bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eye position signals in the dorsal pulvinar during fixation and goal-directed saccades
Authors: Schneider Lukas , Dominguez-Vargas Adan-Ulises , Gibson Lydia , Kagan Igor , Wilke Melanie 
Published: July 2019

AbstractMost sensorimotor cortical areas contain eye position information thought to ensure perceptual stability across saccades and underlie spatial transformations supporting goal-directed actions. One pathway by which eye position signals could be relayed to and across cortical areas is via the dorsal pulvinar. Several studies demonstrated saccade-related activity in the dorsal pulvinar and we have recently shown that many neurons exhibit post-saccadic spatial preference long after the saccade execution. In addition, dorsal pulvinar lesions lead to gaze-holding deficits expressed as nystagmus or ipsilesional gaze bias, prompting us to investigate the effects of eye position. We tested three starting eye positions (−15°/0°/15°) in monkeys performing a visually-cued memory saccade task. We found two main types of gaze dependence. First, ∼50% of neurons showed an effect of static gaze direction during initial and post-saccadic fixation. Eccentric gaze preference was more common than straight ahead. Some of these neurons were not visually-responsive and might be primarily signaling the position of the eyes in the orbit, or coding foveal targets in a head/body/world-centered reference frame. Second, many neurons showed a combination of eye-centered and gaze-dependent modulation of visual, memory and saccadic responses to a peripheral target. A small subset showed effects consistent with eye position-dependent gain modulation. Analysis of reference frames across task epochs from visual cue to post-saccadic target fixation indicated a transition from predominantly eye-centered encoding to representation of final gaze or foveated locations in non-retinocentric coordinates. These results show that dorsal pulvinar neurons carry information about eye position, which could contribute to steady gaze during postural changes and to reference frame transformations for visually-guided eye and limb movements.New & NoteworthyWork on the pulvinar focused on eye-centered visuospatial representations, but position of the eyes in the orbit is also an important factor that needs to be taken into account during spatial orienting and goal-directed reaching. Here we show that dorsal pulvinar neurons are influenced by eye position. Gaze direction modulated ongoing firing during stable fixation, as well as visual and saccade responses to peripheral targets, suggesting involvement of the dorsal pulvinar in spatial coordinate transformations.
Genetic coupling of signal and preference facilitates sexual isolation during rapid speciation
Authors: Xu Mingzi , Shaw Kerry L. 
Published: July 2019

AbstractThe divergence of sexual signals is ultimately a coevolutionary process: while signals and preferences diverge between lineages, they must remain coordinated within lineages for matings to occur. Divergence in sexual signals makes a major contribution to evolving species barriers. Therefore, the genetic architecture underlying signal-preference coevolution is essential to understanding speciation but remains largely unknown. InLaupalacrickets where male song pulse rate and female pulse rate preference have coevolved repeatedly and rapidly, we tested two contrasting hypotheses for the genetic architecture underlying signal-preference coevolution: linkage disequilibrium between unlinked loci and genetic coupling (pleiotropy of a shared locus or tight physical linkage). Through selective introgression and quantitative trait locus (QTL) fine mapping, we estimated the location of QTL underlying interspecific variation in both female preference and male pulse rate from the same mapping populations. Remarkably, map estimates of the pulse rate and preference loci are 0.06-0.23 cM apart, the strongest evidence to date for genetic coupling between signal and preference loci. As the second pair of co-localizing signal and preference loci in theLaupalagenome, our finding supports an intriguing pattern, pointing to a major role for genetic coupling in the quantitative evolution of a reproductive barrier and rapid speciation inLaupala. Due to its effect on suppressing recombination, a coupled, quantitative genetic architecture offers a powerful and parsimonious genetic mechanism for signal-preference coevolution and the establishment of positive genetic covariance on which the Fisherian runaway process of sexual selection relies.
Lek-associated movement of a putative Ebolavirus reservoir, the Hammer-headed fruit bat (Hypsignathus monstrosus), in northern Republic of Congo
Authors: Olson Sarah H. , Bounga Gerard , Ondzie Alain , Bushmaker Trent , Seifert Stephanie N. , Kuisma Eeva , Taylor Dylan W. , Munster Vincent J. , Walzer Chris 
Published: July 2019

AbstractThe biology and ecology of Africa’s largest fruit bat remains largely understudied and enigmatic despite at least two highly unusual attributes. The acoustic lek mating behavior of the hammer-headed bat (Hypsignathus monstrosus) in the Congo basin was first described in the 1970s. Then in the 2000s, molecular testing implicated this species and other fruit bats as potential reservoir hosts for Ebola virus and it was one of only two fruit bat species epidemiologically linked to the 2008 Luebo, Democratic Republic of Congo, Ebola outbreak. Here we share findings from the first pilot study of hammer-headed bat movement using GPS tracking and accelerometry units and a small preceding radio-tracking trial at an apparent lekking site. The radio-tracking revealed adult males had high rates of nightly visitation to the site compared to females (only one visit) and that two of six females day-roosted ∼100 m west of Libonga, the nearest village that is ∼1.6 km southwest. Four months later, in mid-April 2018, five individual bats, comprised of four males and one female, were tracked from two to 306 days, collecting from 67 to 1022 GPS locations. As measured by mean distance to the site and proportion of nightly GPS locations within 1 km of the site (percent visitation), the males were much more closely associated with the site (mean distance 1.4 km; 51% visitation), than the female (mean 5.5 km; 2.2% visitation). Despite the small sample size, our tracking evidence supports our original characterization of the site as a lek, and the lek itself is much more central to male than female movement. Moreover, our pilot demonstrates the technical feasibility of executing future studies on hammer-headed bats that will help fill problematic knowledge gaps about zoonotic spillover risks and the conservation needs of fruit bats across the continent.
Unexpected complexity of everyday manual behaviors
Authors: Yan Yuke , Goodman James M. , Moore Dalton D. , Solla Sara A. , Bensmaia Sliman J. 
Published: July 2019

AbstractHow does the brain control an effector as complex and versatile as the hand? One possibility is that the neural control of the hand is simplified by limiting the space of achievable hand postures. Indeed, hand kinematics can be largely accounted for within a small subspace of postures. This oft replicated finding has been interpreted as evidence that hand postures are confined to this subspace, and that leaving it volitionally is impossible. A prediction from this hypothesis is that measured hand movements that fall outside of this subspace reflect motor or measurement noise. To address this question, we track hand postures of human participants as they perform two distinct tasks – grasping and signing in American Sign Language. We then apply a standard dimensionality reduction technique – principal components analysis – and replicate the finding that hand movements can be largely described within a reduced subspace. However, we show that postural dimensions that fall outside of this subspace are highly structured and task dependent, suggesting that they too are under volitional control. We conclude that hand control occupies a higher dimensional space than previously considered, and propose that controlling the complexity of hand movements is well within the scope of the brain’s computational power.
Nanopore base-calling from a perspective of instance segmentation
Authors: Zhang Yao-zhong , Akdemir Arda , Tremmel Georg , Imoto Seiya , Miyano Satoru , Shibuya Tetsuo , Yamaguchi Rui 
Published: July 2019

AbstractBackgroundNanopore sequencing is a rapidly developing third-generation sequencing technology, which can generate long nucleotide reads of molecules within a portable device in real time. Through detecting the change of ion currency signals during a DNA/RNA fragment’s pass through a nanopore, genotypes are determined. Currently, the accuracy of nanopore base-calling has a higher error rate than short-read base-calling. Through utilizing deep neural networks, the-state-of-the art nanopore base-callers achieve base-calling accuracy in a range from 85% to 95%.ResultIn this work, we proposed a novel base-calling approach from a perspective of instance segmentation. Different from the previous sequence labeling approaches, we formulated the base-calling problem as a multi-label segmentation task. Meanwhile, we proposed a refined U-net model which we call UR-net that can model sequential dependencies for a one-dimensional segmentation task. The experiment results show that the proposed base-caller URnano achieves competitive results compared to recently proposed CTC-featured base-caller Chiron, on the same amount of training and test data for in-domain evaluation. Our results show that formulating the base-calling problem as a one-dimensional segmentation task is a promising approach.AvailabilityThe source code and data are available at https://github.com/yaozhong/URnanoContactyaozhong@ims.u-tokyo.ac.jpSupplementary informationSupplementary data are available at attachment online.
Disruption of prepulse inhibition is associated with severity of compulsive behavior and nucleus accumbens dopamine receptor changes in Sapap3 knockout mice
Authors: Manning Elizabeth E , Wang Abigail Y , Saikali Linda M , Winner Anna S , Ahmari Susanne E 
Published: July 2019

AbstractObsessive compulsive disorder (OCD) is associated with disruption of sensorimotor gating, which may contribute to difficulties inhibiting intrusive thoughts and compulsive rituals. Neural mechanisms underlying these disturbances are unclear; however, striatal dopamine is implicated in regulation of sensorimotor gating and OCD pathophysiology. The goal of this study was to examine the relationships between sensorimotor gating, compulsive behavior, and striatal dopamine receptor levels in Sapap3 knockout mice (KOs), a widely used preclinical model system for OCD research. We found a trend for disruption of sensorimotor gating in Sapap3-KOs using the translational measure prepulse inhibition (PPI); however, there was significant heterogeneity in both PPI and compulsive grooming in KOs. Disruption of PPI was significantly correlated with a more severe compulsive phenotype. In addition, PPI disruption and compulsive grooming severity were associated with reduced dopamine D1 and D2/3 receptor density in the nucleus accumbens core (NAcC). Compulsive grooming progressively worsened in Sapap3-KOs tested longitudinally, but PPI disruption was first detected in high-grooming KOs at 7 months of age. Through detailed characterization of individual differences in OCD-relevant behavioral and neurochemical measures, our findings suggest that NAcC dopamine receptor changes may be involved in disruption of sensorimotor gating and compulsive behavior relevant to OCD.
Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank
Authors: Sun Miao , Folk Ryan A. , Gitzendanner Matthew A. , Smith Stephen A. , Germain-Aubrey Charlotte , Guralnick Robert P. , Soltis Pamela S. , Soltis Douglas E. , Chen Zhiduan 
Published: July 2019

AbstractCurrent advances in sequencing technology have greatly increased the availability of sequence data from public genetic databases. With data from GenBank, we assemble and phylogenetically investigate a 19,740-taxon, five-locus supermatrix (i.e.,atpB, rbcL, matK, matR, and ITS) for rosids, a large clade containing over 90,000 species, or approximately a quarter of all angiosperms (assuming an estimate of 400,000 angiosperm species). The topology and divergence times of the five-locus tree generally agree with previous estimates of rosid phylogeny, and we recover greater resolution and support in several areas along the rosid backbone, but with a few significant differences (e.g., the placement of the COM clade, as well as Myrtales, Vitales, and Zygophyllales). Our five-locus phylogeny is the most comprehensive DNA data set yet compiled for the rosid clade. Yet, even with 19,740 species, current sampling represents only 16-22% of all rosids, and we also find evidence of strong phylogenetic bias in the accumulation of GenBank data, highlighting continued challenges for species coverage. These limitations also exist in other major angiosperm clades (e.g., asterids, monocots) as well as other large, understudied branches of the Tree of Life, highlighting the need for broader molecular sampling. Nevertheless, the phylogeny presented here improves upon sampling by more than two-fold and will be an important resource for macroevolutionary studies of this pivotal clade.
Diversification of Disease Resistance Receptors by Integrated Domain Fusions in Wheat and its Progenitors
Authors: Andersen Ethan J. , Nepal Madhav P. 
Published: July 2019

ABSTRACTPathogenic effectors inhibit plant resistance responses by interfering with intracellular signaling mechanisms. Plant Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) have evolved highly variable effector-recognition sites to detect these effectors. While many NLRs utilize variable Leucine-Rich Repeats (LRRs) to bind to effectors, some have gained Integrated Domains (IDs) necessary for receptor activation or downstream signaling. While a few studies have identified IDs within NLRs, the homology and regulation of these genes have yet to be elucidated. We identified a diverse set of wheat NLR-ID fusion proteins as candidates for NLR functional diversification through ID effector recognition or signal transduction. NLR-ID diversity corresponds directly with the various signaling components essential to defense responses, expanding the potential functions for immune receptors and removing the need for intermediate signaling factors that are often targeted by effectors. ID homologs (>80% similarity) in other grasses indicate that these domains originated as functional, non-NLR-encoding genes and were incorporated into NLR-encoding genes through duplication. Multiple NLR-ID genes encode experimentally verified alternative transcripts that include or exclude IDs. This indicates that plants employ alternative splicing to regulate IDs, possibly using them as baits, decoys, and functional signaling components. Future studies should aim to elucidate differential expression of NLR-ID alternative transcripts.
Active inference, stressors, and psychological trauma: A neuroethological model of (mal)adaptive explore-exploit dynamics in ecological context
Authors: Linson Adam , Parr Thomas , Friston Karl J. 
Published: July 2019

AbstractThis paper offers a formal account of emotional inference and stress-related behaviour, using the notion of active inference. We formulate responses to stressful scenarios in terms of Bayesian belief-updating and subsequent policy selection; namely, planning as (active) inference. Using a minimal model of how creatures or subjects account for their sensations (and subsequent action), we deconstruct the sequences of belief updating and behaviour that underwrite stress-related responses – and simulate the aberrant responses of the sort seen in post-traumatic stress disorder (PTSD). Crucially, the model used for belief-updating generates predictions in multiple (exteroceptive, proprioceptive and interoceptive) modalities, to provide an integrated account of evidence accumulation and multimodal integration that has consequences for both motor and autonomic responses. The ensuing phenomenology speaks to many constructs in the ecological and clinical literature on stress, which we unpack with reference to simulated inference processes and accompanying neuronal responses. A key insight afforded by this formal approach rests on the trade-off between the epistemic affordance of certain cues (that resolve uncertainty about states of affairs in the environment) and the consequences of epistemic foraging (that may be in conflict with the instrumental or pragmatic value of ‘fleeing’ or ‘freezing’). Starting from first principles, we show how this trade-off is nuanced by prior (subpersonal) beliefs about the outcomes of behaviour – beliefs that, when held with unduly high precision, can lead to (Bayes optimal) responses that closely resemble PTSD.
Unlocking the potential of historical abundance datasets to study biomass change in flying insects
Authors: Kinsella Rebecca S. , Thomas Chris D. , Crawford Terry J. , Hill Jane K. , Mayhew Peter J. , Macgregor Callum J. 
Published: July 2019

AbstractTrends in insect abundance are well-established in some datasets, but far less is known about how abundance measures translate into biomass trends. Moths (Lepidoptera) provide particularly good opportunities to study trends and drivers of biomass change at large spatial and temporal scales, given the existence of long-term abundance datasets. However, data on the body masses of moths are required for these analyses, but such data do not currently exist.To address this data gap, we collected empirical data in 2018 on the forewing length and dry mass of field-sampled moths, and used these to train and test a statistical model that predicts the body mass of moth species from their forewing lengths (with refined parameters for Crambidae, Erebidae, Geometridae and Noctuidae).Modelled biomass was positively correlated, with high explanatory power, with measured biomass of moth species (R2 = 0.886 ± 0.0006, across 10,000 bootstrapped replicates) and of mixed-species samples of moths (R2 = 0.873 ± 0.0003), showing that it is possible to predict biomass to an informative level of accuracy, and prediction error was smaller with larger sample sizes.Our model allows biomass to be estimated for historical moth abundance datasets, and so our approach will create opportunities to investigate trends and drivers of insect biomass change over long timescales and broad geographic regions.
Developing single molecule methods for measuring the pathway proteins ERK, AKT, cyclin d and p70s6k in localized colon cancer in relation to mutation status
Authors: Olsen Dorte Aa. , Thomsen Caroline EB. , Andersen Rikke F. , Madsen Jonna S. , Jakobsen Anders , Brandslund Ivan 
Published: July 2019

AbstractBackgroundThe aim of this study was to quantify the intracellular pathway proteins ERK, AKT, cyclin d and p70s6k in localized colon cancer tissue to investigate the possible prognostic values and the ability to be used as screening markers for upstream mutations.MethodsColon cancer tissue and autologous reference tissue were collected from 176 patients who underwent surgery for colon cancer. Assays for quantifying ERK, AKT, cyclin d and p70s6k proteins were developed using single molecule array (Simoa). KRAS/BRAF/PIK3CA mutation status was determined using droplet digital PCR.ResultsPatients with BRAF mutations had decreased concentrations of ERK (p=0.0002), AKT (p=0.00004) and cyclin d (p=0.001) while no significant differences were found between patients with KRAS mutations and Wild type (Wt) patients. None of the investigated protein concentrations were associated with disease free survival or overall survival, if including all patients. However, when stratifying according to mutation status, significant correlations to overall survival were seen for patients with BRAF mutations and AKT (p=0.003) or ERK (p=0.046) and for patients with KRAS mutations and p70s6k (p=0.04). Furthermore, the combination of genetic mutations, stage 2 disease, and all of the investigated pathway proteins showed significant correlations to overall survival.ConclusionsThere is a strong correlation between pathway protein concentrations and mutational BRAF status. Overall survival in colon cancer patients depend both on gene mutation status and pathway protein concentrations. As significant correlations were found between BRAF mutations and ERK, AKT and cyclin d, concentration measurements of these pathway proteins might be useful as screening for upstream mutations.
In-vitro synergistic antibacterial effect of atorvastatin and ampicillin against resistant Staphylococcus spp and E.coli isolated from bovine mastitis
Authors: Sankar Sriraam , Thangamalai Ramasamy , Padmanaban Sriram , Kannan Porteen , Srinivasan M R , Arunaman C S 
Published: July 2019

AbstractThe colossal rise in antimicrobial resistance has led to treatment failures and so mastitis has become cumbersome to treat. The objective of this study was to evaluate the antibacterial effect of non-antibiotic drug, atorvastatin in combination with antimicrobial, ampicillin against two commonly isolated bacterial species Staphylococcus spp and E. coli from bovine mastitis. Milk samples were collected from mastitis cows, visiting Veterinary Clinical Complex. Bacterial isolation was performed using Eosin Methylene Blue (EMB) agar and Mannitol Salt Agar (MSA), followed by characterization and identification by biochemical tests and gram staining. Genotypic confirmation was done by Polymerase Chain Reaction (PCR) with subsequent screening for resistant genes-mec A, blaTEM. Antibiotic Sensitivity Test (ABST) of the isolates against 12 different antimicrobials, atorvastatin only, and combination of atorvastatin with ampicillin were performed using Kirby-Bauer disc diffusion method. Minimum Inhibitory Concentration (MIC) of ampicillin alone and ampicillin in combination with atorvastatin were determined by modified microdilution method. Staphylococcus spp (77.5%) and E.coli (35%) were the two major pathogens isolated in the current study and multi-drug resistance was observed. Among the antimicrobials, the ampicillin showed 100% resistance against Staphylococcus spp and 85.71% resistance against E. coli. Atorvastatin did not display antibacterial effect as a sole agent but displayed synergistic antibacterial activity with ampicillin. There was an average increase in Minimum Inhibitory Concentration of ampicillin for E.coli and Staphylococcus spp isolates and atorvastatin decreased the Minimum Inhibitory Concentration of ampicillin in combination. The ampicillin shows more resistance against both Staphylococcus spp and E.coli, while atorvastatin improves the effect of ampicillin in-vitro. So, atorvastatin may be combined with ampicillin for the treatment of Gram-positive and Gram-negative infections. However, further studies are required to ascertain the exact mechanism of action of atorvastatin with respect to their antibacterial effect for them to be redeployed as an antimicrobial drug in the future.