the core range. Thus, we found no evidence that theB. burgdorferis.l.-induced alterations ofI. ricinusphenotype facilitate the colonisation of marginal habitats in the wild. These findings have implications for a better understanding of eco-evolutionary processes in natural host-parasite systems, as well as the assessment of Lyme borreliosis risk in regions whereI. ricinusis newly emerging.
How optimal foragers should respond to habitat changes? On the consequences of habitat conversion
Authors: Calcagno Vincent , Hamelin Frédéric , Mailleret Ludovic , Grognard Frédéric
Published: March 2018

The Marginal Value Theorem (MVT) provides a framework to predict how habitat modifications related to the distribution of resources over patches should impact the realized fitness of individuals and their optimal rate of movement (or patch residence times) across the habitat. Most MVT theory has focused on the consequences of changing the shape of the gain functions in some patches, describing for instance patch enrichment. However an alternative form of habitat modification is habitat conversion, whereby patches are converted from one existing type to another (e.g. closed habitat to open habitat). In such a case the set of gain functions existing in the habitat does not change, only their relative frequencies does. This has received comparatively very little attention in the context of the MVT. Here we analyze mathematically the consequences of habitat conversion under the MVT. We study how realized fitness and the average rate of movement should respond to changes in the frequency distribution of patch-types, and how they should covary. We further compare the response of optimal and non-plastic foragers. We find that the initial pattern of patch-exploitation in a habitat, characterized by the regression slope of patch yields over residence times, can help predict the qualitative responses of fitness and movement rate following habitat conversion. We also find that for some habitat conversion patterns, optimal and non-plastic foragers exhibit qualitatively different responses, and that adaptive foragers can have opposite responses in the early and late phases following habitat conversion. We suggest taking into account behavioral responses may help better understand the ecological consequences of habitat conversion.
SpiceRx: an integrated resource for the health impacts of culinary spices and herbs
Authors: Nk Rakhi , Tuwani Rudraksh , Garg Neelansh , Mukherjee Jagriti , Bagler Ganesh
Published: March 2018

Spices and herbs are key dietary ingredients used in cuisines across the world. They have been reported to be of medicinal value for a wide variety of diseases through a large body of biomedical investigations. Bioactive phytochemicals in these plant products form the basis of their therapeutic potential as well as adverse effects. A systematic compilation of empirical data involving these aspects of culinary spices and herbs could help unravel molecular mechanisms underlying their effects on health.

SpiceRx provides a platform for exploring the health impact of spices and herbs used in food preparations through a structured database of tripartite relationships with their phytochemicals and disease associations. Starting with an extensive dictionary of culinary spices and herbs, their disease associations were text mined from MEDLINE, the largest database of biomedical abstracts, assisted with manual curation. This information was further combined with spice-phytochemical and phytochemical-disease associations. SpiceRx is an integrated repertoire of evidence-based knowledge pertaining to the health impacts of culinary spices and herbs, and facilitates their disease-specific culinary recommendations as well as exploration of molecular mechanisms underlying their health effects.

Availability and Implementation

SpiceRx is available at http://cosylab.iiitd.edu.in/spicerx and supports all modern browsers. SpiceRx is implemented with Python web development framework Django and relational database PostgreSQL; the front-end was built using HTML, CSS, JavaScript, AJAX, jQuery, JSME Molecular Editor, Bootstrap, Jmol, DataTables and Google Charts.

Supplementary information

Supplementary data are available at Bioinformatics online.
Mapping Local Conformational Landscapes of Proteins in Solution
Authors: ElGamacy M. , Riss M. , Zhu H. , Truffault V. , Coles M.
Published: March 2018

The ability of proteins to adopt multiple conformational states is essential to their function and elucidating the details of such diversity under physiological conditions has been a major challenge. Here we present a generalized method for mapping protein population landscapes by NMR spectroscopy. Experimental NOESY spectra are directly compared to a set of expectation spectra back-calculated across an arbitrary conformational space. Signal decomposition of the experimental spectrum then directly yields the relative populations of local conformational microstates. In this way, averaged descriptions of conformation can be eliminated. As the method quantitatively compares experimental and expectation spectra, it inherently delivers an R-factor expressing how well structural models explain the input data. We demonstrate that our method extracts sufficient information from a single 3D NOESY experiment to perform initial model building, refinement and validation, thus offering a complete de novo structure determination protocol.
IFNβ and TNFα cooperate to induce a STAT1-independent antiviral and immunoregulatory program via non-canonical STAT2 and IRF9 pathways
Authors: Mariani Mélissa K. , Dasmeh Pouria , Fortin Audray , Caron Elise , Kalamujic Mario , Harrison Alexander N. , Kasumba Dacquin M. , Cervantes-Ortiz Sandra , Mukawera Espérance , Serohijos Adrian W.R. , Grandvaux Nathalie
Published: March 2018

IFNβ typically induces an antiviral and immunoregulatory transcriptional program through the activation of ISGF3 (STAT1, STAT2 and IRF9) transcriptional complexes. The response to IFNβ is context-dependent and is prone to crosstalk with other cytokines, such as TNFα IFNβ and TNFα synergize to drive a specific delayed transcriptional program. Previous observation led to the hypothesis that an alternative STAT1-independent pathway involving STAT2 and IRF9 might be involved in gene induction by the combination of IFNβ and TNFα. Using genome wide transcriptional profiling by RNASeq, we found that the costimulation with IFNβ and TNFα induces a broad antiviral and immunoregulatory transcriptional program independently of STAT1. Additionally, STAT2 and IRF9 are involved in the regulation of only a subset of these STAT1-independent genes. Consistent with the growing literature, STAT2 and IRF9 act in concert to regulate a subgroup of these genes. Unexpectedly, STAT2 and IRF9 were also engaged in specific independent pathways to regulate distinct sets of IFNβ and TNFα-induced genes. Altogether these observations highlight the existence of distinct previously unrecognized non-canonical STAT1-independent, but STAT2 and/or IRF9-dependent pathways in the establishment of a delayed antiviral and immunoregulatory transcriptional program in conditions where elevated levels of both IFNβ and TNFα are present.
GiraFFe Browse: A lightweight web based tool for inspecting GFF and FASTA data
Authors: Garland Owen , Clare Amanda , Aubrey Wayne
Published: March 2018

GiraFFe Browse is a tool aimed at making GFF and FASTA data more useful and accessible to researchers. Existing solutions are large in scope and difficult to maintain without specialist knowledge of computer systems. GiraFFe Browse is a lightweight alternative, built using modern software engineering practices with a focus on being developer and user friendly.

Availability and implementation

GiraFFe Browse is open source (GPL) software that is available from the Github repository: https://github.com/bag-man/giraffe-browse

Demo version

An example installation of the application is available at http://giraffe.owen.cymru, using a GFF and FASTA file of Escherichia coli from the European Nucleotide Archive.

Contact

garland.owen@gmail.com
Towards a unification of niche and neutral models of community ecology
Authors: Laan Andres , de Polavieja Gonzalo G.
Published: March 2018

Ecological models of community dynamics fall into two main categories. The neutral theory of biodiversity correctly predicts various large-scale ecosystem characteristics such as the species abundance distributions. On a smaller scale, the niche theory of species competition explains population dynamics and interactions between two to a dozen species. Despite the successes of the two theories, they rely on two contradictory assumptions. In the neutral theory each species is competitively equivalent while in the niche theory every species is specialized to exploit a specific part of its environment. Here we propose a resolution to this contradiction using a game theory model of competition with an attractor hyperplane as its equilibrium solution. When the population dynamics shifts within the hyperplane, it is selectively neutral. However, any movement perpendicular to the hyperplane is subject to restoring forces similar to what is predicted by the niche theory. We show that this model correctly reproduces empirical species abundance distributions and is also compatible with species removal experiments.
FITC Conjugated Polycaprolactone-Glycol-Chitosan Nanoparticles Containing The Longwave Emitting Fluorophore IR 820 For In-Vitro Tracking Of Hyperthermia-Induced Cell Death
Authors: Kumar Piyush , Srivastava Rohit
Published: March 2018

Cancer theranostic agent IR 820 loses its bioimaging ability once therapy is initiated. At the end of therapy, it becomes difficult to track the cancer cells. To address this, FITC conjugated Polycaprolactone glycol chitosan IR 820 nanoparticles (FITC-PCLGC-IR NPs) has been synthesized for in vitro tracking of hyperthemia induced cell death. Two approaches, namely ex situ and in situ have been pursued FITC conjugation to PCLGC-IR NPs. Further comparisons were made to FITC encapsulated PCLGC-IR NPs in terms of biocompatibility, cellular uptake, photothermal mediated cell death and imaging with respect to laser treatment. We have shown that an 808 nm diode laser treatment did not affect the imaging ability of these NPs whereas cancer. Time scanned fluorescence shows the excellent photostability of this formulation for a maximum of 5 min. The detailed studies of these approaches summarize that FITC conjugation to PCLGC-IR nanoparticles is an effective nano-theranostic solution for image-guided photothermal therapy.
Recruitment of Two Dyneins to an mRNA-Dependent Bicaudal D Transport Complex
Authors: Sladewski Thomas E. , Billington Neil , Ali M. Yusuf , Bookwalter Carol S. , Lu Hailong , Krementsova Elena B. , Schroer Trina A. , Trybus Kathleen M.
Published: March 2018

We investigated the role of binding partners of full-lengthDrosophilaBicaudal D (BicD) in the activation of dynein-dynactin motility for mRNA transport on microtubules. In single-molecule assays, full-length BicD robustly activated dynein-dynactin only when both the mRNA binding protein Egalitarian (Egl), andK10mRNA cargo were present. Electron microscopy showed that both Egl and mRNA were needed to disrupt an auto-inhibited, looped BicD conformation that sterically prevents dynein-dynactin binding.In vitroreconstituted messenger ribonucleoprotein (mRNP) complexes with two Egl molecules showed faster speeds and longer run lengths than mRNPs with one Egl, suggesting that cargo binding enhances dynein recruitment. Labeled dynein showed that BicD can recruit two dimeric dyneins to the mRNP, resulting in faster speeds and longer run lengths than with one dynein. The fully reconstituted mRNP provides a model for understanding how adaptor proteins and cargo cooperate to confer optimal transport properties to a dynein-driven transport complex.
Texture Analysis of Dystrophic Muscle Biopsies
Authors: Klonowski Wlodzimierz , Kuraszkiewicz Bozenna , Kaminska Anna M. , Kostera-Pruszczyk Anna
Published: March 2018

Despite the introduction of a full range of genetic diagnostic tests and sophisticated techniques in modern pathology, interpretation of histopathological images obtained from muscle biopsies remains important in the daily practice of neuropathology since it can give indications of the severity and the rate of progression of neuromuscular disease. In this paper, we propose a simple and time saving method for quantitative assessment of severity of Duchenne Muscular Dystrophy (DMD) based on computer-aided analysis of histopathological images obtained from biopsies of dystrophic muscles. Using this method, colour filtration pixel-by-pixel of the whole virtual slides (CFPP method) is adopted to semi-quantitative evaluation of morphological structure of the muscular tissue. Results demonstrate usefulness of the proposed method in neuropathological assessement of DMD severity.
Epigenome-wide study uncovers tau pathology-driven changes of chromatin organization in the aging human brain
Authors: Klein Hans-Ulrich , McCabe Cristin , Gjoneska Elizabeta , Sullivan Sarah E. , Kaskow Belinda J. , Tang Anna , Smith Robert V. , Xu Jishu , Pfenning Andreas R. , Bernstein Bradley E. , Meissner Alexander , Schneider Julie A. , Mostafavi Sara , Tsai Li-Huei , Young-Pearse Tracy L. , Bennett David A. , De Jager Philip L.
Published: March 2018

Accumulation of tau and amyloid-β are two pathologic hallmarks of Alzheimer’s disease (AD). Here, we conducted an epigenome-wide association study using the H3K9 acetylation (H3K9Ac) mark in 669 aged human prefrontal cortices: in contrast to amyloid-β, tau protein burden had a broad effect on the epigenome, affecting 5,590 out of 26,384 H3K9Ac domains. Tau-related alterations aggregated in large genomic segments reflecting spatial chromatin organization, and the magnitude of these effects correlated with the segment’s nuclear lamina association. We confirmed the functional relevance of these chromatin changes by demonstrating (1) consistent transcriptional changes in three independent datasets and (2) similar findings in two AD mouse models. Finally, we found that tau overexpression in iPSC-derived neurons disrupted chromatin organization and that these effects could be blocked by a small molecule predicted to reverse the tau effect. Thus, we report large-scale tau-driven chromatin rearrangements in the aging human brain that may be reversible with HSP90 inhibitors.
A Monte Carlo approach for scattering correction towards quantitative neutron imaging of polycrystals
Authors: Raventós M. , Lehmann E. H. , Boin M. , Morgano M. , Hovind J. , Harti R. , Valsecchi J. , Kaestner A. , Carminati C. , Boillat P. , Trtik P. , Schmid F. , Siegwart M. , Mannes D. , Strobl M. , Grünzweig C.
Published: March 2018

The development of neutron imaging from a qualitative inspection tool towards a quantitative technique in materials science has increased the requirements for accuracy significantly. Quantifying the thickness or the density of polycrystalline samples with high accuracy using neutron imaging has two main problems: (i) the scattering from the sample creates artefacts on the image and (ii) there is a lack of specific reference attenuation coefficients. This work presents experimental and simulation results to explain and approach these problems. Firstly, a series of neutron radiography and tomography experiments of iron, copper and vanadium are performed and serve as a reference. These materials were selected because they attenuate neutrons mainly through coherent (Fe and Cu) and incoherent (V) scattering. Secondly, an ad hoc Monte Carlo model was developed, based on beamline, sample and detector parameters, in order to simulate experiments, understand the physics involved and interpret the experimental data. The model, developed in the McStas framework, uses a priori information about the sample geometry and crystalline structure, as well as beamline settings, such as spectrum, geometry and detector type. The validity of the simulations is then verified with experimental results for the two problems that motivated this work: (i) the scattering distribution in transmission imaging and (ii) the calculated attenuation coefficients.
New applications of the X-ray rotation tilt technique
Authors: Heckert Mirko , Enghardt Stefan , Bauch Jürgen
Published: March 2018

The piezoelectric materials langasite (LGS) and calcium tantalum gallium silicate (CTGS) have been investigated with the X-ray rotation tilt (XRRT) technique using a new evaluation method. The XRRT technique is a microdiffraction method where diffraction lines are registered on a two-dimensional detector. These lines can be described using conic sections analogous to Kossel lines. Their form and position depend upon the lattice parameters and orientation of the investigated crystal. They can, therefore, be used to obtain these parameters. The new evaluation method allows for an automatic indexing of XRRT and Kossel reflections without knowledge of the pattern centre and detector-to-sample distance. This enables the investigation of more complex crystal structures like LGS and CTGS, where in this work the lattice constants and orientation were measured at various points on the sample.
The development of powder profile refinement at the Reactor Centre Netherlands at Petten
Authors: van Laar Bob , Schenk Henk
Published: March 2018

With thousands of references to `Rietveld refinement' it is forgotten that the method did not suddenly appear in a flash of inspiration of a single person, but was the result of the work of three individuals working in the 1960s at the Reactor Centre Netherlands at Petten, Loopstra, van Laar and Rietveld. This paper outlines the origins of `profile refinement', as it was called at Petten, and also looks at why it took so long for the scientific community to recognize its importance. With the recent passing of Hugo Rietveld, the death of Bert Loopstra in 1998 and before other pioneers also disappear, it is important to set down a first-hand account.
Monoclinic sphere packings. II. Trivariant lattice complexes with mirror symmetry
Authors: Sowa Heidrun
Published: March 2018

All homogeneous sphere packings were derived that refer to the three trivariant monoclinic lattice complexes with mirror symmetry. In total, 29 types of sphere packings have been found. Only for three types is the maximal inherent symmetry of their sphere packings monoclinic whereas the inherent symmetry is orthorhombic for 13 types, tetragonal for eight types, hexagonal for four types and cubic for one type.
Constitutive modelling of mechanically induced martensitic transformations
Authors: de Bortoli Daniel , Adziman Fauzan , de Souza Neto Eduardo A. , Pires Francisco M. Andrade
Published: March 2018

Purpose

The purpose of this work is to apply a recently proposed constitutive model for mechanically induced martensitic transformations to the prediction of transformation loci. Additionally, this study aims to elucidate if a stress-assisted criterion can account for transformations in the so-called strain-induced regime.

Design/methodology/approach

The model is derived by generalising the stress-based criterion of Patel and Cohen (1953), relying on lattice information obtained using the Phenomenological Theory of Martensite Crystallography. Transformation multipliers (cf. plastic multipliers) are introduced, from which the martensite volume fraction evolution ensues. The associated transformation functions provide a variant selection mechanism. Austenite plasticity follows a classical single crystal formulation, to account for transformations in the strain-induced regime. The resulting model is incorporated into a fully implicit RVE-based computational homogenisation finite element code.

Findings

Results show good agreement with experimental data for a meta-stable austenitic stainless steel. In particular, the transformation locus is well reproduced, even in a material with considerable slip plasticity at the martensite onset, corroborating the hypothesis that an energy-based criterion can account for transformations in both stress-assisted and strain-induced regimes.

Originality/value

A recently developed constitutive model for mechanically induced martensitic transformations is further assessed and validated. Its formulation is fundamentally based on a physical metallurgical mechanism and derived in a thermodynamically consistent way, inheriting a consistent mechanical dissipation. This model draws on a reduced number of phenomenological elements and is a step towards the fully predictive modelling of materials that exhibit such phenomena.