bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Five Host Plant Species on the Life History and Population Growth Parameters of Myzus persicae (Hemiptera: Aphididae)
Authors: Hong Feng , Han Hong-Liang , Pu Po , Wei Dong , Wang Jia , Liu Yinghong 
Published: September 2019

AbstractThe green peach aphid, Myzus persicae Sulzer (Hemiptera: Aphididae), is an important agricultural pest with a wide range of host plants. To study effects of host species on the life history traits of M. persicae, aphids were individually reared on five host plants: Brassica campestris L. (Brassicales: Brassicaceae), Capsicum annuum L. (Tubiflorae: Solanaceae), Nicotiana tabacum L. (Tubiflorae: Solanaceae), Raphanus sativus L. (Brassicales: Brassicaceae), and Vicia faba L. (Rosales: Leguminosae). TWOSEX-MSchart software was used for the statistical analysis according to the age-stage, two-sex life table theory. The results showed that the shortest preadult stage and adult/total prereproductive period of M. persicae were 6.48, 0.19, and 6.67 d on V. faba, respectively. While the adult and total longevity of M. persicae on R. sativus (25.00 and 31.62 d) and N. tabacum (24.40 and 30.56 d) were significantly longer than that on the other three hosts, as was the reproductive period. The fecundity of M. persicae on R. sativus (80.83 nymphs per female), N. tabacum (71.72 nymphs per female), and V. faba (70.39 nymphs per female) was also greater than that on B. campestris and C. annuum. It was demonstrated that V. faba, R. sativus, and N. tabacum were more suitable plants for the growth of M. persicae exhibiting a shorter preadult stage, longer longevity, and greater fecundity than the remaining two species, as confirmed by the higher intrinsic rate of increase and net reproductive rate.
A Process for Decomposing Total Survey Error in Probability and Nonprobability Surveys: A Case Study Comparing Health Statistics in US Internet Panels
Authors: Unangst Jennifer , Amaya Ashley E , Sanders Herschel L , Howard Jennifer , Ferrell Abigail , Karon Sarita , Dever Jill A 
Published: August 2019

Abstract
As survey methods evolve, researchers require a comprehensive understanding of the error sources in their data. Comparative studies, which assess differences between the estimates from emerging survey methods and those from traditional surveys, are a popular tool for evaluating total error; however, they do not provide insight on the contributing error sources themselves. The Total Survey Error (TSE) framework is a natural fit for evaluations that examine survey error components across multiple data sources. In this article, we present a case study that demonstrates how the TSE framework can support both qualitative and quantitative evaluations comparing probability and nonprobability surveys. Our case study focuses on five internet panels that are intended to represent the US population and are used to measure health statistics. For these panels, we analyze the total survey error in two ways: (1) using a qualitative assessment that describes how panel construction and management methods may introduce error and (2) using a quantitative assessment that estimates and partitions the total error for two probability-based panels into coverage error and nonresponse error. This work can serve as a “proof of concept” for how the TSE framework may be applied to understand and compare the error structure of probability and nonprobability surveys. For those working specifically with internet panels, our findings will further provide an example of how researchers may choose the panel option best suited to their study aims and help vendors prioritize areas of improvement.
GBTrans: a commensal search for radio pulses with the Green Bank 20-m telescope
Authors: Golpayegani Golnoosh , Lorimer Duncan R , Ellingson Steven W , Agarwal Devansh , Young Olivia , Ghigo Frank , Prestage Richard , Rajwade Kaustubh , McLaughlin Maura A , Mingyar Michael 
Published: September 2019

ABSTRACT
We describe GBTrans, a real-time search system designed to find fast radio bursts (FRBs) using the 20-m radio telescope at the Green Bank Observatory. The telescope has been part of the Skynet educational programme since 2015. We give details of the observing system and report on the non-detection of FRBs from a total observing time of 503 d. Single pulses from four known pulsars were detected as part of the commensal observing. The system is sensitive enough to detect approximately half of all currently known FRBs and we estimate that our survey probed redshifts out to about 0.3 corresponding to an effective survey volume of around 124 000 Mpc3. Modelling the FRB rate as a function of fluence, ${\cal F}$, as a power law with ${\cal F}^{-\alpha }$, we constrain the index α &lt; 2.5 at the 90 per cent confidence level. We discuss the implications of this result in the context of constraints from other FRB surveys.
Ingredients for solar-like systems: protostar IRAS 16293-2422 B versus comet 67P/Churyumov–Gerasimenko
Authors: Drozdovskaya Maria N , van Dishoeck Ewine F , Rubin Martin , Jørgensen Jes K , Altwegg Kathrin 
Published: September 2019

ABSTRACT
Our modern day Solar System has 4.6 × 109 yr of evolution behind it with just a few relics of its birth conditions remaining. Comets are thought to be some of the most pristine tracers of the initial ingredients that were combined to produce the Earth and the other planets. Other low-mass protostars may be analogous to our proto-Sun and hence, could be used to study the building blocks necessary to form Solar-like systems. This study tests this idea on the basis of new high sensitivity, high spatial resolution ALMA data on the protoplanetary disc-scales (∼70 au) of IRAS 16293-2422 and the bulk composition of comet 67P/Churyumov-Gerasimenko, as determined for the first time with the unique in situ monitoring carried out by Rosetta. The comparative analysis of the observations from the Protostellar Interferometric Line Survey (PILS) and the measurements made with Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) shows that the relative abundances of CHO-, N-, and S-bearing molecules correlate, with some scatter, between protostellar and cometary data. A tentative correlation is seen for the first time for P- and Cl-bearing compounds. The results imply that the volatile composition of cometesimals and planetesimals is partially inherited from the pre- and protostellar phases of evolution.
A resting-state network comparison of combat-related PTSD with combat-exposed and civilian controls
Authors: Vanasse Thomas J , Franklin Crystal , Salinas Felipe S , Ramage Amy E , Calhoun Vince D , Robinson Paul C , Kok Mitchell , Peterson Alan L , Mintz Jim , Litz Brett T , Young-McCaughan Stacey , Resick Patricia A , Fox Peter T ,   STRONG STAR Consortium
Published: August 2019

Abstract
Resting-state functional connectivity (rsFC) is an emerging means of understanding the neurobiology of combat-related post-traumatic stress disorder (PTSD). However, most rsFC studies to date have limited focus to cognitively related intrinsic connectivity networks (ICNs), have not applied data-driven methodologies or have disregarded the effect of combat exposure. In this study, we predicted that group independent component analysis (GICA) would reveal group-wise differences in rsFC across 50 active duty service members with PTSD, 28 combat-exposed controls (CEC), and 25 civilian controls without trauma exposure (CC). Intranetwork connectivity differences were identified across 11 ICNs, yet combat-exposed groups were indistinguishable in PTSD vs CEC contrasts. Both PTSD and CEC demonstrated anatomically diffuse differences in the Auditory Vigilance and Sensorimotor networks compared to CC. However, intranetwork connectivity in a subset of three regions was associated with PTSD symptom severity among executive (left insula; ventral anterior cingulate) and right Fronto-Parietal (perigenual cingulate) networks. Furthermore, we found that increased temporal synchronization among visuospatial and sensorimotor networks was associated with worse avoidance symptoms in PTSD. Longitudinal neuroimaging studies in combat-exposed cohorts can further parse PTSD-related, combat stress-related or adaptive rsFC changes ensuing from combat.
A phylogenomic framework for Vetigastropoda (Mollusca)
Authors: Cunha Tauana Junqueira , Giribet Gonzalo 
Published: August 2019

AbstractAbalones, turban snails, top snails, keyhole limpets and slit shells are just some of the diverse marine Vetigastropoda. With major lineages having ancient divergences in the Paleozoic Era, basal nodes in the phylogeny have been largely unresolved. Here we present the first genomic-scale dataset focused on vetigastropods, including a comprehensive sampling of taxa with all superfamilies and about half of the extant families (41 new transcriptomes, 49 total ingroup terminals). Our recovered topology is congruent among inference methods for the majority of nodes, and differs from previous studies, in which long branch attraction artifacts seem to be pervasive. The first three divergences sequentially separate Pleurotomarioidea, Seguenzioidea and Haliotoidea from remaining vetigastropods. Fissurelloidea is sister group to Scissurelloidea, Lepetodriloidea and Lepetelloidea, which all together are the sister group to Trochoidea. A methodological discordance exists in the position of Haliotidae and Fissurellidae, possibly due to a compounded effect of small sample bias derived from gene-wide partitioning. Dense sampling of trochoids and fissurellids also provides a backbone for family and subfamily-level relationships, with Tegulidae not monophyletic.
CoRNeA: A pipeline to decrypt the inter protein interfaces from amino acid sequence information
Authors: Chopra Kriti , Burdak Bhawna , Sharma Kaushal , Kembavi Ajit , Mande Shekhar C. , Chauhan Radha 
Published: August 2019

AbstractComputational methods have been devised in the past to predict the interface residues using amino acid sequence information but have been majorly applied to predict for prokaryotic protein complexes. Since the composition and rate of evolution of the primary sequence are different between prokaryotes and eukaryotes, it is important to develop a method specifically for eukaryotic complexes. Here we report a new hybrid pipeline for the prediction of protein-protein interaction interfaces from the amino acid sequence information alone based on the framework of Co-evolution, machine learning (Random forest) and Network Analysis named CoRNeA trained specifically on eukaryotic protein complexes. We incorporate the intra contact information of the individual proteins to eliminate false positives from the predictions as the amino acid sequence also holds information for its own folding along with the interface propensities. Our prediction on various case studies shows that CoRNeA can successfully identify minimal interacting regions of two partner proteins with higher precision and recall.
EDEM3 modulates plasma triglyceride level through its regulation of LRP1 expression
Authors: Xu Yu-Xin , Peloso Gina M. , Nagai Taylor H. , Mizoguchi Taiji , Deik Amy , Bullock Kevin , Lin Honghuang , Musunuru Kiran , Yang Qiong , Vasan Ramachandran S. , Gerszten Robert E. , Clish Clary B. , Rader Daniel , Kathiresan Sekar 
Published: August 2019

SummaryHuman genetics studies have uncovered genetic variants that can be used to guide biological research and prioritize molecular targets for therapeutic intervention for complex diseases and metabolic conditions. We have identified a missense variant (P746S) inEDEM3associated with lower blood triglyceride (TG) levels in >300,000 individuals. Functional analyses in cell and mouse models show that EDEM3 deficiency strongly increased the uptake of very low-density lipoprotein and thereby reduced the plasma TG level, as a result of up-regulated expression of LRP1 receptor. We demonstrate that EDEM3 deletion up-regulated the pathways for RNA and ER protein processing and transport, and consequently increased the cell surface mannose-containing glycoproteins, including LRP1. Metabolomics analyses reveal a cellular TG accumulation under EDEM3 deficiency, a profile consistent with individuals with carryingEDEM3P746S. Our study identifies EDEM3 as a regulator of blood TG, and targeted inhibition of EDEM3 may provide a complementary approach for lowering elevated blood TG concentrations.
Land use impacts poison frog chemical defenses through changes in leaf litter ant communities
Authors: Moskowitz Nora A. , Dorritie Barbara , Fay Tammy , Nieves Olivia C. , Vidoudez Charles ,   Cambridge Rindge and Latin 2017 Biology Class,   Masconomet 2017 Biotechnology Class, Fischer Eva K. , Trauger Sunia A. , Coloma Luis A. , Donoso David A. , O’Connell Lauren A. 
Published: August 2019

AbstractMuch of the world’s biodiversity is held within tropical rainforests, which are increasingly fragmented by agricultural practices. In these threatened landscapes, there are many organisms that acquire chemical defenses from their diet and are therefore intimately connected with their local food webs. Poison frogs (Family Dendrobatidae) are one such example, as they acquire alkaloid-based chemical defenses from their diet of leaf litter ants and mites. It is currently unknown how habitat fragmentation impacts chemical defense across trophic levels, from arthropods to frogs. We examined the chemical defenses and diets of the Diablito poison frog (Oophaga sylvatica), and the diversity of their leaf litter ant communities in secondary forest and reclaimed cattle pasture. Notably, this research was performed in collaboration with two high school science classrooms. We found that the leaf litter of forest and pasture frog habitats differed significantly in ant community structure. We also found that forest and pasture frogs differed significantly in diet and alkaloid profiles, where forest frogs contained more of specific alkaloids and ate more ants in both number and volume. Finally, ant species composition of frog diets resembled the surrounding leaf litter, but diets were less variable. This suggests that frogs tend to consume particular ant species within each habitat. To better understand how ants contribute to the alkaloid chemical profiles of frogs, we chemically profiled several ant species and found some alkaloids to be common across many ant species while others are restricted to a few species. At least one alkaloid (223H) found in ants from disturbed sites was also found in skins from pasture. Our experiments are the first to link anthropogenic land use changes to dendrobatid poison frog chemical defenses through variation in leaf litter communities, which has implications for conservation management of these threatened amphibians.
Genetic description of Manania handi and Manania gwilliami
Authors: Hanson Mark A. , Westlake Hannah E. , Page Louise R. 
Published: September 2019

AbstractStaurozoa is an intriguing lineage of cnidarians bearing both polypoid and medusoid characters in the adult body plan. Miranda et al. (2016) provided a massive descriptive effort of specimen collection, sequencing, and character evolution. We also recently described the neuromusculature of two staurozoan species: Manania handi and Haliclystus “sanjuanensis.” We found that our M. handi samples genetically matched Manania gwilliami samples used in Miranda et al. (2016). Taking advantage of newly-deposited M. gwilliami sequence data, we confirm the identity of our M. handi samples, and provide additional sequence data for M. handi and H. sanjuanensis for future staurozoan identification efforts.
Oxidative stress underlies heritable impacts of paternal cigarette smoke exposure
Authors: Murphy Patrick J , Guo Jingtao , Jenkins Timothy G , James Emma R , Hoidal John R , Huecksteadt Thomas , Broberg Dallin , Hotaling James M , Alonso David F , Carrell Douglas T , Cairns Bradley R , Aston Kenneth I 
Published: August 2019

SUMMARYPaternal cigarette smoke (CS) exposure is associated with increased risk of behavioral disorders and cancer in offspring, but the mechanism has not been identified. This study used mouse models to evaluate: 1) what impact paternal CS exposure has on sperm DNA methylation (DNAme), 2) whether sperm DNAme changes persist after CS exposure ends, 3) the degree to which DNAme and gene expression changes occur in offspring and 4) the mechanism underlying impacts of CS exposure. We demonstrate that CS exposure induces sperm DNAme changes that are partially corrected within 28 days of removal from CS exposure. Additionally, paternal smoking causes changes in neural DNAme and gene expression in offspring. Remarkably, the effects of CS exposure are largely recapitulated in oxidative stress-compromisedNrf2-/-mice and their offspring, independent of paternal smoking. These results demonstrate that paternal CS exposure impacts offspring phenotype and that oxidative stress underlies CS induced heritable epigenetic changes.
NETGE-PLUS: standard and network-based gene enrichment analysis in human and model organisms
Authors: Bovo Samuele , Martelli Pier Luigi , Di Lena Pietro , Casadio Rita 
Published: August 2019

ABSTRACTOmics techniques provide a spectrum of information that needs to be disentangled to characterize complex traits at the molecular level. The gap between genotype and phenotype must be closed by reconciling the genome information with the set of molecular pathways and biological processes describing the phenotype. In dealing with this problem, gene enrichment analysis has become the most widely adopted strategy. Here, we present NETGE-PLUS, a web-server for standard and network-based functional interpretation of gene sets of human and of model organisms, including S. scrofa, S. cerevisiae, E. coli and A. thaliana. NETGE-PLUS enables the functional enrichment of both simple and ranked lists of genes, also introducing the possibility of exploring relationships among KEGG pathways. A web interface makes data retrieval complete and user-friendly. NETGE-PLUS is publicly available at http://net-ge2.biocomp.unibo.it
Google matrix analysis of bi-functional SIGNOR network of protein-protein interactions
Authors: Frahm Klaus M. , Shepelyansky Dima L. 
Published: September 2019

AbstractMotivationDirected protein networks with only a few thousand of nodes are rather complex and do not allow to extract easily the effective influence of one protein to another taking into account all indirect pathways via the global network. Furthermore, the different types of activation and inhibition actions between proteins provide a considerable challenge in the frame work of network analysis. At the same time these protein interactions are of crucial importance and at the heart of cellular functioning.ResultsWe develop the Google matrix analysis of the protein-protein network from the open public database SIGNOR. The developed approach takes into account the bi-functional activation or inhibition nature of interactions between each pair of proteins describing it in the frame work of Ising-spin matrix transitions. We also apply a recently developed linear response theory for the Google matrix which highlights a pathway of proteins whose PageRank probabilities are most sensitive with respect to two proteins selected for the analysis. This group of proteins is analyzed by the reduced Google matrix algorithm which allows to determine the effective interactions between them due to direct and indirect pathways in the global network. We show that the dominating activation or inhibition function of each protein can be characterized by its magnetization. The results of this Google matrix analysis are presented for three examples of selected pairs of proteins. The developed methods work rapidly and efficiently even for networks with several million of nodes and can be applied to various biological networks.AvailabilityThe Google matrix data and executive code of described algorithms are available at http://www.quantware.ups-tlse.fr/QWLIB/google4signornet/
Machine learning guided association of adverse drug reactions with in vitro target-based pharmacology
Authors: Ietswaart Robert , Arat Seda , Chen Amanda X. , Farahmand Saman , Kim Bumjun , DuMouchel William , Armstrong Duncan , Fekete Alexander , Sutherland Jeffrey J. , Urban Laszlo 
Published: August 2019

AbstractAdverse drug reactions (ADRs) are one of the leading causes of morbidity and mortality in health care. Understanding which drug targets are linked to ADRs can lead to the development of safer medicines. Here, we analyze in vitro secondary pharmacology of common (off) targets for 2134 marketed drugs. To associate these drugs with human ADRs, we utilized FDA Adverse Event Reports and developed random forest models that predict ADR occurrences from in vitro pharmacological profiles. By evaluating Gini importance scores of model features, we identify 221 target-ADR associations, which co-occur in PubMed abstracts to a greater extent than expected by chance. Among these are established relations, such as the association of in vitro hERG binding with cardiac arrhythmias, which further validate our machine learning approach. Evidence on bile acid metabolism supports our identification of associations between the Bile Salt Export Pump and renal, thyroid, lipid metabolism, respiratory tract and central nervous system disorders. Unexpectedly, our model suggests PDE3 is associated with 40 ADRs. These associations provide a comprehensive resource to support drug development and human biology studies.
Interactions across life stages and thermal tolerance plasticity inTigriopus californicus
Authors: Healy Timothy M. , Bock Antonia K. , Burton Ronald S. 
Published: August 2019

AbstractIn response to rapid environmental change, organisms rely on both genetic adaptation and phenotypic plasticity to adjust key traits that are necessary for survival and reproduction. Given the accelerating rate of climate change, plasticity may be particularly important. For organisms in warming aquatic habitats, upper thermal tolerance is likely to be a key trait, and many organisms express plasticity in this trait in response to developmental or adulthood temperatures. Although plasticity at one life stage may influence plasticity at another life stage, relatively little is known about these interactive effects for thermal tolerance. Here we used locally adapted populations of the intertidal copepodTigriopus californicusto investigate these interactions in a marine ectotherm. We found that low latitude populations had greater critical thermal maxima (CTmax) than high latitude populations, and variation in developmental temperature altered CTmaxplasticity in adulthood. After development at 25°C, CTmaxwas plastic in adults, whereas no adult plasticity in this trait was observed after 20°C development. This pattern was identical across four populations, suggesting that local thermal adaptation has not shaped this interactive effect. However, differences in the capacities to maintain ATP synthesis rates and to induce heat shock proteins at high temperatures, two likely mechanisms of local adaptation in this species, were consistent with changes in CTmaxdue to developmental temperatures, suggesting there is mechanistic overlap between plastic interactions and adaptation in general. These results indicate that interactive effects of plasticity across life stages may have substantial impacts on upper thermal tolerance in ectothermic organisms.Summary statementDevelopmental temperatures alter the plasticity of thermal limits in adults of a marine ectotherm, and differences in ATP synthesis rate and heat shock protein expression parallel the changes in tolerance.