bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions
Authors: Bailey Paul C. , Schudoma Christian , Jackson William , Baggs Erin , Dagdas Gulay , Haerty Wilfried , Moscou Matthew , Krasileva Ksenia V. 
Published: January 2017

AbstractBackgroundThe plant immune system is innate, encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes.ResultsWe showed that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncovered a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events revealed that homologous receptors can be fused to diverse domains. Furthermore, we discovered a 43 amino acids long motif that was associated with this dominant integration clade and was located immediately upstream of the fusion site. Sequence analysis revealed that DNA transposition and/or ectopic recombination are the most likely mechanisms of NLR-ID formation.ConclusionsThe identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen ‘baits’.
The effect of dietary ginseng polysaccharide supplementation on the immune responses involved in porcine milk-derived esRNAs
Authors: Sun Jiajie , Yao Liyuan , Chen Ting , Xi Qianyun , Zhang Yongliang 
Published: January 2017

AbstractGinseng and its polysaccharides (GPS) have been well known as an immune modulator. This study was conducted to investigate the effects of dietary supplemental GPS on the immune responses involved in sow’s milk-derived exosomal shuttle RNAs (esRNAs) using RNA-Seq and miRNA-Seq. Of the 213 identified miRNA types, a total of 26 conserved miRNAs were differently expressed in response to GPS supplementation, including 10 up-regulated and 16 down-regulated miRNAs in GPS feeding group. In addition, exosomal transcriptome analysis identified 14,696 protein-coding genes in sow’s milk exosomes, and 283 genes with 204 and 79 candidates showing up and down-regulation were significantly responded to GPS supplementation. Integrated analysis of each differently expressed miRNA with significantly expressed genes further revealed the presence of 51 highly conserved miRNA-gene interactions that were annotated to be related to immunoregulatory functions. This work provided an important advance in the functional identification of dietary GPS supplementation and more fundamental information about how GPS promoted the immune response and healthy growth of the infant from mothers at molecular levels.
Reduced foraging investment as an adaptation to patchy food sources: a phasic army ant simulation
Authors: Teseo Serafino , Delloro Francesco 
Published: January 2017

AbstractColonies of several ant species within the subfamily Dorylinae alternate stereotypical discrete phases of foraging and reproduction. Such phasic cycles are thought to be adaptive because they minimize the amount of foraging and the related costs, and at the same time enhance the colony-level ability to rely on patchily distributed food sources. In order to investigate these hypotheses, we use here a simple computational approach to study the population dynamics of two species of virtual ant colonies that differ quantitatively in their foraging investment. One species, which we refer to as “phasic”, forages only half of the time, mirroring the phasic activity of some army ants; the other “non-phasic” species forages instead all the time. We show that, when foraging costs are relatively high, populations of phasic colonies grow on average faster than non-phasic populations, outcompeting them in mixed populations. Interestingly, such tendency becomes more consistent as food becomes more difficult to find but locally abundant. According to our results, reducing the foraging investment, for example by adopting a phasic lifestyle, can result in a reproductive advantage, but only in specific conditions. We thus suggest phasic colony cycles to have emerged together with the doryline specialization in feeding on the brood of other eusocial insects, a resource that is hard to obtain but highly abundant if available.
Symptoms of Depression in a Large Healthy Population Cohort are related to Subjective Memory Complaints and Memory Performance in Negative Contexts
Authors: Schweizer Susanne , Kievit Rogier A. , Emery Tina ,   Cam-CAN, Henson Richard N. 
Published: January 2017

AbstractDecades of research have investigated the impact of clinical depression on memory, which has revealed biases and in some cases impairments. However, little is understood about the effects of sub-clinical symptoms of depression on memory performance in the general population. Here we report the effects of symptoms of depression on memory problems in a large population-derived cohort (N = 2544), 87% of whom reported at least one symptom of depression. Specifically, we investigate the impact of depressive symptoms on subjective memory complaints, objective memory performance on a standard neuropsychological task and, in a subsample (n = 288), objective memory in affective contexts. There was a dissociation between subjective and objective memory performance, with depressive symptoms showing a robust relationship with self-reports of memory complaints, even after adjusting for age, gender, general cognitive ability and symptoms of anxiety, but not with performance on the standardised measure of verbal memory. Contrary to our expectations, hippocampal volume (assessed in a subsample, n = 592) did not account for significant variance in subjective memory, objective memory or depressive symptoms. Nonetheless, depressive symptoms were related to poorer memory for pictures presented in negative contexts, even after adjusting for memory for pictures in neutral contexts. Thus the symptoms of depression, associated with subjective memory complaints, appear better assessed by memory performance in affective contexts, rather than standardised memory measures. We discuss the implications of these findings for understanding the impact of depressive symptoms on memory functioning in the general population.
asymptoticMK: A web-based tool for the asymptotic McDonald–Kreitman test
Authors: Haller Benjamin C. , Messer Philipp W. 
Published: January 2017

ABSTRACTThe McDonald–Kreitman (MK) test is a widely used method for quantifying the role of positive selection in molecular evolution. One key shortcoming of this test lies in its sensitivity to the presence of slightly deleterious mutations, which can severely bias its estimates. An asymptotic version of the MK test was recently introduced that addresses this problem by evaluating polymorphism levels for different mutation frequencies separately, and then extrapolating a function fitted to that data. Here we present asymptoticMK, a web-based implementation of this asymptotic McDonald–Kreitman test. Our web service provides a simple R-based interface into which the user can upload the required data (polymorphism and divergence data for the genomic test region and a neutrally evolving reference region). The web service then analyzes the data and provides plots of the test results. This service is free to use, open-source, and available athttp://benhaller.com/messerlab/asymptoticMK.html.
Rapidde novoassembly of the European eel genome from nanopore sequencing reads
Authors: Jansen Hans J. , Liem Michael , Jong-Raadsen Susanne A. , Dufour Sylvie , Weltzien Finn-Arne , Swinkels William , Koelewijn Alex , Palstra Arjan P. , Pelster Bernd , Spaink Herman P. , van den Thillart Guido E. , Dirks Ron P. , Henkel Christiaan V. 
Published: January 2017

AbstractWe have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, the entire computational process takes two days on a single CPU. The resulting genome assembly significantly improves on a previous draft based on short reads only, both in terms of contiguity (N50 1.2 Mbp) and structural quality. This combination of affordable nanopore sequencing and light-weight assembly promises to make high-quality genomic resources accessible for many non-model plants and animals.
DNA-dependent RNA cleavage by the Natronobacterium gregoryi Argonaute
Authors: Ye Sunghyeok , Bae Taegeun , Kim Kyoungmi , Habib Omer , Lee Seung Hwan , Kim Yoon Young , Lee Kang-In , Kim Seokjoong , Kim Jin-Soo 
Published: January 2017

AbstractWe show here that, unlike most other prokaryotic Argonaute (Ago) proteins, which are DNA-guided endonucleases, the Natronobacterium gregoryi-derived Ago (NgAgo) can function as a DNA-guided endoribonuclease, cleaving RNA, rather than DNA, in a targeted manner. The NgAgo protein, in complex with 5’-hydroxylated or 5’-phosphrylated oligodeoxyribonucleotides (ODNs) of variable lengths, split RNA targets into two or more fragments in vitro, suggesting its physiological role in bacteria and demonstrating a potential for degrading RNA molecules such as mRNA or lncRNA in eukaryotic cells in a targeted manner.
Lacking conservation genomics in the giant Galápagos tortoise
Authors: Loire Etienne , Galtier Nicolas 
Published: January 2017

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100031).Conservation policy in the giant Galápagos tortoise, an iconic endangered animal, has been assisted by genetic markers for ∼15 years: a dozen loci have been used to delineate thirteen (sub)species, between which hybridization is prevented. Here, comparative reanalysis of a previously published NGS data set reveals a conflict with traditional markers. Genetic diversity and population substructure in the giant Galápagos tortoise are found to be particularly low, questioning the genetic relevance of current conservation practices. Further examination of giant Galapagos tortoise population genomics is critically needed.
Production of the antibiotic secondary metabolite solanapyrone A by the fungal plant pathogen Ascochyta rabiei during fruiting body formation in saprobic growth
Authors: Kim Wonyong , Park Jeong‐Jin , Dugan Frank M. , Peever Tobin L. , Gang David R. , Vandemark George , Chen Weidong 
Published: January 2017

SummaryFungi are noted producers of a diverse array of secondary metabolites, many of which are of pharmacological importance. However, the biological roles of the vast majority of these molecules during the fungal life cycle in nature remain elusive. Solanapyrones are polyketide‐derived secondary metabolites produced by diverse fungal species including the plant pathogen Ascochyta rabiei. This molecule was originally thought to function as a phytotoxin facilitating pathogenesis of A. rabiei. Chemical profiling and gene expression studies showed that solanapyrone A was specifically produced during saprobic, but not parasitic growth of A. rabiei. Expression of the gene encoding the final enzymatic step in solanapyrone biosynthesis was specifically associated with development of the asexual fruiting bodies of the fungus on certain substrates. In confrontation assays with saprobic fungi that were commonly found in chickpea debris in fields, A. rabiei effectively suppressed the growth of all competing fungi, such as Alternaria, Epicoccum and Ulocladium species. Solanapyrone A was directly detected in the inhibitory zone using a MALDI‐imaging mass spectrometry, and the purified compound showed significant antifungal activities against the potential saprobic competitors. These results suggest that solanapyrone A plays an important role for competition and presumably the survival of the fungus.
Endemic cyanophages and the puzzle of phage‐bacteria coevolution
Authors: Cordero Otto X. 
Published: January 2017

SummaryA recent genomic analysis of Synechococcus cyanophages sampled for over 15 years reveals a remarkable pattern of stable phage population structure, highly reminiscent of the ecotype structure observed in bacteria and archaeal ecotypes. In this highlight I discuss the importance of this finding and the questions and opportunities it opens to learn more about the nature of phage‐bacterial coevolution in the environment.
Misoprostol for cervical priming prior to hysteroscopy in postmenopausal and premenopausal nulliparous women; a multicentre randomised placebo controlled trial
Authors: Tasma ML , Louwerse MD , Hehenkamp WJ , Geomini PM , Bongers MY , Veersema S , van Kesteren PJ , Tromp E , Huirne JA , Graziosi GC 
Published: January 2017

ObjectiveTo evaluate the reduction of pain by misoprostol compared with placebo prior to hysteroscopy in postmenopausal and premenopausal nulliparous women.DesignRandomised multicentre double‐blind placebo controlled trial.SettingTwo Dutch teaching hospitals and one Dutch university medical centre.PopulationPostmenopausal and premenopausal nulliparous women undergoing office hysteroscopy.MethodsPatients were randomised to receive either 400 microgram misoprostol or placebo 12 and 24 hours before hysteroscopy. Pain was quantified by the use of real time pain measurement using the continuous pain score meter (CPSM) and VAS scores.Main outcome measuresPrimary outcome was pain measured by the CPSM during passage of the hysteroscope through the cervical canal, quantified by the area under the curve (AUC). Secondary outcomes included VAS scores, other CPSM parameters, failures and side effects.ResultsIn all, 149 patients were randomly assigned to either misoprostol (n = 74) or placebo (n = 75). The AUC during introduction did not significantly differ between the intervention and the placebo group. The VAS score during introduction, however, demonstrated a significant difference in premenopausal nulliparous women favouring misoprostol: 2.9 (95% CI 1.3–4.4) versus placebo 5.5 (95% CI 3.9–7.1), P = 0.02, as well as the AUC during the entire procedure: 618 (95% CI 410–827) versus 1126 (95% CI 671–1580), P = 0.04. Failures were equally distributed between the misoprostol (16%) and placebo group (13%). Intestinal side effects occurred significantly more frequently in the misoprostol group (67%) than in the placebo group (32%) [OR 4.2 (95% CI 2.1–8.3), P < 0.01].ConclusionMisoprostol prior to hysteroscopy reduces pain in premenopausal nulliparous women but not in postmenopausal women. It does cause side effects.Tweetable abstractRCT: misoprostol versus placebo prior to hysteroscopy in 149 women significantly reduces some pain parameters.
The Impact of a Soiled Airway on Intubation Success in the Emergency Department When Using the GlideScope or the Direct Laryngoscope
Authors: Sakles John C. , Corn G. Judson , Hollinger Patrick , Arcaris Brittany , Patanwala Asad E. , Mosier Jarrod M. 
Published: January 2017

AbstractBackgroundThe objective was to determine the impact of a soiled airway on firstpass success when using the GlideScope video laryngoscope or the direct laryngoscope for intubation in the emergency department (ED).MethodsData were prospectively collected on all patients intubated in an academic ED from July 1, 2007, to June 30, 2016. Patients ≥ 18 years of age, who underwent rapid sequence intubation by an emergency medicine resident with the GlideScope or the direct laryngoscope, were included in the analysis. Data were stratified by device used (GlideScope or direct laryngoscope). The primary outcome was firstpass success. Patients were categorized as those without blood or vomitus (CLEAN) and those with blood or vomitus (SOILED) in their airway. Multivariate regression models were developed to control for confounders.ResultsWhen using the GlideScope, the firstpass success was lower in the SOILED group (249/306; 81.4%) than the in CLEAN group (586/644, 91.0%; difference = 9.6%; 95% confidence interval [CI] = 4.7%–14.5%). Similarly, when using the direct laryngoscope, the firstpass success was lower in the SOILED group (186/284, 65.5%) than in the CLEAN group (569/751, 75.8%; difference = 10.3%; 95% CI = 4.0%–16.6%). The SOILED airway was associated with a decreased firstpass success in both the GlideScope cohort (adjusted odds ratio [aOR] = 0.4; 95% CI = 0.3–0.7) and the direct laryngoscope cohort (aOR = 0.6; 95% CI = 0.5–0.8).ConclusionSoiling of the airway was associated with a reduced firstpass success during emergency intubation, and this reduction occurred to a similar degree whether using either the GlideScope or the direct laryngoscope.
The Australian Census Longitudinal Dataset: using record linkage to create a longitudinal sample from a series of cross‐sections
Authors: Chipperfield James , Brown James J. , Watson Nicole 
Published: January 2017

SummaryThe Australian Bureau of Statistics is creating a longitudinal sample, called the Australian Census Longitudinal Dataset (ACLD), by linking person records across its five‐yearly Census of Population and Housing. This paper proposes a Multi‐Panel framework for selecting and weighting records in the ACLD. This framework can be applied more generally to selecting longitudinal samples from a series of cross‐sectional administrative files. The proposed framework avoids some significant limitations of the popular ‘Top‐Up’ sampling approach to maintaining the cross‐sectional and longitudinal representativeness of a sample over time.
Amplitude‐integrated electroencephalography can predict neurodevelopmental outcome at 12 months of corrected age in very preterm infants
Authors: Ralser Elisabeth , Neubauer Vera , Pupp‐Peglow Ulrike , Kiechl‐Kohlendorfer Ursula , Griesmaier Elke 
Published: January 2017

AbstractAimIt is difficult to find diagnostic tools than can reliably predict neurodevelopmental outcomes in very preterm infants in clinical practice. This study evaluated whether amplitude‐integrated electroencephalography predicted neurodevelopmental outcome in preterm infants when they reached 12 months of corrected age.MethodsBetween October 2007 and December 2013, we studied 232 preterm infants (51% male) at Innsbruck Medical University Hospital, Austria. Their mean birthweight was 1264 g, and their mean gestational age was 29.5 weeks. Amplitude‐integrated electroencephalography was evaluated using the Burdjalov score, and outcomes were assessed using the Bayley Scales of Infant Development – Second Edition.ResultsThe cohort was divided into three subgroups: 154 infants with normal outcomes, 53 infants with moderate delays and 25 infants with severe delays. The amplitude‐integrated electroencephalography Burdjalov scores were lower in infants with moderate delays than in infants with normal outcomes and even lower in infants with severe delays. The highest area under the curve (0.776) for the Burdjalov score was at 18–24 hours of life.ConclusionOur study confirmed the predictive value of amplitude‐integrated electroencephalography and showed that this needed to be carried out early in life to provide reliable information on neurodevelopmental outcomes in very preterm infants.
Comparative cardiovascular risks of dipeptidyl peptidase 4 inhibitors with other second‐ and third‐line antidiabetic drugs in patients with type 2 diabetes
Authors: Ou Huang‐Tz , Chang Kai‐Cheng , Li Chung‐Yi , Wu Jin‐Shang 
Published: January 2017

AimsDipeptidyl peptidase 4 inhibitors (DPP4is) are suggested as a second‐ and third‐line antidiabetic treatment for type 2 diabetes. Previous studies assessed only the cardiovascular effects of DPP4is as a second‐line treatment, included sulphonylurea as the only comparator, and yielded inconclusive results on the risk of heart failure. The present study therefore evaluated the comparative cardiovascular risks of DPP4is with other second‐ and third‐line antidiabetic drugs.MethodsBased on a large nationwide diabetic cohort, 113 051 patients with type 2 diabetes newly on metformin‐based dual or triple therapy were identified in 2009–2011 and followed until 2013, or death if this occurred sooner. Primary interest targeted hospitalizations for ischaemic stroke, myocardial infarction and heart failure. Secondary outcomes were hypoglycaemia and all‐cause mortality. Cox proportional hazards models were performed to assess time‐to‐event hazard ratio between propensity score‐matched antidiabetic treatment groups.ResultsDPP4is as a second‐line add‐on to metformin had a significantly lower stroke risk [hazard ratio (HR) 0.817 (95% confidence interval 0.687, 0.971)] and all‐cause mortality [HR 0.825 (0.687, 0.992)] than those for sulphonylurea. DPP4is as a third‐line add‐on to metformin and sulphonylurea combined dual therapy had a significantly lower risk for stroke [HR 0.826 (0.740, 0.923)] and all‐cause mortality [HR 0.784 (0.701, 0.878)] than those for acarbose, and significantly lower risks for stroke [HR 0.653 (0.542, 0.786)], heart failure [HR 0.721 (0.568, 0.917)] and all‐cause mortality [HR 0.689 (0.594, 0.703)] than those for meglitinide.ConclusionsDPP4is as a second‐ or third‐line add‐on treatment provided cardiovascular benefits and posed no increased risks for heart failure, hypoglycaemia or death.
A novel dual amylin and calcitonin receptor agonist, KBP‐089, induces weight loss through a reduction in fat, but not lean mass, while improving food preference
Authors: Gydesen Sofie , Hjuler Sara Toftegaard , Freving Zenia , Andreassen Kim Vietz , Sonne Nina , Hellgren Lars I , Karsdal Morten Asser , Henriksen Kim 
Published: January 2017

Background and PurposeObesity and associated co‐morbidities, such as type 2 diabetes and non‐alcoholic fatty liver disease, are major health challenges. Hence, there is an important need to develop weight loss therapies with the ability to reduce the co‐morbidities.Experimental ApproachThe effect of the dual amylin and calcitonin receptor agonist (DACRA), KBP‐089, on body weight, glucose homeostasis and fatty acid accumulation in liver and muscle tissue and on food preference was investigated. Furthermore, we elucidated weight‐independent effects of KBP‐089 using a weight‐matched group.Key ResultsRats fed a high‐fat diet were treated, s.c., with KBP‐089 0.625, 1.25, 2.5 μg·kg−1 or vehicle. KB‐089 induced in a dose‐dependent and sustained weight loss (~17% by 2.5 μg·kg−1). Moreover, KBP‐089 reduced fat depot size and reduced lipid accumulation in muscle and liver. In Zucker Diabetic Fatty rats, KBP‐089 improved glucose homeostasis through improved insulin action. To obtain a weight‐matched group, significantly less food was offered (9% less than in the KBP‐089 group). Weight matching led to improved glucose homeostasis by reducing plasma insulin; however, these effect were inferior compared to those of KBP‐089. In the food preference test, rats fed a normal diet obtained 74% of their calories from chocolate. KBP‐089 reduced total caloric intake and induced a relative increase in chow consumption while drastically reducing chocolate consumption compared with vehicle.Conclusions and ImplicationsThe novel DACRA, KBP‐089, induces a sustained weight loss, leading to improved metabolic parameters including food preference, and these are beyond those observed simply by diet‐induced weight loss.