bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational and robotic modeling reveal parsimonious combinations of interactions between individuals in schooling fish
Authors: Lei Liu , Escobedo Ramón , Sire Clément , Theraulaz Guy 
Published: June 2019

AbstractCoordinated motion and collective decision-making in fish schools result from complex interactions by which individuals integrate information about the behavior of their neighbors. However, little is known about how individuals integrate this information to take decisions and control their movements. Here, we combine experiments with computational and robotic approaches to investigate the impact of different strategies for a fish to interact with its neighbors on collective swimming in groups of rummy-nose tetra (Hemigrammus rhodostomus). By means of a data-based agent model describing the interactions between pairs ofH. rhodostomus(Caloviet al., 2018), we show that the simple addition of the pairwise interactions with two neighbors quantitatively reproduces the collective behavior observed in groups of five fish. Increasing the number of interacting neighbors does not significantly improve the simulation results. Remarkably, we find that groups remain cohesive and polarized even when each agent only interacts with only one of its neighbors: the one that has the strongest contribution to the heading variation of the focal agent. However, group cohesion is lost when each agent only interacts with its nearest neighbor. We then investigate by means of a swarm robotic platform the collective motion in groups of five robots. Our platform combines the implementation of the fish behavioral model and an engineering-minded control system to deal with real-world physical constraints. We find that swarms of robots are able to reproduce the behavioral patterns observed in groups of five fish when each robot only interacts with its neighbor having the strongest effect on its heading variation, whereas increasing the number of interacting neighbors does not significantly improve the group coordination. Overall, our results suggest that fish have to acquire only a minimal amount of information about their environment to coordinate their movements when swimming in groups.Author SummaryHow do fish combine and integrate information from multiple neighbors when swimming in a school? What is the minimum amount of information about their environment needed to coordinate their motion? To answer these questions, we combine experiments with computational and robotic modeling to test several hypotheses about how individual fish could combine and integrate the information on the behavior of their neighbors when swimming in groups. Our research shows that, for both simulated agents and robots, using the information of two neighbors is sufficient to qualitatively reproduce the collective motion patterns observed in groups of fish. Remarkably, our results also show that it is possible to obtain group cohesion and coherent collective motion over long periods of time even when individuals only interact with their most influential neighbor, that is, the one that exerts the most important effect on their heading variation.
Stochastic Modeling Reveals Kinetic Heterogeneity in Post-replication DNA Methylation
Authors: Busto-Moner Luis , Morival Julien , Fahim Arjang , Reitz Zachary , Downing Timothy L. , Read Elizabeth L. 
Published: June 2019

AbstractDNA methylation is a heritable epigenetic modification that plays an essential role in mammalian development. Genomic methylation patterns are dynamically maintained, with DNA methyltransferases mediating inheritance of methyl marks onto nascent DNA over cycles of replication. A recently developed experimental technique employing immunoprecipitation of bromodeoxyuridine labeled nascent DNA followed by bisulfite sequencing (Repli-BS) measures post-replication temporal evolution of cytosine methylation, thus enabling genome-wide monitoring of methylation maintenance. In this work, we combine statistical analysis and stochastic mathematical modeling to analyze Repli-BS data from human embryonic stem cells. We estimate site-specific kinetic rate constants for the restoration of methyl marks on >10 million uniquely mapped cytosines within the CpG (cytosine-phosphate-guanine) dinucleotide context across the genome using Maximum Likelihood Estimation. We find that post-replication remethylation rate constants span approximately two orders of magnitude, with half-lives of per-site recovery of steady-state methylation levels ranging from shorter than ten minutes to five hours and longer. Furthermore, we find that kinetic constants of maintenance methylation are correlated among neighboring CpG sites. Stochastic mathematical modeling provides insight to the biological mechanisms underlying the inference results, suggesting that enzyme processivity and/or collaboration can produce the observed kinetic correlations. Our combined statistical/mathematical modeling approach expands the utility of genomic datasets and disentangles heterogeneity in methylation patterns arising from replication-associated temporal dynamics versus stable cell-to-cell differences.
Quantifying transmission of emerging zoonoses: Using mathematical models to maximize the value of surveillance data
Authors: Ambrose Monique R. , Kucharski Adam J. , Formenty Pierre , Muyembe-Tamfum Jean-Jacques , Rimoin Anne W. , Lloyd-Smith James O. 
Published: June 2019

AbstractUnderstanding and quantifying the transmission of zoonotic pathogens is essential for directing public health responses, especially for pathogens capable of transmission between humans. However, determining a pathogen’s transmission dynamics is complicated by challenges often encountered in zoonotic disease surveillance, including unobserved sources of transmission (both human and zoonotic), limited spatial information, and unknown scope of surveillance. In this work, we present a model-based inference method that addresses these challenges for subcritical zoonotic pathogens using a spatial model with two levels of mixing. After demonstrating the robustness of the method using simulation studies, we apply the new method to a dataset of human monkeypox cases detected during an active surveillance program from 1982-1986 in the Democratic Republic of the Congo (DRC). Our results provide estimates of the reproductive number and spillover rate of monkeypox during this surveillance period and suggest that most human-to-human transmission events occur over distances of 30km or less. Taking advantage of contact-tracing data available for a subset of monkeypox cases, we find that around 80% of contact-traced links could be correctly recovered from transmission trees inferred using only date and location. Our results highlight the importance of identifying the appropriate spatial scale of transmission, and show how even imperfect spatiotemporal data can be incorporated into models to obtain reliable estimates of human-to-human transmission patterns.Author SummarySurveillance datasets are often the only sources of information about the ecology and epidemiology of zoonotic infectious diseases. Methods that can extract as much information as possible from these datasets therefore provide a key advantage for informing our understanding of the disease dynamics and improving our ability to choose the optimal intervention strategy. We developed and tested a likelihood-based inference method based on a mechanistic model of the spillover and human-to-human transmission processes. We first used simulated datasets to explore which information about the disease dynamics of a subcritical zoonotic pathogen could be successfully extracted from a line-list surveillance dataset with non-localized spatial information and unknown geographic coverage. We then applied the method to a dataset of human monkeypox cases detected during an active surveillance program in the Democratic Republic of the Congo between 1982 and 1986 to obtain estimates of the reproductive number, spillover rate, and spatial dispersal of monkeypox in humans.
Activation ofShigella flexneritype 3 secretion requires a host-induced conformational change to the translocon pore
Authors: Russo Brian C. , Duncan Jeffrey K. , Wiscovitch Alexandra L. , Hachey Austin C. , Goldberg Marcia B. 
Published: June 2019

AbstractType 3 secretion systems (T3SSs) are conserved bacterial nanomachines that inject virulence proteins (effectors) into eukaryotic cells during infection. Due to their ability to introduce heterologous protein into human cells, these systems are being developed as therapeutic delivery devices. The T3SS assembles a translocon pore in the plasma membrane and then docks onto the pore. Docking activates effector secretion through the pore and into the host cytosol. Here, usingShigella flexneri, a model pathogen for the study of type 3 secretion, we determined the molecular mechanisms by which host intermediate filaments trigger docking and enable effector secretion. We show that the interaction of intermediate filaments with the translocon pore protein IpaC changed the pore’s conformation in a manner that was required for docking. Intermediate filaments repositioned residues of theShigellapore protein IpaC that are located on the surface of the pore and in the pore channel. Restricting these conformational changes blocked docking in an intermediate filament-dependent manner. These data demonstrate that a host-induced conformational change to the pore enables T3SS docking and effector secretion, providing new mechanistic insight into the regulation of type 3 secretion.Author summaryThe movement of bacterial proteins across membranes is essential for bacterial physiology and bacterial virulence. The type 3 secretion system moves bacterial virulence proteins from the inside of bacterial pathogens into human cells. To do so, the type 3 secretion system forms a pore in the plasma membrane of the target cell, attaches (docks) onto the pore, and delivers virulence proteins through the pore. Docking is essential for establishing a continuous channel from the inside of the bacteria to the inside of the human cell. What enables the type 3 secretion system to dock onto pores is not understood. We show that structural proteins in human cells, intermediate filament proteins, induce structural rearrangements to the type 3 secretion pore that trigger docking and that enable the subsequent delivery of virulence proteins into human cells. Due to the wide prevalence of type 3 secretion systems among human pathogens, these findings are likely to broadly enhance our understanding of type 3 secretion.
Controlling Strawberry Mites: Comparison of New Bio-Pesticides and Conventional Chemical Pesticides
Authors: Zhu Jiahong , Li Zhuo , Ren Zongjie , Cao Aocheng , Yan Dongdong , Wang Qiuxia , Ouyang Canbin , Li Yuan 
Published: June 2019

AbstractBACKGROUNDTetranychus cinnabarinusis one of the pest insects most severely influencing strawberry production. It has a high attack rate and causes severe economic losses. Laboratory toxicity tests and greenhouse experiments were carried out using 13 acaricides to determine their efficacy and potential mechanisms of action.RESULTSAbamectin showed the highest efficacy againstT. cinnabarinusfemale mites; its LC50value was 0.18mg L-1. Pyridaben, cyhalothrin, veratrine, and carbosulfan showed reasonably high efficacy; their LC50values were 2.69 mg L-1, 3.94 mg L-1, 5.98 mg L-1, and 6.75 mg L-1, respectively. Less effective were hexythiazox and bifenthrin, their LC50values were 9.82 mg L-1and 19.09 mg L-1, respectively. Other acaricides such as spirodiclofen, chlorantraniliprole, chlorfenapyr, spinosad, and bifenazate did not show good efficacy. The status of female mites treated with avermectin, pyridaben, kanghebio and cyhalothrin changed significantly under a fluorescence microscope. There were no significant differences among female mites treated with spirotetramat, chlorantraniliprole, spinosad and bifenazate. Enzyme activity tests showed that Kanghebio and cyhalothrin obviously inhibited Ca2+-adenosine triphosphatase (Ca2+-ATPase), while veratrine and kanghebi obviously inhibited acetylcholinesterase (TChE) and monoamine oxidase (MAO). Cyhalothrinexerted an auxo-action on MAO. Greenhouse experiment indicated that abamectin showed the best efficacy, as well as the longest duration of efficacy, pyridaben, cyhalothrin, veratrine, and kanghebio followed, while carbosulfan, hexythiazox, and bifenthrin performed the worst.CONCLUSIONSOur study provided a scientific basis for chemical pesticides to be replaced by these and potentially other new bio-pesticides.
Chronic Repeated Predatory Stress Induces Resistance to Quinine Adulteration of Ethanol in Male Mice
Authors: Shaw Gladys A. , Bent Maria Alexis M. , Council Kimaya R. , Pais A. Christian , Amstadter Ananda , Wolstenholme Jennifer T. , Miles Michael F. , Neigh Gretchen N. 
Published: June 2019

AbstractBackgroundTrauma related psychiatric disorders, such as posttraumatic stress disorder (PTSD), and alcohol use disorder (AUD) are highly comorbid illnesses that separately present an opposing, sex-specific pattern, with increased prevalence of PTSD in females and increased prevalence of AUD diagnoses in males. Likewise, PTSD is a risk factor in the development of AUD, with conflicting data on the impact of sex in the comorbid development of both disorders. Because the likelihood of experiencing more than one traumatic event is high, we aim to utilize chronic repeated predatory stress (CRPS) to query the extent to which sex interacts with CRPS to influence alcohol consumption, or cessation of consumption.MethodsMale (n=16) and female (n=15) C57BL/6J mice underwent CRPS or daily handling for two weeks during adolescence (P35-P49) and two weeks during adulthood (P65-P79). Following the conclusion of two rounds of repeated stress, behavior was assessed in the open field. Mice subsequently underwent a two-bottle choice intermittent ethanol access (IEA) assessment (P90-131) with the options of 20% ethanol or water. After establishing drinking behavior, increasing concentrations of quinine were added to the ethanol to assess the drinking response to adulteration of the alcohol.ResultsCRPS increased fecal corticosterone concentrations and anxiety-like behaviors in the open field in both male and female mice as compared to control mice that had not been exposed to CRPS. Consistent with previous reports, we observed a sex difference in alcohol consumption such that females consumed more ethanol per gram of body mass than males. In addition, CRPS reduced alcohol aversion in male mice such that higher concentrations of quinine were necessary to reduce alcohol intake as compared to control mice. CRPS did not alter alcohol-related behaviors in female mice.ConclusionCollectively, we demonstrate that repeated CRPS can induce anxiety-like behavior in both sexes but selectively influences the response to ethanol adulteration in males.
Atypical MEG inter-subject correlation during listening to continuous natural speech in dyslexia
Authors: Thiede A. , Glerean E. , Kujala T. , Parkkonen L. 
Published: June 2019

AbstractListening to speech elicits brain activity time-locked to the speech sounds. This so-called neural entrainment to speech was found to be atypical in dyslexia, a reading impairment associated with neural speech processing deficits. We hypothesized that the brain responses of dyslexic vs. normal readers to real-life speech would be different, and thus the strength of inter-subject correlation (ISC) would differ from that of typical readers and be reflected in reading-related measures.We recorded magnetoencephalograms (MEG) of 23 dyslexic and 21 typically-reading adults during listening to ∼10 min of natural Finnish speech consisting of excerpts from radio news, a podcast, a self-recorded audiobook chapter and small talk. The amplitude envelopes of band-pass-filtered MEG source signals were correlated between subjects in a cortically-constrained source space in six frequency bands. The resulting ISCs of dyslexic and typical readers were compared with a permutation-based t-test. Neuropsychological measures of phonological processing, technical reading, and working memory were correlated with the ISCs utilizing the Mantel test.During listening to speech, ISCs were reduced in dyslexic compared to typical readers in delta (0.5–4 Hz), alpha (8–12 Hz), low gamma (25–45 Hz) and high gamma (55–90 Hz) frequency bands. In the beta (12–25 Hz) band, dyslexics had mainly enhanced ISC to speech compared to controls. Furthermore, we found that ISCs across both groups were associated with phonological processing, technical reading, and working memory.The atypical ISC to natural speech in dyslexics supports the temporal sampling deficit theory of dyslexia. It also suggests over-synchronization to phoneme-rate information in speech, which could indicate more effort-demanding sampling of phonemes from speech in dyslexia. These irregularities in parsing speech are likely some of the complex neural factors contributing to dyslexia. The associations between neural coupling and reading-related skills further support this notion.Research HighlightsMEG inter-subject correlation (ISC) of dyslexics was atypical while listening to speech.Depending on the frequency band, dyslexics had stronger or weaker ISC than controls.Reading-related measures correlated with the strength of ISC.
Mobile phones: The effect of its presence on learning and memory
Authors: Tanil Clarissa T. , Yong Min Hooi 
Published: June 2019

AbstractOur aim was to examine the effect of mobile phone’s presence on learning and memory among undergraduates. A total of 119 undergraduates completed a memory task and the Smartphone Addiction Scale (SAS). As predicted, those without phones had higher recall accuracy compared to those with phones. Results showed a significant negative relationship between phone conscious thought and memory recall but not for SAS and memory recall. Phone conscious thought significantly predicted memory accuracy. We found that the presence of a phone and high phone conscious thought affects one’s memory learning and recall, indicating the negative effect of a mobile phone proximity to our learning and memory.
The expression of equine keratins K42 and K124 is restricted to the hoof epidermal lamellae ofEquus caballus
Authors: Armstrong Caitlin , Cassimeris Lynne , Silva Santos Claire Da , Micoogullari Yagmur , Wagner Bettina , Babasyan Susanna , Brooks Samantha , Galantino-Homer Hannah 
Published: June 2019

AbstractThe equine hoof inner epithelium is folded into primary and secondary epidermal lamellae which increase the dermo-epidermal junction surface area of the hoof and can be affected by laminitis, a common disease of equids. Two keratin proteins (K), K42 and K124, are the most abundant keratins in the hoof lamellar tissue ofEquus caballus. We hypothesize that these keratins are lamellar tissue-specific and could serve as differentiation- and disease-specific markers. Our objective was to characterize the expression of K42 and K124 in equine stratified epithelia and to generate monoclonal antibodies against K42 and K124. By RT-PCR analysis, keratin gene (KRT)KRT42andKRT124expression was present in lamellar tissue, but not cornea, haired skin, or hoof coronet. In situ hybridization studies showed thatKRT124localized to the suprabasal and, to a lesser extent, basal cells of the lamellae, was absent from haired skin and hoof coronet, and abruptly transitions fromKRT124-negative coronet toKRT124-positive proximal lamellae. A monoclonal antibody generated against full-length recombinant equine K42 detected a lamellar keratin of the appropriate size, but also cross-reacted with other epidermal keratins. Three monoclonal antibodies generated against N- and C-terminal K124 peptides detected a band of the appropriate size in lamellar tissue and did not cross-react with proteins from haired skin, corneal limbus, hoof coronet, tongue, glabrous skin, oral mucosa, or chestnut on immunoblots. K124 localized to lamellar cells by indirect immunofluorescence. This is the first study to demonstrate the localization and expression of a hoof lamellar-specific keratin, K124, and to validate anti-K124 monoclonal antibodies.
Plant-mediated community structure of spring-fed, coastal rivers
Authors: Lauretta Matthew V. , Pine William E. , Walters Carl J. , Frazer Thomas K. 
Published: June 2019

AbstractQuantifying ecosystem-level processes that drive community structure and function is key to the development of effective environmental restoration and management programs. To assess the effects of large-scale aquatic vegetation loss on fish and invertebrate communities in Florida estuaries, we quantified and compared the food webs of two adjacent spring-fed rivers that flow into the Gulf of Mexico. We constructed a food web model using field-based estimates of community absolute biomass and trophic interactions of a highly productive vegetated river, and modeled long-term simulations of vascular plant decline coupled with seasonal production of filamentous macroalgae. We then compared ecosystem model predictions to observed community structure of the second river that has undergone extensive vegetative habitat loss, including extirpation of several vascular plant species. Alternative models incorporating bottom-up regulation (decreased primary production resulting from plant loss) versus coupled top-down effects (compensatory predator search efficiency) were ranked by goodness-of-fit tests of model predictions to the empirical community observations. Our best model for predicting community responses to vascular plant loss incorporated coupled effects of decreased primary production (bottom-up), increased prey search efficiency of large-bodied fishes at low vascular plant density (top-down), and decreased prey search efficiency of small-bodied fishes with increased biomass of filamentous macroalgae (bottom-up). The results of this study indicate that the loss of vascular plants from the coastal river ecosystem may alter the food web structure and result in a net decline in the biomass of fishes. These results are highly relevant to ongoing landscape-level restoration programs intended to improve aesthetics and ecosystem function of coastal spring-fed rivers by highlighting how the structure of these communities can be regulated both by resource availability and consumption. Restoration programs will need to acknowledge and incorporate both to be successful.
An integrated solution for space shuttle launching ramp
Authors: Yücenur G. Nilay , Subaşı Anıl Sezer 
Published: June 2019

Purpose
The purpose of this study is to select the most appropriate city in Turkey for space shuttle launching ramp.

Design/methodology/approach
In the proposed approach, an integrated methodology is used. The SWARA method is used in the first phase of the solution for determining criteria’s importance weights. Based on the criteria weights obtained by the SWARA method, the WASPAS method is used for selecting the best alternative.

Findings
Mugla is selected for the most suitable city for the first space shuttle launching pad according to determined criteria and proposed model.

Research limitations/implications
Although there are 81 cities in Turkey, 4 alternatives were selected for evaluation. It is possible to eliminate this limitation by the future studies with the implementation of proposed model to entire of Turkey.

Practical implications
This proposed model can be used by the countries which want to have a new or first space shuttle launching ramp in the world.

Originality/value
Although some climatic conditions are pointed out on the location of the space shuttle launching ramp, in literature, there is not a comprehensive and detailed evaluation example as much as the model proposed in this study. Therefore, this study is the first in terms of the proposed model and applied techniques in the sectoral sense. In addition, the study is also a guide for solving the original model which is revealed in the selection of the most suitable alternative city for space shuttle launching ramp by different multi-criteria decision-making methods.