bluuebunny/crossref_metadata_2025 huggingface dataset:
Philhellenic attitudes. Eduard Schaubert’s Wrocław collection: an account of its antiquities and the circumstances of its formation
Authors: Kubala Agata
Published: May 2018

This paper considers the figure of the Wrocław collector Eduard Schaubert (1804–1860) and the collection he amassed during his twenty-year stay in Greece, paying particular attention to his collecting activities and the motives that lay behind them. The collection was built up over at least a dozen years and was gradually expanded in two ways: through personal exploration in Athens and in other regions of Greece, and through purchases. Schaubert’s collection forms an expression of its creator’s philhellenic attitudes and an example of a new, scholarly approach to collecting in which artefacts were chosen according to a pre-defined principle. It also represents an interesting example of a markedly heterogeneous group, comprising not only Greek objects but also items of Egyptian and Roman provenance, so forming what might be described as a typical nineteenth-century private collection of antiquities.
Urinary [TIMP-2]·[IGFBP7]-guided randomized controlled intervention trial to prevent acute kidney injury in the emergency department
Authors: Schanz Moritz , Wasser Christoph , Allgaeuer Sebastian , Schricker Severin , Dippon Juergen , Alscher Mark Dominik , Kimmel Martin
Published: May 2018

Background

Early detection and prevention of acute kidney injury (AKI) is important to reduce morbidity and mortality. Discovery of early-detection biomarkers has enabled early preventive approaches. There are no data on early biomarker-guided intervention with nephrological consultation in emergency departments (EDs).

Methods

In this prospective randomized controlled intervention trial, patients at high risk for AKI were screened with urinary [TIMP-2]·[IGFBP7] in the ED of Robert-Bosch-Hospital (Stuttgart, Germany). We screened 257 eligible patients of whom 100 met the inclusion criteria, with urinary [TIMP-2]·[IGFBP7] >0.3, and were included. The intervention group received immediate one-time nephrological consultation after randomization, implementing Kidney Disease: Improving Global Outcomes (KDIGO) 2012 recommendations on AKI. The primary outcome was the incidence of moderate to severe AKI within the first day after admission. Secondary outcomes were AKI occurrence within 3 days after admission, need for renal replacement therapy (RRT), length of hospital stay and death.

Results

The primary outcome did not differ significantly (P = 0.9) between the groups, neither within the first day nor within the first 3 days after admission. The intervention group had significantly (P < 0.05) lower serum creatinine (SCr) on Day 2 and lower maximum SCr and tended (P = 0.08) to have higher urine output (UOP) at Day 3 than the non-intervention group. No patient in the intervention group needed RRT (0 versus 3) during the hospital stay (P = 0.09).

Conclusions

One-time routine nephrologist-guided application of the KDIGO bundle in ED patients with a risk for AKI cannot currently be recommended. However, due to the uniform trend of study endpoints in favour of intervention, further trials to investigate larger cohorts of more severely ill patients are warranted.

Trial registration

www.ClinicalTrials.gov, study number NCT02730637.
Money, Sex and Broken Promises: Politicians’ Bad Behaviour Reduces Trust
Authors: Rose Richard , Wessels Bernhard
Published: May 2018

This article develops and tests empirically a theory of the effect on political trust of forms of behaviour that violate social, political and legal norms about how politicians ought to behave. These include taking money for favours, over-indulging in private life and making misleading promises to win votes. The evidence comes from a specially designed survey in Britain, France and Spain, countries where popular distrust of politicians appears greater than illegal political behaviour. Bad behaviours, especially abandoning election promises once in office, have a much stronger effect on distrust of political parties that do differences in partisanship. Comparing national regressions shows that the impact of bad behaviours is very similar in Britain, France and Spain.
‘Space is blue and birds fly through it’
Authors: Rovelli Carlo
Published: May 2018

Quantum mechanics is not about ‘quantum states’: it is about values of physical variables. I give a short fresh presentation and update on therelationalperspective on the theory, and a comment on its philosophical implications.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Role of long-range aromatic clique and community in protein stability
Authors: Mahanta P , Bhardwaj A , Reddy VS , Ramakumar S
Published: May 2018

Aromatic interactions make an important contribution to protein structure, function, folding and have attracted intense study. Earlier studies on a recombinant xylanase from Bacillus sp. NG-27 (RBSX), which has the ubiquitous (beta/alpha)8-triosephosphate isomerase barrel fold showed that three aromatic residues to alanine substitutions, in the N-terminal and C-terminal regions, significantly decreased the stability of the enzyme. Of these mutations, F4A mutation decreased the stability of the enzyme by ∼4 degree C, whereas W6A mutation and Y343A mutation remarkably decreased the stability of the enzyme by ∼10 degree C. On the other hand, the F4W mutation did not affect the thermal stability of RBSX. We provide here a network perspective of aromatic-aromatic interactions in terms of aromatic clique community and long-range association. Our study reveals that disruption of long-range k-clique aromatic interaction cluster holding the N- and C-terminal regions are associated with the decreased stability of the enzyme. The present work reiterates as well as expands on those findings concerning the role of interactions between the N- and C-terminus in protein stability. Furthermore, comparative analyses of crystal structures of homologous pairs of proteins from thermophilic and mesophilic organisms emphasize the prevalence of long-range k-clique communities of aromatic interaction that may be playing an important role and highlights an additional source of stability in thermophilic proteins. The design principle based on clustering of long-range aromatic residues in the form of aromatic-clique and clique community may be effectively applied to enhance the stability of enzymes for biotechnological applications.

Database

The coordinates o fF4A, F4W, W6A, and Y343A are deposited in the PDB database under the accession numbers 5EFF, 5E58, 5EFD, and 5EBA respectively.

Abbreviations

BSX, xylanase from Bacilllus sp. NG-27; RBSX, recombinant BSX xylanase; TIM, Triosephosphate isomerase; GH10, Glycosyl hydrolase family 10; 3D, three-dimensional; r.m.s.d, root mean square deviation; RSA, relative solvent accessible surface area; Tm, melting temperature; CD, Circular Dichroism; BHX, GH10 xylanase from Bacillus halodurans; BFX, GH10 xylanase from Bacillus firmus; TmxB, GH10 xylanase from Thermotoga maritima
Isolation and antibiotic profile ofVibriospp. in final effluents of two wastewater treatment plants in the Eastern Cape of South Africa
Authors: Osuolale Olayinka , Okoh Anthony
Published: May 2018

Background

Poorly or partially treated wastewater disposed of can contaminate water and even properly treated sewage can have its problems. The highlight of this danger is wastewater treatment plants serving as reservoir for proliferation of antibiotic resistant organisms. We have reported the state of two wastewater treatment in the Eastern Cape of South Africa which discharge poorly and partially treated effluents. Our aims to identify Vibrio spp. and their antibiotic profiles in treated final effluent discharge from wastewater treatment plant.

Methods

Culture based approach using the TCBS agar for isolationVibriospp., presumptive isolates were purified and confirmed using PCR. The confirmed isolated were also genotyped to identify the species present. The antibiotic profiling of the confirmed isolates was using the CLSI recommended first line antibiotics for Vibrio.

Results

Out of the 786 presumptive isolates, 374 were confirmed asVibriospp. None of the Vibrio spp. pathotypes were present in the confirmed isolates. Randomized isolates of 100 Vibrio spp. were selected, > 90 % of the isolates were susceptible to Ciprofloxacin, and > 50 – 80 % for Ampicillin, Chloramphenicol, Tetracycline, Cefotaxime, and Trimethoprim-sulfamethoxazole respectively.

Conclusions

We are able to isolate Vibrio spp. from treated effluents but none of their pathotypes were present. The antibiotic agents considered for primary testing which are ciprofloxacin was the most effective of the antibiotic drugs, followed by cefotaxime, tetracycline with less susceptibility. Contamination from discharged effluents from wastewater treatment can lead to spread of spread of disease in this environment. The WWTPs studied are sources of pollution to surface water with environmental and public health.
Optimization of Experiment Design for Mass Spectrometric Isotopic Labeling Kinetics
Authors: Lathwal Shefali , Raaisa Raaisa , Alves Tiago C. , Kibbey Richard G. , Jha Abhishek K. , Mason Graeme F.
Published: May 2018

Determination of metabolic fluxes by measurement of time-dependent sampling of isotopic enrichments during the administration of labeled substrates provides rich information. Because such experiments are resource-intensive and frequently push the limits of sensitivity of the measurement techniques, optimization of experiment design can improve feasibility with respect to financial and labor costs, time to completion, and increase precision and accuracy of the results. Here we used a previously published set of data acquired in cultured insulinoma cells to evaluate contributions to the sensitivity and variability of the rate of citrate synthase (CS). Specifically, we calculated changes in uncertainty in CS if sample times were dropped or new ones were added, and we observed that some sampling times can be dropped with little effect, while improvements can be made with a strategic choice of when to add samples. We measured the contributions of data sampled at different times on the sensitivity of CS, finding that CS had greater sensitivity at early time points. We tested the concept that if two estimated parameters are correlated significantly, then refining one might constrain the other. In this case, the rate of Beta-oxs was found to be correlated with CS, and narrower variability in Beta-ox did indeed improve the sensitivity of CS. The tests described here might be applied at the initial design stage and then after a pilot phase to improve sensitivities of targeted fluxes and the reduction of materials, time, labor, and other experimental resources. The correlation analyses can be used to consider what orthogonal measurements might be beneficial for further improvement of measurements. While this study used a specific example of a set of time-dependent kinetic isotopic measurements, the results illustrate some generalizable behaviors that can be tested in other experimental systems.
Temporal alignment and latent Gaussian process factor inference in population spike trains
Authors: Duncker Lea , Sahani Maneesh
Published: May 2018

We introduce a novel scalable approach to identifying common latent structure in neural population spike-trains, which allows for variability both in the trajectory and in the rate of progression of the underlying computation. Our approach is based on shared latent Gaussian processes (GPs) which are combined linearly, as in the Gaussian Process Factor Analysis (GPFA) algorithm. We extend GPFA to handle unbinned spike-train data by incorporating a continuous time point-process likelihood model, achieving scalability with a sparse variational approximation. Shared variability is separated into terms that express condition dependence, as well as trial-to-trial variation in trajectories. Finally, we introduce a nested GP formulation to capture variability in the rate of evolution along the trajectory. We show that the new method learns to recover latent trajectories in synthetic data, and can accurately identify the trial-to-trial timing of movement-related parameters from motor cortical data without any supervision.
Explainable machine learning prediction of synergistic drug combinations for precision cancer medicine
Authors: Janizek Joseph D. , Celik Safiye , Lee Su-In
Published: May 2018

Although combination therapy has been a mainstay of cancer treatment for decades, it remains challenging, both to identify novel effective combinations of drugs and to determine the optimal combination for a particular patient’s tumor. While there have been several recent efforts to test drug combinationsin vitro, examining the immense space of possible combinations is far from being feasible. Thus, it is crucial to develop datadriven techniques to computationally identify the optimal drug combination for a patient. We introduce TreeCombo, an extreme gradient boosted tree-based approach to predict synergy of novel drug combinations, using chemical and physical properties of drugs and gene expression levels of cell lines as features. We find that TreeCombo significantly outperforms three other state-of-theart approaches, including the recently developed DeepSynergy, which uses the same set of features to predict synergy using deep neural networks. Moreover, we found that the predictions from our approach were interpretable, with genes having well-established links to cancer serving as important features for prediction of drug synergy.
Host protein CD63 enhances viral RNA replication by interacting with human astrovirus nonstructural protein nsP1a/4
Authors: zhao wei , liu Nian , Tao Xiao Li , Zheng Chun hong , Li Xiang yu , Yu Man , Li Yong gang
Published: May 2018

Human astrovirus nonstructural protein nsP1a/4, located at the C-terminal end of nsP1a, is thought to be involved in the regulation of RNA replication and capsid maturation;however, its rolesviral growth and virulence are not well understood. We investigated the intracellular host proteins that interact with nsP1a and explored the potential roles of the interaction in the pathogenesis of human astrovirus infection. We screened 14 independent proteins with a cDNA library derived from Caco-2 cells using a yeast two-hybrid technique. Deletion analysis revealed that interaction between the nsP1a/4 domain and the large extracellular loop (LEL) domain of the human protein CD63 is necessary for astrovirus replication. The interaction was confirmed by glutathione-S-transferase (GST) pull-down assays and co-immunoprecipitation assays. Confocal microscopy showed that nsP1a/4 and CD63 co-localized in the cytoplasm of infected cells. Over expression of CD63 promoted viral RNA synthesis, whereas knockdown of CD63 markedly decreased viral RNA levels. Those results suggest that CD63 plays a critical role in human astrovirus RNA replication. The interaction between CD63 and nsP1a/4 provides a channel to further understand the roles of interactions between host and virus proteins in astrovirus infection and release.

IMPORTANCE

Human astroviruses cause gastroenteritis in young children and immunocompromised patients. In this study, we provide evidence that nsP1a/4, a nonstructural protein located at the C-terminal end of the human astrovirus nsP1a polyprotein, interacts with the host protein CD63. Over expression of CD63 promoted viral RNA replication, whereas knockdown of CD63 decreased virus RNA replication, indicating that CD63 plays a critical role in the human astrovirus life cycle.
Using molecular ecological network analysis to explore the effects of chemotherapy on intestinal microbial communities of colorectal cancer patients
Authors: Cong Jing , Zhu Jingjuan , Zhang Chuantao , Li Tianjun , Liu Kewei , Liu Dong , Zhou Na , Jiang Man , Hou Helei , Zhang Xiaochun
Published: May 2018

Intestinal microbiota is now widely known to be key roles in the nutrition uptake, metabolism, and the regulation of human immune responses. However, we do not know how changes the intestinal microbiota in response to the chemotherapy. In this study, we used network-based analytical approaches to explore the effects of five stages of chemotherapy on the intestinal microbiota of colorectal cancer patients. The results showed that chemotherapy greatly reduced the alpha diversity and changed the specie-specie interaction networks of intestinal microbiota, proved by the network size, network connectivity and modularity. The OTU167 and OTU8 from the genus Fusobacterium and Bacteroides were identified as keystone taxa by molecular ecological networks in the first two stages of chemotherapy, and were significantly correlated with tumor makers (P < 0.05). Five stages of chemotherapy did not make the intestinal micro-ecosystem regain a steady state, because of the lower alpha diversity and more complicated ecological networks compared to the healthy individuals. Furthermore, combing the changes of ecological networks with the tumor markers, the intestinal microbiota was closely linked with clinical chemotherapeutic effects.

Importance

A deeply understanding of the role of intestinal microbiota contributes to help us find path forward for improving the prognosis of colorectal cancer patients. In addition, diet or probiotics interventions will be a possible attempt to improve the clinical chemotherapeutic effects for colorectal cancer patients.
Global mycorrhizal plant distribution linked to terrestrial carbon stocks
Authors: Soudzilovskaia Nadejda A. , van Bodegom Peter M. , Terrer César , van’t Zelfde Maarten , McCallum Ian , McCormack M. Luke , Fisher Joshua B. , Brundrett Mark , de Sá Nuno César , Tedersoo Leho
Published: May 2018

Vegetation impacts on ecosystem functioning are mediated by mycorrhiza, a plant-fungal association formed by most plant species. Ecosystems dominated by distinct mycorrhizal types differ strongly in their biogeochemistry. Quantitative analyses of mycorrhizal impacts on ecosystem functioning are hindered by the absence of information on mycorrhizal distribution. We present the first global high-resolution maps of vegetation biomass distribution among main types of mycorrhizal associations. Arbuscular, ecto-, ericoid and non-mycorrhizal vegetation store 241±15, 100±17, 7±1.8 and 29 ± 5.5 GT carbon in aboveground biomass, respectively. Soil carbon stocks in both topsoil and subsoil are positively related to the biomass fraction of ectomycorrhizal plants in the community, though the strength of this relationship varies across biomes. We show that human-induced transformations of Earth’s ecosystems have reduced ectomycorrhizal vegetation, with potential knock-on effects on terrestrial carbon stocks. Our work provides a benchmark for spatially explicit global quantitative assessments of mycorrhizal impacts on ecosystem functioning and biogeochemical cycles.

One Sentence Summary

First maps of the global distribution of mycorrhizal plants reveal global losses of ectomycorrhizal vegetation, and quantitative links between mycorrhizal vegetation patterns and terrestrial carbon stocks.
Activation of the TRKB receptor mediates the panicolytic-like effect of NOS inhibitor aminoguanidine
Authors: Ribeiro DE , Casarotto PC , Spiacci A , Fernandes GG , Pinheiro LC , Tanus-Santos JE , Zangrossi H , Guimarães FS , Joca SRL , Biojone C
Published: May 2018

Nitric oxide (NO) triggers escape reactions in the dorsal periaqueductal gray matter (dPAG), a core structure mediating panic-associated responses, and decreases the release of BDNFin vitro. BDNF mediates the panicolytic effect induced by antidepressant drugs and produces these effectsper sewhen injected into the dPAG. Based on these findings, we hypothesize that nitric oxide synthase (NOS) inhibitors would have panicolytic properties associated with increased BDNF signaling in the dPAG. We observed that the repeated (7 days), but not acute (1day), systemic administration of the NOS inhibitor aminoguanidine (AMG; 15 mg/kg/day) increased the latency to escape from the open arm of the elevated T-maze (ETM) and inhibited the number of jumps in hypoxia-induced escape reaction in rats, suggesting a panicolytic-like effect. Repeated, but not acute, AMG administration (15mg/kg) also decreased nitrite levels and increased TRKB phosphorylation at residues Y706/7 in the dPAG. Notwithstanding the lack of AMG effect on total BDNF levels in that structure, the microinjection of the TRK antagonist K252a into the dPAG blocked the anti-escape effect of this drug in the ETM. Taken together our data suggest that the inhibition of NO production by AMG increased the levels of pTRKB, which is required for the panicolytic-like effect observed.
Prioritizing Small Molecule as Candidates for Drug Repositioning using Machine Learning
Authors: Shameer Khader , Johnson Kipp W. , Glicksberg Benjamin S. , Hodos Rachel , Readhead Ben , Tomlinson Max S. , Dudley Joel T.
Published: May 2018

Drug repositioning, i.e. identifying new uses for existing drugs and research compounds, is a cost-effective drug discovery strategy that is continuing to grow in popularity. Prioritizing and identifying drugs capable of being repositioned may improve the productivity and success rate of the drug discovery cycle, especially if the drug has already proven to be safe in humans. In previous work, we have shown that drugs that have been successfully repositioned have different chemical properties than those that have not. Hence, there is an opportunity to use machine learning to prioritize drug-like molecules as candidates for future repositioning studies. We have developed a feature engineering and machine learning that leverages data from publicly available drug discovery resources: RepurposeDB and DrugBank. ChemVec is the chemoinformatics-based feature engineering strategy designed to compile molecular features representing the chemical space of all drug molecules in the study. ChemVec was trained through a variety of supervised classification algorithms (Naïve Bayes, Random Forest, Support Vector Machines and an ensemble model combining the three algorithms). Models were created using various combinations of datasets as Connectivity Map based model, DrugBank Approved compounds based model, and DrugBank full set of compounds; of which RandomForest trained using Connectivity Map based data performed the best (AUC=0.674). Briefly, our study represents a novel approach to evaluate a small molecule for drug repositioning opportunity and may further improve discovery of pleiotropic drugs, or those to treat multiple indications.
Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses andFusarium graminearumresistance in maize seedling roots
Authors: Zhou Shaoqun , Zhang Ying K. , Kremling Karl A. , Ding Yezhang , Bennett John S. , Bae Justin S. , Kim Dean K. , Kolomiets Michael V. , Schmelz Eric A. , Schroeder Frank C. , Buckler Edward S. , Jander Georg
Published: May 2018

The production and regulation of defensive specialized metabolites plays a central role in pathogen resistance in maize (Zea mays) and other plants. Therefore, identification of genes involved in plant specialized metabolism can contribute to improved disease resistance.

We used comparative metabolomics to identify previously unknown antifungal metabolites in maize seedling roots, and investigated the genetic and physiological mechanisms underlying their natural variation using quantitative trait locus (QTL) mapping and comparative transcriptomics approaches.

Two maize metabolites, smilaside A (3,6-diferuloyl-3′,6′-diacetylsucrose) and smiglaside C (3,6-diferuloyl-2′,3′,6′-triacetylsucrose), that may contribute to maize resistance againstFusarium graminearumand other fungal pathogens were identified. Elevated expression of an ethylene receptor gene,ETHYLENE INSENSITIVE 2(ZmEIN2), co-segregated with decreased smilaside A/smiglaside C ratio. Pharmacological and genetic manipulation of ethylene availability and sensitivityin vivoindicated that, whereas ethylene was required for the production of both metabolites, the smilaside A/smiglaside C ratio was negatively regulated by ethylene sensitivity. This ratio, rather than the absolute abundance of these two metabolites, was important for maize seedling root defense againstF. graminearum.

Ethylene signaling regulates the relative abundance of the twoF. graminearum-resistance-related metabolites and affects resistance againstF. graminearumin maize seedling roots.
Disease and climate effects on individuals jointly drive post-reintroduction population dynamics of an endangered amphibian
Authors: Joseph Maxwell B. , Knapp Roland A.
Published: May 2018

The emergence of novel pathogens often has dramatic negative effects on previously unexposed host populations. Subsequent disease can drive populations and even species to extinction. After establishment in populations, pathogens can continue to affect host dynamics, influencing the success or failure of species recovery efforts. However, quantifying the effect of pathogens on host populations in the wild is challenging because individual hosts and their pathogens are difficult to observe. Here we use long-term mark-recapture data to describe the dynamics of reintroduced populations of an endangered amphibian (Rana sierrae) and evaluate the success of these recovery efforts in the presence of a recently-emerged pathogen, the amphibian chytrid fungusBatrachochytrium dendrobatidis. We find that highB. dendrobatidisinfection intensities are associated with increases in detectability, reductions in survival, and more infected adults. We also find evidence for intensity-dependent survival, with heavily infected individuals suffering higher mortality. These results highlight the need in disease ecology for probabilistic approaches that account for uncertainty in infection intensity using imperfect observational data. Such approaches can advance the understanding of disease impacts on host population dynamics, and in the current study will improve the effectiveness of species conservation actions.
Cryo-EM structure of the circumsporozoite protein of Plasmodium falciparum with a vaccine-elicited antibody reveals maturation of inter-antibody contacts
Authors: Oyen David , Torres Jonathan L. , Cottrell Christopher A. , Richter King C. , Wilson Ian A. , Ward Andrew B.
Published: May 2018

The circumsporozoite protein (CSP) on the surface of Plasmodium falciparum sporozoites is important for parasite development, motility, and host hepatocyte invasion. However, intrinsic disorder of the NANP repeat sequence in the central region of CSP has hindered its structural and functional characterization. Here, the cryo-EM structure at ∼3.4 Å resolution of a recombinant shortened CSP construct (rsCSP) with the variable domains (Fabs) of a highly protective monoclonal antibody reveals an extended spiral conformation of the central NANP repeat region surrounded by antibodies. This unusual structure appears to be stabilized and/or induced by interaction with an antibody where contacts between adjacent Fabs are somatically mutated and enhance the interaction. Such maturation in non-antigen contact residues may be an effective mechanism for antibodies to target tandem repeat sequences and provide novel insights into malaria vaccine design.

An unusual spiral conformation is formed for the NANP repeat region in Plasmodium falciparum circumsporozoite protein (CSP) in complex with antibodies generated by the RTS,S vaccine and is stabilized by affinity-matured inter-Fab interactions.
Revealing nonlinear neural decoding by analyzing choices
Authors: Yang Qianli , Walker Edgar , Cotton R. James , Tolias Andreas S. , Pitkow Xaq
Published: May 2018

Sensory data about most natural task-relevant variables are entangled with task-irrelevant nuisance variables. The neurons that encode these relevant signals typically constitute a nonlinear population code. Here we present a theoretical framework for quantifying how the brain uses or decodes its nonlinear information. Our theory obeys fundamental mathematical limitations on information content inherited from the sensory periphery, identifying redundant codes when there are many more cortical neurons than primary sensory neurons. The theory predicts that if the brain uses its nonlinear population codes optimally, then more informative patterns should be more correlated with choices. More specifically, the theory predicts a simple, easily computed quantitative relationship between fluctuating neural activity and behavioral choices that reveals the decoding efficiency. We analyze recordings from primary visual cortex of monkeys discriminating the distribution from which oriented stimuli were drawn, and find these data are consistent with the hypothesis of near-optimal nonlinear decoding.
Dynamics of the Previte-Hoffman food web model with small immigrations
Authors: Hassan Sk. Sarif
Published: May 2018

The ecological dynamics of prey-predator systems are extensively studied over a century.Previte and Hoffmanintroduced a three species(predator-prey with an omnivore) model in 2013. We demonstrate the asymptotic stability of the Previte and Hoffman modified model adding with small immigration into the prey or predator or omnivore population. A comparison of dynamics is also drawn with immigration and without immigration. It is worth noting that the qualitative dynamics is unchanged among the immigration system over the classical Previte-Hoffman system.
Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes
Authors: Toju Hirokazu , Tanaka Yu
Published: May 2018

Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, as effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics, and agricultural practices, more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes [Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales), and Purpureocillium (Hypocreales)] co-occurred in the soybean rhizosphere at a small spatial scale. Overall, this study suggests how “consortia” of anti-nematode microbes can derive from indigenous (resident) microbiomes, thereby providing basic information for managing anti-nematode microbial communities in agroecosystems.
A quantitative framework for investigating the reliability of network construction
Authors: Cirtwill Alyssa R. , Eklöf Anna , Roslin Tomas , Wootton Kate , Gravel Dominique
Published: May 2018

Descriptions of ecological networks typically assume that the same interspecific interactions occur each time a community is observed. This contrasts with the known stochasticity of ecological communities: community composition, species abundances, and link structure all vary in space and time. Moreover, finite sampling generates variation in the set of interactions actually observed. Here we develop the conceptual and analytical tools needed to capture uncertainty in the estimation of pairwise interactions. To define the problem, we identify the different contributions to the uncertainty of an interaction and its implications for the estimation of network properties. We then outline a framework to quantify the uncertainty around each interaction. We illustrate this framework using the most extensively sampled network to date. We found significant uncertainty in estimates for the probability of most pairwise interactions which we could, however, limit with informative priors. Through these efforts, we demonstrate the utility of our approach and the importance of acknowledging the uncertainty inherent in network studies. Most importantly, we stress that networks are best thought of as systems constructed from random variables, the stochastic nature of which must be acknowledged for an accurate representation. Doing so will fundamentally change networks analyses and yield greater realism.
Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise
Authors: Pertea Mihaela , Shumate Alaina , Pertea Geo , Varabyou Ales , Chang Yu-Chi , Madugundu Anil K. , Pandey Akhilesh , Salzberg Steven L.
Published: May 2018

We assembled the sequences from 9,795 RNA sequencing experiments, collected from 31 human tissues and hundreds of subjects as part of the GTEx project, to create a new, comprehensive catalog of human genes and transcripts. The new human gene database contains 43,162 genes, of which 21,306 are protein-coding and 21,856 are noncoding, and a total of 323,824 transcripts, for an average of 7.5 transcripts per gene. Our expanded gene list includes 4,998 novel genes (1,178 coding and 3,819 noncoding) and 97,511 novel splice variants of protein-coding genes as compared to the most recent human gene catalogs. We detected over 30 million additional transcripts at more than 650,000 sites, nearly all of which are likely to be nonfunctional, revealing a heretofore unappreciated amount of transcriptional noise in human cells.
Mental health consumer participation in undergraduate occupational therapy student assessment: No negative impact
Authors: Logan Alexandra , Yule Elisa , Taylor Michael , Imms Christine
Published: May 2018

Background/aim

Australian accreditation standards for occupational therapy courses require consumer participation in the design, delivery and evaluation of programs. This study investigated whether a mental health consumer – as one of two assessors for an oral assessment in a mental health unit – impacted engagement, anxiety states and academic performance of undergraduate occupational therapy students.

Methods

Students (n = 131 eligible) self‐selected into two groups but were blinded to the group differences (assessor panel composition) until shortly prior to the oral assessment. Control group assessors were two occupational therapy educators, while consumer group assessors included an occupational therapy educator and a mental health consumer.

Results

Pre‐ and post‐assessment data were successfully matched for 79 students (overall response rate = 73.1%). No evidence was found of significant differences between the two groups for engagement, anxiety or academic performance (all P values >0.05).

Conclusion

Including mental health consumers as assessors did not negatively impact student engagement and academic performance, nor increase student anxiety beyond that typically observed in oral assessment tasks. The findings provide support for expanding the role of mental health consumers in the education and assessment of occupational therapy students. Development of methods to determine the efficacy of consumer involvement remains an area for future research.
The Association of Proxy Care Engagement with Proxy Reports of Patient Experience and Quality of Life
Authors: Roydhouse Jessica K. , Gutman Roee , Keating Nancy L. , Mor Vincent , Wilson Ira B.
Published: May 2018

Objective

To assess the association of proxy‐specific covariates with proxy‐reported patient cancer care experience, quality rating, and quality of life.

Data Sources/Study Setting

Secondary analysis of data from the Cancer Care Outcomes Research and Surveillance (CanCORS) study.

Study Design

Cross‐sectional observational study. The respondents were proxies for patients with incident colorectal or lung cancer.

Data Collection/Extraction Methods

Analyses used linear regression models and adjusted for patient sociodemographic and clinical characteristics. Outcomes included patients’ experiences with medical care, nursing care, and care coordination, overall quality ratings, and physical and mental health, all scored on 0–100 scales (0 = worst, 100 = best). Independent variables included the proxy's relationship with the patient and engagement in patient care.

Principal Findings

Of 1,011 proxies, most were the patient's spouse (50 percent) or child (36 percent). Although most proxies (66 percent) always attended medical visits, 3 percent reported never attending. After adjustment, on average children reported worse experiences and poorer quality care than spouses (4–9 points lower across outcomes). Proxies who never attended medical visits reported significantly worse medical care (−11 points, 95 percent CI = −18 to −3) and care coordination (−13 points, 95 percent CI = −20 to −6).

Conclusions

Collecting data on proxy engagement in care is warranted if proxy responses are used.
Far‐Infrared Optimization of the Fragrance‐Improving Process with Temperature and Humidity Control for Green Tea
Authors: Hua Jin‐Jie , Yuan Hai‐Bo , Deng Yu‐Liang , Jiang Yong‐Wen , Wang Jin‐Jin , Dong Chun‐Wang , Li Jia
Published: May 2018

In this study, a Box–Behnken design was used to explore the effect of a new technology on green tea fragrance improvement and to optimize fragrance‐improving with a bilayer far‐infrared fragrance‐improving machine with temperature and humidity control. Based on the results of previous single‐factor experiments, the main biochemical composition and sensory evaluation scores of the fragrance‐improved samples were used as investigation indices. The new fragrance‐improving technology was compared with the traditional far‐infrared fragrance‐improving process, roller pot fragrance improvement, and hot air rotary fragrance improvement. The results show that the optimal parameter combination of the new technology consists of a temperature of 128.00 °C, relative humidity of 70.00 g/h, and transmission speed of 435.00 r/min. With these process parameters, the amino acids, tea polyphenols, flavonoids, soluble sugar, catechins, and caffeine in the fragrance‐improved samples reached 3.86%, 32.29%, 5.59%, 4.45%, 8.97%, and 2.75%, respectively. The quality material weight value was 11.72%. The shape, color, taste, and aroma of the fragrance‐improved samples made using these parameters were found to be best, with a sensory quality score of 87.40, which is significantly higher than that of other fragrance‐improving methods. The energy consumption was 0.19 RMB/kg, which was reduced by more than 50% compared with the other methods, and the production efficiency was more than 30% higher than the traditional methods. This new far‐infrared fragrance‐improving technology overcomes the yellowish and grayish color of fragrance‐improved tea samples that is caused by the traditional fragrance‐improving approach, and will provide technical guidance for actual green tea production.

Practical Application

Our proposed approach innovatively integrates humidity and rotational speed as factors for fragrance improvement in Chinese tea process. The findings of this work provide new technical for fragrance improvement processes.
Microbial community analyses of produced waters from high‐temperature oil reservoirs reveal unexpected similarity between geographically distant oil reservoirs
Authors: Kim Daehyun D. , O'Farrell Corynne , Toth Courtney R. A. , Montoya Oscar , Gieg Lisa M. , Kwon Tae‐Hyuk , Yoon Sukhwan
Published: May 2018

As a preliminary investigation for the development of microbial‐enhanced oil recovery strategies for high‐temperature oil reservoirs (~70 to 90°C), we have investigated the indigenous microbial community compositions of produced waters from five different high‐temperature oil reservoirs near Segno, Texas, U.S. (~80 to 85°C) and Crossfield, Alberta, Canada (~75°C). The DNA extracted from these low‐biomass‐produced water samples were analysed with MiSeq amplicon sequencing of partial 16S rRNA genes. These sequences were analysed along with additional sequence data sets available from existing databases. Despite the geographical distance and difference in the physicochemical properties, the microbial compositions of the Segno and Crossfield produced waters exhibited unexpectedly high similarity, as indicated by the results of beta diversity analyses. The major operational taxonomic units included acetoclastic and hydrogenotrophic methanogens (Methanosaetaceae, Methanobacterium and Methanoculleus), as well as bacteria belonging to the families Clostridiaceae and Thermotogaceae, which have been recognized to include thermophilic, thermotolerant, and/or spore‐forming subtaxa. The sequence data retrieved from the databases exhibited different clustering patterns, as the communities from close geographical locations invariably had low beta diversity and the physicochemical properties and conditions of the reservoirs apparently did not have a substantial role in shaping of microbial communities.
Diagnostic value of microRNAs derived from exosomes in bronchoalveolar lavage fluid of early‐stage lung adenocarcinoma: A pilot study
Authors: Kim Ji Eun , Eom Jung Seop , Kim Won‐young , Jo Eun Jung , Mok Jeongha , Lee Kwangha , Kim Ki Uk , Park Hye‐kyung , Lee Min Ki , Kim Mi‐hyun
Published: May 2018

Background

Low‐dose computed tomography can identify smaller nodules more often than chest radiography in lung screening. However, complications from invasive diagnostic procedures performed to detect nodules are common. Exosomes contain a diverse array of biomolecules that reflect the biological state of the cell from which they are released. The aim of this study was to investigate the diagnostic value of bronchoalveolar lavage (BAL) fluid exosomal microRNAs (miRNAs) for early‐stage lung adenocarcinoma.

Methods

We evaluated miRNAs (miR‐7, miR‐21, miR‐126, Let‐7a, miR‐17, and miR‐19) known to have diagnostic value for lung adenocarcinoma. Exosomes were isolated from the BAL fluid of control subjects (n = 15) and patients with lung adenocarcinoma (n = 13). Exosomal miRNA was analyzed using a commercial kit containing probes targeting six selected miRNAs. Results were validated via quantitative PCR.

Results

The presence of miRNAs was confirmed in exosomes from BAL fluid of both lung adenocarcinoma patients and control subjects. miR‐126 (P < 0.001) and Let‐7a (P = 0.015) levels were significantly higher in the BAL fluid of lung adenocarcinoma patients than in control subjects. The BAL fluid miRNA signature was confirmed using an independent set of paired adenocarcinoma and normal tissue samples (n = 4). Lung adenocarcinoma tissues showed increased expression of miR‐126 (P = 0.039) compared to normal tissue samples.

Conclusion

We identified a close correlation between BAL fluid exosomal miRNAs and tumor miRNAs. BAL fluid exosomal miRNAs obtained through noninvasive methods could serve as diagnostic biomarkers in early‐stage lung adenocarcinoma.
Intronic variant of EGFR is associated with GBAS expression and survival outcome of early‐stage non‐small cell lung cancer
Authors: Hong Mi Jeong , Lee Shin Yup , Choi Jin Eun , Kang Hyo‐Gyoung , Do Sook Kyung , Lee Jang Hyuck , Yoo Seung Soo , Lee Eung Bae , Seok Yangki , Cho Sukki , Jheon Sanghoon , Lee Jaehee , Cha Seung Ick , Kim Chang Ho , Park Jae Yong
Published: May 2018

Background

Genome‐wide association studies have indicated that most of the currently identified disease and trait‐associated single nucleotide polymorphisms (SNPs) are intronic or intergenic. RegulomeDB is a recently developed database that provides functional annotations for regulatory features of SNPs located in non‐coding regions. We evaluated the potential regulatory SNPs in the EGFR gene region using RegulomeDB and their associations with prognosis after surgery in non‐small cell lung cancer (NSCLC) patients.

Methods

A total of 698 patients with surgically resected NSCLC were enrolled and seven SNPs were selected based on the RegulomeDB database. All SNPs were genotyped using SEQUENOM MassARRAY iPLEX assay.

Results

Among the seven SNPs evaluated, rs9642391 (EGFR ivs19+2851C>G) was significantly associated with survival outcome (adjusted hazard ratio [HR] for overall survival = 0.70, 95% confidence interval [CI] 0.56–0.87, P = 0.001; adjusted HR for disease‐free survival = 0.82, 95% CI 0.70–0.97, P = 0.02; under a codominant model). According to RegulomeDB, rs9642391C>G, which is located in intron 19 of EGFR, was predicted to influence the expression of GBAS but not EGFR. As predicted, rs9642391C>G was associated with GBAS (P = 0.024) but not EGFR messenger RNA expression in tumor tissues.

Conclusion

In conclusion, our study provides evidence that rs9642391C>G in the intron of EGFR is associated with GBAS expression and survival outcomes of patients with surgically resected early‐stage NSCLC.
babette: BEAUti 2, BEAST2 and Tracer for R
Authors: Bilderbeek Richèl J. C. , Etienne Rampal S.
Published: May 2018

In the field of phylogenetics, BEAST2 is one of the most widely used software tools. It comes with the graphical user interfaces BEAUti 2, DensiTree and Tracer, to create BEAST2 configuration files and to interpret BEAST2's output files. However, when many different alignments or model setups are required, a workflow of graphical user interfaces is cumbersome.

Here, we present a free, libre and open‐source package,babette: ‘BEAUti 2, BEAST2 and Tracer for R’, for the R programming language.babettecreates BEAST2 input files, runs BEAST2 and parses its results, all from an R function call.

We describebabette's usage and the novel functionality it provides compared to the original tools and we give some examples.

Asbabetteis designed to be of high quality and extendable, we conclude by describing the further development of the package.