bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of selective treatment onHaematobia irritansinfestation of untreated cattle
Authors: Miraballes Cecilia , Stryhn Henrik , Barros Antonio Thadeu M. , Lucas Martin , Domingues Luísa Nogueira , Ribeiro Rodrigo , Monge Macarena , Fraga Alvaro , Riet-Correa Franklin 
Published: October 2019

AbstractTo reduce the use of insecticide treatments againstHaematobia irritanswe evaluated the impact of treating 15% of the bovines, with the greatest number of flies including bulls, with 40% diazinon ear tags, on the infestation of untreated cows. Horn fly susceptibility to diazinon was measured before and after treatment, and peaks of infestation were recorded. Three groups of Bradford bovines were evaluated: Group 1 (control untreated), Group 2 (15% treated) and Group 3 (control 100% treated). Weekly counts of horn flies were performed on the same animals for 78 days. Two peaks of infestation were recorded, and a higher number of horn flies occurred in the untreated control group than in the untreated cows of the selectively treated group throughout the entire period of the study, except for a single week. The horn fly field population was significantly more susceptible to diazinon than the reference susceptible strain both before and after insecticide treatment. In conclusion, treatment of 15% of the most infested animals from a herd, with 40% diazinon ear tags, quickly reduced horn fly infestations of the entire herd and may be a practical approach for horn fly control, reducing costs and chemical use.
rsCaMPARI: an erasable marker of neuronal activity
Authors: Sha Fern , Abdelfattah Ahmed S. , Patel Ronak , Schreiter Eric R. 
Published: October 2019

AbstractIdentifying and comparing active neuron ensembles underlying complex behaviors is a key challenge in neuroscience. Recent tools such as CaMPARI have enabled the optical marking and selection of active neuron populations. However, CaMPARI photoconversion is permanent and irreversible, limiting its utility when multiple activity snapshots must be compared within the same sample. We sought to overcome these limitations by developing an erasable neuronal activity marker based on a reversibly switchable fluorescent protein. Here we introduce rsCaMPARI, a reversibly switchable calcium marker that enables spatiotemporally precise marking, erasing, and remarking of active neuron populations under brief, user-defined time windows of light exposure. rsCaMPARI photoswitching kinetics are modulated by calcium concentration when illuminating with blue light, and the fluorescence can be reset with violet light. We demonstrate the utility of rsCaMPARI for marking and remarking active neuron populations in freely-swimming zebrafish.
Multivoxel Pattern of Blood Oxygen Level Dependent Activity can be sensitive to stimulus specific fine scale responses
Authors: Vizioli Luca , De Martino Federico , Petro Lucy S , Kersten Daniel , Ugurbil Kamil , Yacoub Essa , Muckli Lars 
Published: October 2019

1.AbstractAt ultra-high field, fMRI voxels can span the sub-millimeter range, allowing the recording of blood oxygenation level dependent (BOLD) responses at the level of fundamental units of neural computation, such as cortical columns and layers. This sub-millimeter resolution, however, is only nominal in nature as a number of factors limit the spatial acuity of functional voxels. Multivoxel Pattern Analysis (MVPA) may provide a means to detect information at finer spatial scales that may otherwise not be visible at the single voxel level due to limitations in sensitivity and specificity. Here, we evaluate the spatial scale of stimuli specific BOLD responses in multivoxel patterns exploited by linear Support Vector Machine, Linear Discriminant Analysis and Naïve Bayesian classifiers across cortical depths in V1. To this end, we artificially misaligned the testing relative to the training portion of the data in increasing spatial steps, then investigated the breakdown of the classifiers’ performances. A one voxel shift led to a significant decrease in decoding accuracy (p<.05) across all cortical depths, indicating that stimulus specific responses in a multivoxel pattern of BOLD activity exploited by multivariate decoders can be as precise as the nominal resolution of single voxels (here .8 mm isotropic). Our results further indicate that large draining vessels, prominently residing in proximity of the pial surface, do not, in this case, hinder the ability of MVPA to exploit fine scale patterns of BOLD signals. We argue that tailored analytical approaches can help overcoming limitations in high-resolution fMRI and permit studying the mesoscale organization of the human brain with higher sensitivities.
Multimodal Study of the Effects of Varying Task Load Utilizing EEG, GSR and Eye-Tracking
Authors: Born Jannis , Ramachandran Babu Ram Naidu , Romero Pinto Sandra Alejandra , Winkler Stefan , Ratnam Rama 
Published: October 2019

AbstractObjectiveThe effect of task load on performance is investigated by simultaneously collecting multi-modal physiological data and participant response data. Periodic response to a questionnaire is also obtained. The goal is to determine combinations of modalities that best serve as predictors of task performance.ApproachA group of participants performed a computer-based visual search task mimicking postal code sorting. A five-digit number had to be assigned to one of six different non-overlapping numeric ranges. Trials were presented in blocks of progressively increasing task difficulty. The participants’ responses were collected simultaneously with 32 channels of electroencephalography (EEG) data, eye-tracking data, and Galvanic Skin Response (GSR) data. The NASA Task-Load-Index self-reporting instrument was administered at discrete time points in the experiment.Main resultsLow beta frequency EEG waves (12.5-18 Hz) were more prominent as cognitive task load increased, with most activity in frontal and parietal regions. These were accompanied by more frequent eye blinks and increased pupillary dilation. Blink duration correlated strongly with task performance. Phasic components of the GSR signal were related to cognitive workload, whereas tonic components indicated a more general state of arousal. Subjective data (NASA TLX) as reported by the participants showed an increase in frustration and mental workload. Based on one-way ANOVA, EEG and GSR provided the most reliable correlation to perceived workload level and were the most informative measures (taken together) for performance prediction.SignificanceNumerous modalities come into play during task-related activity. Many of these modalities can provide information on task performance when appropriately grouped. This study suggests that while EEG is a good predictor of task performance, additional modalities such as GSR increase the likelihood of more accurate predictions. Further, in controlled laboratory conditions, the most informative or minimum number of modalities can be isolated for monitoring in real work environments.
Chromosome-level genome assembly of the greenfin horse-faced filefish (Thamnaconus septentrionalis) using Oxford Nanopore PromethION sequencing and Hi-C technology
Authors: Bian Li , Li Fenghui , Ge Jianlong , Wang Pengfei , Chang Qing , Zhang Shengnong , Li Jie , Liu Changlin , Liu Kun , Liu Xintian , Li Xuming , Chen Hongju , Chen Siqing , Shao Changwei , Lin Zhishu 
Published: October 2019

AbstractThe greenfin horse-faced filefish, Thamnaconus septentrionalis, is a valuable commercial fish species that is widely distributed in the Indo-West Pacific Ocean. It has characteristic blue-green fins, rough skin and spine-like first dorsal fin. T. septentrionalis is of a conservation concern as a result of sharply population decline, and it is an important marine aquaculture fish species in China. The genomic resources of this filefish are lacking and no reference genome has been released. In this study, the first chromosome-level genome of T. septentrionalis was constructed using Nanopore sequencing and Hi-C technology. A total of 50.95 Gb polished Nanopore sequence were generated and were assembled to 474.31 Mb genome, accounting for 96.45% of the estimated genome size of this filefish. The assembled genome contained only 242 contigs, and the achieved contig N50 was 22.46 Mb, reaching a surprising high level among all the sequenced fish species. Hi-C scaffolding of the genome resulted in 20 pseudo-chromosomes containing 99.44% of the total assembled sequences. The genome contained 67.35 Mb repeat sequences, accounting for 14.2% of the assembly. A total of 22,067 protein-coding genes were predicted, of which 94.82% were successfully annotated with putative functions. Furthermore, a phylogenetic tree was constructed using 1,872 single-copy gene families and 67 unique gene families were identified in the filefish genome. This high quality assembled genome will be a valuable genomic resource for understanding the biological characteristics and for facilitating breeding of T. septentrionalis.
Rest-task Modulation of fMRI-derived Global Signal Topography is Mediated by Transient Co-activation Patterns
Authors: Zhang Jianfeng , Huang Zirui , Tumati Shankar , Northoff Georg 
Published: October 2019

AbstractRecent resting-state fMRI studies have revealed that the global signal (GS) exhibits a non-uniform spatial distribution across the gray matter. Whether this topography is informative remains largely unknown. We therefore tested rest-task modulation of global signal topography by analyzing static global signal correlation and dynamic co-activation patterns in a large sample of fMRI dataset (n=837) from the Human Connectome Project. The GS topography in the resting-state and in seven different tasks was first measured by correlating the global signal with the local timeseries (GSCORR). In the resting state, high GSCORR was observed mainly in the primary sensory and motor regions, while low GSCORR was seen in the association brain areas. This pattern changed during the seven tasks, with mainly decreased GSCORR in sensorimotor cortex. Importantly, this rest-task modulation of GSCORR could be traced to transient co-activation patterns at the peak period of global signal (GS-peak). By comparing the topography of GSCORR and respiration effects, we observed that the topography of respiration mimicked the topography of global signal in the resting-state whereas both differed during the task states; due to such partial dissociation, we assume that GSCORR could not be equated with a respiration effect. Finally, rest-task modulation of GS topography could not be exclusively explained by other sources of physiological noise. Together, we here demonstrate the informative nature of global signal topography by showing its rest-task modulation, the underlying dynamic co-activation patterns, and its partial dissociation from respiration effects during task states.
Persistent transmission of shigellosis in England is associated with a recently emerged multi-drug resistant strain ofShigella sonnei
Authors: Bardsley Megan , Jenkins Claire , Mitchell Holly D , Mikhail Amy FW , Baker Kate S , Foster Kirsty , Hughes Gwenda , Dallman Timothy J 
Published: October 2019

AbstractBackgroundWhole genome sequencing has enhanced surveillance and facilitated detailed monitoring of transmission ofShigellaspecies in England.MethodsWe undertook an epidemiological and phylogenetic analysis of isolates from all cases of shigellosis referred to Public Health England between 2015 to 2018 to explore recent strain characteristics and transmission dynamics ofShigellaspecies.ResultsOf the 4950 confirmed cases of shigellosis identified during this period, the highest proportion of isolates wereS. sonnei(54.4%), followed byS. flexneri(39.2%),S. boydii(4.1%) andS. dysenteriae(2.2%). Most cases were adults (82.9%) and male (59.5%), and 34.9% cases reported recent travel outside the UK. Throughout the study period diagnoses ofS. flexneriandS. sonneiwere most common in men with no history of recent travel abroad. Species prevalence was not static with cases ofS. flexneriin men decreasing from 2015-2016, and the number of cases ofS. sonneiincreasing from 2017. Phylogenetic analysis showed this recent increase inS. sonneiwas attributed to a novel clade exhibiting resistance to ciprofloxacin and azithromycin, which had emerged from a Central Asia sub-lineage.ConclusionsDespite changes in species prevalence,Shigelladiagnoses in England are persistently the most common in adult males without reported travel history, consistent with sexual transmission amongst men who have sex with men. The trend in increasing ciprofloxacin resistance, in addition to plasmid-mediated azithromycin resistance, inS. sonneiis of significant public health concern with respect to transmission of multi-drug resistant gastrointestinal pathogens and the risk of treatment failures.SummaryShigelladiagnoses in England are most prevalent amongst men who have sex with men.S. sonneiexhibiting resistance to both azithromycin and ciprofloxacin has replaced azithromycin-resistantS. flexnerias the most commonly isolated species in this setting.
Area-specific synapse structure in branched axons reveals a subcellular level of complexity in thalamocortical networks
Authors: Rodriguez-Moreno Javier , Porrero Cesar , Rollenhagen Astrid , Rubio-Teves Mario , Casas-Torremocha Diana , Alonso-Nanclares Lidia , Yakoubi Rachida , Santuy Andrea , Merchan-Pérez Angel , DeFelipe Javier , Lübke Joachim HR , Clasca Francisco 
Published: October 2019

AbstractThalamocortical Posterior nucleus (Po) axons innervating the somatosensory (S1) and motor (MC) vibrissal cortices are key links in the brain neuronal network that allows rodents to explore the environment whisking with their motile vibrissae. Here, using high-end 3D electron microscopy, we demonstrate massive differences between MC vs. S1 Po synapses in a) bouton and active zone size; b) neurotransmitter vesicle pool size; c) mitochondria distribution near synapses; and d) proportion of non-spinous dendrite contacts. These differences are as large, or bigger, than those between Po and ventroposterior thalamic nucleus synapses in S1. Moreover, using single-axon transfection labeling, we show that the structure of boutons in the MC vs. S1 branches of individual Po axons is different. These structural differences parallel striking, recently-discovered divergences in functional efficacy and plasticity between S1 and MC Po synapses, and overall reveal a new, subcellular level of thalamocortical circuit complexity, unaccounted for in current models.
MARSHAL, a novel tool for virtual phenotyping of maize root system hydraulic architectures
Authors: Meunier Félicien , Heymans Adrien , Draye Xavier , Couvreur Valentin , Javaux Mathieu , Lobet Guillaume 
Published: October 2019

AbstractFunctional-structural root system models combine functional and structural root traits to represent the growth and development of root systems. In general, they are characterized by a large number of growth, architectural and functional root parameters, generating contrasted root systems evolving in a highly nonlinear environment (soil, atmosphere), which makes unclear what impact of each single root system on root system functioning actually is. On the other end of the root system modelling continuum, macroscopic root system models associate to each root system instance a set of plant-scale, easily interpretable parameters. However, as of today, it is unclear how these macroscopic parameters relate to root-scale traits and whether the upscaling of local root traits are compatible with macroscopic parameter measurements. The aim of this study was to bridge the gap between these two modelling approaches by providing a fast and reliable tool, which eventually can help performing plant virtual breeding.We describe here the MAize Root System Hydraulic Architecture soLver (MARSHAL), a new efficient and user-friendly computational tool that couples a root architecture model (CRootBox) with fast and accurate algorithms of water flow through hydraulic architectures and plant-scale parameter calculations, and a review of architectural and hydraulic parameters of maize.To illustrate the tool’s potential, we generated contrasted maize hydraulic architectures that we compared with architectural (root length density) and hydraulic (root system conductance) observations. Observed variability of these traits was well captured by model ensemble runs We also analyzed the multivariate sensitivity of mature root system conductance, mean depth of uptake, root system volume and convex hull to the input parameters to highlight the key parameters to vary for efficient virtual root system breeding. MARSHAL enables inverse optimisations, sensitivity analyses and virtual breeding of maize hydraulic root architecture. It is available as an R package, an RMarkdown pipeline, and a web application.One-sentence summaryWe developed a dynamic hydraulic-architectural model of the root system, parameterized for maize, to generate contrasted hydraulic architectures, compatible with field and lab observations and that can be further analyzed in soil-root system models for virtual breeding.Authors contributionsF.M., X.D., M.J. and G.L. designed the study and defined its scope; F.M. and G.L. developed the model while associated tools were created by A.H. and G.L.; F.M. ran the model simulations and analyzed the results together with M.J and G.L.; F.M. and M.J. wrote the first version of this manuscript; all co-authors critically revised it.
New Targeted Approaches for Epigenetic Age Predictions
Authors: Han Yang , Franzen Julia , Stiehl Thomas , Gobs Michael , Kuo Chao-Chung , Nikolić Miloš , Hapala Jan , Koop Barbara Elisabeth , Strathmann Klaus , Ritz‐Timme Stefanie , Wagner Wolfgang 
Published: October 2019

AbstractAging causes epigenetic modifications, which are utilized as a biomarker for the aging process. While genome-wide DNA methylation profiles enable robust age-predictors by integration of many age-associated CG dinucleotides (CpGs), there are various alternative approaches for targeted measurements at specific CpGs that better support standardized and cost-effective high-throughput analysis. In this study, we utilized 4,650 Illumina BeadChip datasets of blood to select the best suited CpG sites for targeted analysis. DNA methylation analysis at these sites with either pyrosequencing or droplet digital PCR (ddPCR) revealed a high correlation with chronological age. In comparison, bisulfite barcoded amplicon sequencing (BBA-seq) gave slightly lower precision at individual CpGs. However, BBA-seq data revealed that the correlation of methylation levels with age at neighboring CpG sites follows a bell-shaped curve, often accompanied by a CTCF binding site at the peak. We demonstrate that within individual BBA-seq reads the DNA methylation at neighboring CpGs is not coherently modified but reveals a stochastic pattern. Based on this, we have developed an alternative model for epigenetic age predictions based on the binary sequel of methylated and non-methylated sites in individual reads, which reflects heterogeneity in epigenetic aging within a sample. Thus, the stochastic evolution of age-associated DNA methylation patterns, which seems to resemble epigenetic drift, enables epigenetic clocks for individual DNA strands.
Efficient sampling and noisy decisions
Authors: Heng Joseph , Woodford Michael , Polania Rafael 
Published: October 2019

AbstractThe precision of human decisions is limited by both processing noise and basing decisions on finite information. But what determines the degree of such imprecision? Here we develop an efficient coding framework for higher-level cognitive processes, in which information is represented by a finite number of discrete samples. We characterize the sampling process that maximizes perceptual accuracy or fitness under the often-adopted assumption that full adaptation to an environmental distribution is possible, and show how the optimal process differs when detailed information about the current contextual distribution is costly. We tested this theory on a numerosity discrimination task, and found that humans efficiently adapt to contextual distributions, but in the way predicted by the model in which people must economize on environmental information. Thus, understanding decision behavior requires that we account for biological restrictions on information coding, challenging the often-adopted assumption of precise prior knowledge in higher-level decision systems.
Sub-optimality of the early visual system explained through biologically plausible plasticity
Authors: Chauhan Tushar , Masquelier Timothée , Cottereau Benoit R. 
Published: October 2019

AbstractThe early visual cortex is the site of crucial pre-processing for more complex, biologically relevant computations that drive perception and, ultimately, behaviour. This pre-processing is often viewed as an optimisation which enables the most efficient representation of visual input. However, measurements in monkey and cat suggest that receptive fields in the primary visual cortex are often noisy, blobby, and symmetrical, making them sub-optimal for operations such as edge-detection. We propose that this suboptimality occurs because the receptive fields do not emerge through a global minimisation of the generative error, but through locally operating biological mechanisms such as spike-timing dependent plasticity. Using an orientation discrimination paradigm, we show that while sub-optimal, such models offer a much better description of biology at multiple levels: single-cell, population coding, and perception. Taken together, our results underline the need to carefully consider the distinction between information-theoretic and biological notions of optimality in early sensorial populations.
Native and invasive populations of the ectomycorrhizal death capAmanita phalloidesare highly sexual but dispersal limited
Authors: Golan Jacob , Adams Catherine A. , Cross Hugh , Elmore Holly , Gardes Monique , Glassman Sydney I. , Gonçalves Susana C. , Hess Jaqueline , Richard Franck , Wang Yen-Wen , Wolfe Benjamin , Pringle Anne 
Published: October 2019

AbstractThe authors have withdrawn this manuscript and do not wish it to be cited. As we have moved more deeply into population genomics, we have discovered the analyses we initially used do not answer our questions well. We are recalibrating and intend to submit a new manuscript in the future. If you have any questions, please contact the corresponding author.
Electrochemical and biological response of titanium (cp-Ti) after silicon ion implantation
Authors: Deen K.M. , Farooq A. , Rizwan M. , Ahmad A. , Haider W. 
Published: October 2019

PurposeThis study/paper aims to the authors applied low “Si” ions dose over cp-Ti-2, and the potent dose level was optimized for adequate corrosion resistance and effective proliferation of stem cells.Design/methodology/approachThe cp-Ti surface was modified by silicon (Si) ions beam at 0.5 MeV in a Pelletron accelerator. Three different ion doses were applied to the polished samples, and the surface was characterized by XRD and AFM analysis.FindingsAt moderate “Si” ion dose (6.54 × 1012ions-cm−2), the potential shifted to a noble value. The small “icorr” (1.22 µA.cm−2) and relatively large charge transfer resistance (43.548 kΩ-cm2) in the ringer‘s lactate solution was confirmed through Potentiodynamic polarization and impedance spectroscopy analysis. Compared to cp-Ti and other doses, this dose level also provided the effective proliferation of mesenchymal stem cells.Originality/valueThe dosage levels used were different to previous work and provided the effective proliferation of mesenchymal stem cells.