bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemoreception of Meloidogyne incognita and Caenorhabditis elegans on botanical nematicidals
Authors: Sobkowiak Robert , Bojarska Natalia , Krzyżaniak Emilia , Wągiel Karolina , Ntalli Nikoletta 
Published: March 2018

AbstractPlant–parasitic nematodes cause serious damage to various agricultural crops worldwide, and their control necessitates environmentally safe measures. Plant secondary metabolites of botanical origin are tested here–in to study their effect in Meloidogyne incognita locomotion, being this an important factor affecting host inoculation inside the soil. We compare the effect to the respective behavioral responses of the model organism Caenorhabditis elegans. The tested botanical nematicidals, all reported of activity against Meloidogyne sp. in our previous works, belong to different chemical groups of small molecular weight molecules encompassing acids, alcohols, aldehydes and ketones. Specifically we report on the attractant or repellent properties of trans–anethole, (E,E)–2,4–decadienal, (E)–2–decenal, fostiazate, and 2–undecanone. The treatments for both nematode species were made at sublethal concentration levels, namely 1mM (<EC50), and the chemical control used for the experiment was the commercial nematicide fosthiazate and oxamyl. According to our results, trans–anethole, decenal, and oxamyl act as C. elegans attractants. 2–undecanone strongly attracts M. incognita. These findings can be of use in the development of nematicidal formulates, contributing to the disruption of nematode chemotaxis to root systems.
Interindividual variability in HRV reactivity: autonomic flexibility or regression to the mean?
Authors: Dimitriev Dimitriy A. , Saperova Elena V. , Indeykina Olga S. , Dimitriev Aleksey D. 
Published: March 2018

AbstractObjectiveThere is now a substantial body of evidence linking the baseline level of heart rate variability (HRV) with the magnitude of stress-induced reduction in respiratory sinus arrhythmia. However, it remains to be proved to what extent these interindividual differences in stress responses may be attributed to the statistical phenomenon of regression to the mean (RTM). We sought to test the hypothesis that the statistical artifact RTM explains part of the baseline effect.ApproachHeart rate recording was carried out in 1,156 volunteers. To obtain an estimate of the stress response, 148 persons were randomly selected. Participants were monitored on a rest day and just before an academic examination for state anxiety and HRV. Participants were divided into quartiles according to baseline HRV levels and were compared for response to academic stress.Main resultsWe observed a significant reduction in HRV in subjects with a high baseline HRV (> 75th percentile), while a significant increase was found in the group with low baseline HRV. Regression analysis demonstrated that the value of baseline HRV correlated with the magnitude of stress reaction consistent with the RTM model. Baseline-adjusted ANCOVA does not reveal significant intergroup differences in the changes in heart rate (HR) and HRV from rest to exam. RTM-adjusted estimates confirmed an exam effect for HR and HRV.SignificanceThe results of our study strongly support RTM as the source of variability of stress-related changes in HRV.
Dopamine is a double-edged sword: Enhancing memory retrieval performance at the expense of metacognition
Authors: Clos Mareike , Bunzeck Nico , Sommer Tobias 
Published: March 2018

AbstractWhile memory encoding and consolidation processes have been linked with dopaminergic signaling for a long time, the role of dopamine in episodic memory retrieval remained mostly unexplored. Based on previous observations of striatal activity during memory retrieval, we used pharmacological fMRI to investigate the effects of dopamine on retrieval performance and metacognitive memory confidence in healthy humans. Dopaminergic modulation by the D2 antagonist haloperidol administered acutely during the retrieval phase improved recognition accuracy of previously learned pictures significantly and was associated with increased activity in the SN/VTA, locus coeruleus, hippocampus and amygdala during retrieval. In contrast, confidence for new-decisions was impaired by unsystematically increased activity of the striatum across confidence levels and restricted range of responsiveness in frontostriatal networks under haloperidol. These findings offer new insights into the mechanisms underlying memory retrieval and metacognition and provide a broader perspective on the presence of memory problems in dopamine-related diseases and the treatment of memory disorders.
Can we use routinely collected hospital and GP data for epidemiological study of common hand conditions? A UK Biobank based validation project
Authors: Lane Jennifer C.E. , Schnier Christian , Green Jane , Lam Wee L. , Furniss Dominic , Sudlow Cathie L.M. 
Published: March 2018

AbstractObjectiveRoutine health records can be of great value in epidemiological and genetic studies if they are able to reliably identify true disease cases, especially when linked to large cohort studies. Little research has been undertaken into whether coding within UK electronic health records (EHR) is able to accurately identify clinical disease cases of common hand conditions. There is therefore a relative paucity of hand surgical research using EHRs due to concerns that cases cannot be accurately identified.The aim of this study was to investigate the accuracy of hospital and primary care coding of routine EHRs for carpal tunnel syndrome (CTS) and base of thumb osteoarthritis (BTOA). Self-reported disease state as recorded in UK Biobank, a large prospective cohort study was also investigated.MethodsCode lists for each condition were generated by a team of clinicians, clinical coders and epidemiologists. All patients recruited to UK Biobank in one geographical region (Lothian, Scotland) where linked primary and secondary care coded datasets available were included. A decision- making algorithm was designed to define an administratively-confirmed or a clinically confirmed disease case. Patient electronic medical records (EMRs) were independently interrogated by two clinicians and inter-observer reliability calculated.ResultsOf the 17,201 Biobank participants in NHS Lothian, 268 had at least one code for CTS and 82 for BTOA. For CTS, 159 cases were confirmed, 100 cases had insufficient information and 9 cases were refuted. Excluding missing data, the positive predictive value (PPV) for true clinical disease cases was 96% for incident disease (90% for prevalent disease; overall 94%).For BTOA, 27 cases were confirmed, 46 cases had insufficient information, and 9 cases were refuted. Excluding missing data, PPV for incident disease was 81% (prevalent disease 56%, overall PPV 75%). Interrogation of the disease cases with insufficient information noted a large proportion arising from primary care and self-report coding systems.Analyzing code combinations revealed that secondary care codes had the highest PPV for CTS and BTOA, emphasizing a more robust evaluation of PPV for patients requiring hospital based care. Overall, inter-observer reliability was good, with agreement in 90% of cases (Cohen’s kappa of 0.79) for clinical disease cases in CTS and agreement of 98%, (kappa 0.96) for BTOA.ConclusionsWe have demonstrated that coding within UK Biobank is of sufficient quality to enable use of the resource for epidemiological and genetic research into common hand conditions, and that EMRs can be used for manual validation of UK health coding systems. Further work is needed to consider potential regional and interdisciplinary differences in coding practice, in strategies for dealing with missing data in EHRs, and to validate coding of common hand conditions in primary care.
Cryo-EM visualization of an active high open probability CFTR ion channel
Authors: Fay Jonathan F. , Aleksandrov Luba A. , Jensen Timothy J. , Cui Liying L. , Kousouros Joseph N. , He Lihua , Aleksandrov Andrei A. , Gingerich Drew S. , Riordan John R. , Chen James Z. 
Published: March 2018

AbstractThe Cystic fibrosis transmembrane conductance regulator (CFTR) anion channel, crucial to epithelial salt and water homeostasis, and defective due to mutations in its gene in patients with cystic fibrosis is a unique member of the large family of ATP-binding cassette transport proteins. Regulation of CFTR channel activity is stringently controlled by phosphorylation and nucleotide binding. Structural changes that underlie transitions between active and inactive functional states are not yet fully understood. Indeed the first 3D structures of dephosphorylated, ATP-free and phosphorylated ATP-bound states were only recently reported. Here we have determined the structure of inactive and active states of a thermally stabilized CFTR with very high channel open probability, confirmed after reconstitution into proteoliposomes. The unique repositioning of the TMHs and R domain density that we observe provide insights into the structural transition between active and inactive functional states of CFTR.HighlightsStructures of thermostabilized avian CFTR in dephosphorylated or phosphorylated forms at 4.3 Å and 6.6 Å resolution, respectively.Conformational differences of transmembrane helices 7 & 8 compared to zebra fish and human CFTR structures reveal an extracellular vestibule that may provide anion access to the pore.R-domain density appears to “plug” the intercellular vestibule in the dephosphorylated avian CFTR cryo-EM map.
Comprehensive analysis of lung cancer pathology images to discover tumor shape features that predict survival outcome
Authors: Wang Shidan , Chen Alyssa , Yang Lin , Cai Ling , Xie Yang , Fujimoto Junya , Gazdar Adi , Xiao Guanghua 
Published: March 2018

ABSTRACTPathology slide images capture tumor histomorphological details in high resolution. However, manual detection and characterization of tumor regions in pathology slides is labor intensive and subjective. Using a deep convolutional neural network (CNN), we developed an automated tumor region recognition system for lung cancer pathology slides. From the identified regions, we extracted 22 well-defined tumor shape features and found that 15 of them were significantly associated with patient survival outcome in lung adenocarcinoma patients from the National Lung Screening Trial. A tumor shape-based prognostic model was developed and validated in an independent patient cohort (n=389). The predicted high-risk group had significantly worse survival than the low-risk group (p value = 0.0029). Predicted risk group serves as an independent prognostic factor (high-risk vs. low-risk, hazard ratio = 2.25, 95% CI 1.34-3.77, p value = 0.0022) after adjusting for age, gender, smoking status, and stage. This study provides new insights into the relationship between tumor shape and patient prognosis.
Thermoneutrality induces skeletal muscle myopathy via brown adipose tissue in an IRF4- and myostatin-dependent manner
Authors: Kong Xingxing , Zhou Peng , Yao Ting , Kazak Lawrence , Tenen Danielle , Lyubetskaya Anna , Dawes Brian A. , Tsai Linus , Kahn Barbara B. , Spiegelman Bruce M. , Liu Tiemin , Rosen Evan D. 
Published: March 2018

SummarySkeletal muscle and brown adipose tissue (BAT) share a common lineage and have been functionally linked, as exercise increases browning through the actions of various myokines. It is unknown, however, whether BAT can affect skeletal muscle function. Our prior work has shown that loss of the transcription factor IRF4 in BAT (BATI4KO) reduces adaptive thermogenesis. Here, we note that these mice also have reduced exercise capacity relative to wild-type littermates, associated with diminished mitochondrial function, ribosomal protein synthesis, and mTOR signaling in muscle, in addition to the signature ultrastructural abnormalities of tubular aggregate myopathy. Within brown adipose tissue, loss of IRF4 caused the induction of a myogenic gene expression signature, which includes an increase in the secreted factor myostatin, a known inhibitor of muscle function. Reduction of myostatin activity by the injection of neutralizing antibodies or soluble ActRIIB receptor rescued the exercise capacity of BATI4KO mice. Additionally, overexpression of IRF4 in brown adipocytes reduced serum myostatin and increased mitochondrial function and exercise capacity in muscle. A physiological role for this system is suggested by the observation that mice housed at thermoneutrality show lower exercise capacity with increased serum myostatin; both of these abnormalities are corrected by surgical removal of BAT. Collectively, our data point to an unsuspected level of BAT-muscle cross-talk driven by IRF4 and myostatin.HighlightsMice lacking IRF4 in BAT have a decrease in exercise capacity, accompanied by histological, ultrastructural, signaling, gene expression, and bioenergetic evidence of myopathy in white vastus.Loss of IRF4 promotes the expression of a myogenic signature in BAT, including the myokine myostatin.Neutralization of serum myostatin rescues the ability of BATI4KO mice to exercise normally, while overexpression of IRF4 in BAT allows mice to run better than wild-type counterparts.Thermoneutrality reduces the level of IRF4 in BAT of WT mice, resulting in a myopathic phenotype that can be reversed by surgical excision of BAT.
Both functional trait divergence and trait plasticity confer polyploid advantage in changing environments
Authors: Wei Na , Cronn Richard , Liston Aaron , Ashman Tia-Lynn 
Published: March 2018

ABSTRACTPolyploidy, or whole genome duplication, exists in all eukaryotes and is thought to drive ecological and evolutionary success especially in plants. The mechanisms of polyploid success in ecologically relevant contexts, however, remain largely unknown. Here we conducted an extensive test of functional trait divergence and trait plasticity in conferring polyploid fitness advantage in changing environments by growing clonal replicates of a worldwide genotype collection of six polyploid and five diploid wild strawberry (Fragaria) species in three climatically different common gardens. Among leaf functional traits, we detected divergence in means but not plasticities between polyploids and diploids, suggesting that increased genomic redundancy does not necessarily translate into broader phenotypic amplitude in polyploids. Across the heterogeneous garden environments, however, polyploids exhibited fitness advantage, which was conferred by both trait means and adaptive trait plasticities, supporting a ‘jack-and-master’ hypothesis for polyploids. Our findings provide unparalleled insight into the prevalence and persistence of polyploidization.
Machine learning as an effective method for identifying true SNPs in polyploid plants
Authors: Korani Walid , Clevenger Josh P. , Chu Ye , Ozias-Akins Peggy 
Published: March 2018

AbstractSingle Nucleotide Polymorphisms (SNPs) have many advantages as molecular markers since they are ubiquitous and co-dominant. However, the discovery of true SNPs especially in polyploid species is difficult. Peanut is an allopolyploid, which has a very low rate of true SNP calling. A large set of true and false SNPs identified from the Arachis 58k Affymetrix array was leveraged to train machine learning models to select true SNPs straight from sequence data. These models achieved accuracy rates of above 80% using real peanut RNA-seq and whole genome shotgun (WGS) re-sequencing data, which is higher than previously reported for polyploids. A 48K SNP array, Axiom Arachis2, was designed using the approach which revealed 75% accuracy of calling SNPs from different tetraploid peanut genotypes. Using the method to simulate SNP variation in peanut, cotton, wheat, and strawberry, we show that models built with our parameter sets achieve above 98% accuracy in selecting true SNPs. Additionally, models built with simulated genotypes were able to select true SNPs at above 80% accuracy using real peanut data, demonstrating that our model can be used even if real data are not available to train the models. This work demonstrates an effective approach for calling highly reliable SNPs from polyploids using machine learning. A novel tool was developed for predicting true SNPs from sequence data, designated as SNP-ML (SNP-Machine Learning, pronounced “snip mill”), using the described models. SNP-ML additionally provides functionality to train new models not included in this study for customized use, designated SNP-MLer (SNP-Machine Learner, pronounced “snip miller”). SNP-ML is freely available for public use.
Architecture of Marine Food Webs: to be or not be a ‘small-world’
Authors: Marina Tomás Ignacio , Saravia Leonardo A. , Cordone Georgina , Salinas Vanesa , Doyle Santiago R. , Momo Fernando R. 
Published: March 2018

AbstractThe search for general properties in network structure has been a central issue for food web studies in recent years. One such property is the small-world topology that combines a high clustering and a small distance between nodes of the network. This property may increase food web resilience but make them more sensitive to the extinction of connected species. Food web theory has been developed principally from freshwater and terrestrial ecosystems, largely omitting marine habitats. If theory needs to be modified to accommodate observations from marine ecosystems, based on major differences in several topological characteristics is still on debate. Here we investigated if the small-world topology is a common structural pattern in marine food webs. We developed a novel, simple and statistically rigorous method to examine the largest set of complex marine food webs to date. More than half of the analyzed marine networks exhibited a similar or lower characteristic path length than the random expectation, whereas 39% of the webs presented a significantly higher clustering than its random counterpart. Our method proved that 5 out of 28 networks fulfilled both features of the small-world topology: short path length and high clustering. This work represents the first rigorous analysis of the small-world topology and its associated features in high-quality marine networks. We conclude that such topology is a structural pattern that is not maximized in marine food webs; thus it is probably not an effective model to study robustness, stability and feasibility of marine ecosystems.
Quantifying the unquantifiable: why Hymenoptera – not Coleoptera – is the most speciose animal order
Authors: Forbes Andrew A. , Bagley Robin K. , Beer Marc A. , Hippee Alaine C. , Widmayer Heather A. 
Published: March 2018

AbstractBackgroundWe challenge the oft-repeated claim that the beetles (Coleoptera) are the most species-rich order of animals. Instead, we assert that another order of insects, the Hymenoptera, are more speciose, due in large part to the massively diverse but relatively poorly known parasitoid wasps. The idea that the beetles have more species than other orders is primarily based on their respective collection histories and the relative availability of taxonomic resources, which both disfavor parasitoid wasps. Though it is unreasonable to directly compare numbers of described species in each order, the ecology of parasitic wasps – specifically, their intimate interactions with their hosts – allows for estimation of relative richness. We present a simple logical model that shows how the specialization of many parasitic wasps on their hosts suggests few scenarios in which there would be more beetle species than parasitic wasp species. We couple this model with an accounting of what we call the “genus-specific parasitoid-host ratio” from four well-studied genera of insect hosts, a metric by which to generate extremely conservative estimates of the average number of parasitic wasp species attacking a given beetle or other insect host species. Synthesis of our model with data from real host systems suggests that the Hymenoptera may have 2.5 - 3.2× more species than the Coleoptera. While there are more described species of beetles than all other animals, the Hymenoptera are almost certainly the larger order.
How strong are correlations in strongly recurrent neuronal networks?
Authors: Darshan Ran , Vreeswijk Carl van , Hansel David 
Published: March 2018

ABSTRACTCross-correlations in the activity in neural networks are commonly used to characterize their dynamical states and their anatomical and functional organizations. Yet, how these latter network features affect the spatiotemporal structure of the correlations in recurrent networks is not fully understood. Here, we develop a general theory for the emergence of correlated neuronal activity from the dynamics in strongly recurrent networks consisting of several populations of binary neurons. We apply this theory to the case in which the connectivity depends on the anatomical or functional distance between the neurons. We establish the architectural conditions under which the system settles into a dynamical state where correlations are strong, highly robust and spatially modulated. We show that such strong correlations arise if the network exhibits an effective feedforward structure. We establish how this feedforward structure determines the way correlations scale with the network size and the degree of the connectivity. In networks lacking an effective feedforward structure correlations are extremely small and only weakly depend on the number of connections per neuron. Our work shows how strong correlations can be consistent with highly irregular activity in recurrent networks, two key features of neuronal dynamics in the central nervous system.
Retronasal Habituation: Characterization and Impact on Flavor Perception using Time-Intensity
Authors: Pellegrino Robert , Atchley Addison , Ali Simrah , Shingleton Joel , Luckett Curtis R. 
Published: March 2018

AbstractOlfactory habituation results from prolonged exposure to an odor, leading to perceptual changes defined by several characteristics. To date, human habituation research has focused on orthonasal olfaction which is perceived externally while ignoring internal routes of odor perception related to flavor. In our study, we conducted two experiments to characterize retronasal olfactory habituation and measured its impact on flavor perception. In Experiment 1, 22 participants rhythmically breathed a food odor (lime), non-food odor (lavender), and blank (propylene glycol) that was presented using an orally-adhered strip, while rating the odor intensity using the time-intensity procedure. After a 10-minute exposure, the participants ate a lime-flavored gummy and rated the lime flavor. In Experiment 2, the same procedure was performed for a low-level lime odor, a simple (lime oil) and complex (lime oil + sucrose + citric acid) beverage as the flavor stimuli. Our results demonstrated two known principles of habituation for retronasally presented odors: 1) prolonged exposure lead to decreased perception, 2) weaker stimuli lead to more rapid habituation. Additionally, we found that the non-food odor habituated slower than the food odor; however, the participants seemed to recover simultaneously upon food and beverage consumption leading to no change in flavor perception.