bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insect herbivory reshapes a native leaf microbiome
Authors: Humphrey Parris T , Whiteman Noah K 
Published: April 2019

AbstractInsect herbivory is pervasive in plant communities, but its impact on microbial plant colonizers is not well-studied in natural systems. By calibrating sequencing-based bacterial detection to absolute bacterial load, we find that the within-host abundance of most leaf microbiome (phyllosphere) taxa colonizing a native forb is amplified within leaves impacted by insect herbivory. Herbivore-associated bacterial amplification reflects community-wide compositional shifts towards lower ecological diversity, but the extent and direction of such compositional shifts can be interpreted only by quantifying absolute abundance. Experimentally eliciting anti-herbivore defenses reshaped within-host fitness ranks among Pseudomonas spp. field isolates and amplified a subset of putative P. syringae phytopathogens in a manner causally consistent with observed field-scale patterns. Herbivore damage was inversely correlated with plant reproductive success and was highly clustered across plants, which predicts tight co-clustering with putative phytopathogens across hosts. Insect herbivory may thus drive the epidemiology of plant-infecting bacteria as well as the structure of a native plant microbiome by generating variation in within-host bacterial fitness at multiple phylogenetic and spatial scales. This study emphasizes that “non-focal” biotic interactions between hosts and other organisms in their ecological settings can be crucial drivers of the population and community dynamics of host-associated microbiomes.
Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs
Authors: Williams Rachel C. , Blanco Marina B. , Poelstra Jelmer W. , Hunnicutt Kelsie E. , Comeault Aaron A. , Yoder Anne D. 
Published: April 2019

AbstractMadagascar’s biodiversity is notoriously threatened by deforestation and climate change. Many of these organisms are rare, cryptic, and severely threatened, making population-level sampling unrealistic. Such is the case with Madagascar’s dwarf lemurs (genusCheirogaleus), the only obligate hibernating primate. We here apply comparative genomic approaches to generate the first genome-wide estimates of genetic diversity within dwarf lemurs. We generate a reference genome for the fat-tailed dwarf lemur,Cheirogaleus medius, and use this resource to facilitate analyses of high-coverage (~30x) genome sequences for wild-caught individuals representing species:C. sp. cf. medius, C. major, C. crossleyiandC. sibreei. This study represents the largest contribution to date of novel genomic resources for Madagascar’s lemurs. We find concordant phylogenetic relationships among the four lineages ofCheirogaleusacross most of the genome, and yet detect a number of discordant genomic regions consistent with ancient admixture. We hypothesized that these regions could have resulted from adaptive introgression related to hibernation, indeed finding that genes associated with hibernation are present, though most significantly, that gene ontology categories relating to transcription are over-represented. We estimate levels of heterozygosity and find particularly low levels in an individual sampled from an isolated population ofC. mediusthat we refer to asC. sp. cf. medius. Results are consistent with a recent decline in effective population size, which is evident across species. Our study highlights the power of comparative genomic analysis for identifying species and populations of conservation concern, as well as for illuminating possible mechanisms of adaptive phenotypic evolution.
Multi-view Co-training for microRNA Prediction
Authors: Hassani Mohsen Sheikh , Green James R. 
Published: April 2019

AbstractMicroRNA (miRNA) are short, non-coding RNAs involved in cell regulation at post-transcriptional and translational levels. Numerous computational predictors of miRNA been developed that generally classify miRNA based on either sequence- or expression-based features. While these methods are highly effective, they require large labelled training data sets, which are often not available for many species. Simultaneously, emerging high-throughput wet-lab experimental procedures are producing large unlabelled data sets of genomic sequence and RNA expression profiles. Existing methods use supervised machine learning and are therefore unable to leverage these unlabelled data. In this paper, we design and develop a multi-view co-training approach for the classification of miRNA to maximize the utility of unlabelled training data by taking advantage of multiple views of the problem. Starting with only 10 labelled training data, co-training is shown to significantly increase classification accuracy of both sequence- and expression-based classifiers, without requiring any new labelled training data. After 11 iterations of co-training, the expression-based view of miRNA classification experiences an average increase in AUPRC of 15.81% over six species, compared to 11.90% for self-training and 4.84% for passive learning. Similar results are observed for sequence-based classifiers with increases of 46.47%, 39.53% and 29.43%, for co-training, self-training, and passive learning, respectively. The final co-trained sequence and expression-based classifiers are integrated into a final confidence-based classifier which shows improved performance compared to each individual view. This study represents the first application of multi-view co-training to miRNA prediction and shows great promise, particularly for understudied species with few available training data.AvailabilityCode is available athttps://github.com/GreenCUBIC/miRNA_MVCT. All datasets are publicly available with accession numbers listed in the manuscript.Contactjrgreen@sce.carleton.ca
All-Assay-Max2 pQSAR: Activity predictions as accurate as 4-concentration IC50s for 8,558 Novartis assays
Authors: Martin Eric J , Polyakov Valery R , Zhu Xiang-Wei , Mukherjee Prasenjit , Tian Li , Liu Xin 
Published: April 2019

ABSTRACTProfile-QSAR (pQSAR) is a massively multi-task, 2-step machine learning method with unprecedented scope, accuracy and applicability domain. In step one, a “profile” of conventional single-assay random forest regression (RFR) models are trained on a very large number of biochemical and cellular pIC50assays using Morgan 2 sub-structural fingerprints as compound descriptors. In step two, a panel of PLS models are built using the profile of pIC50predictions from those RFR models as compound descriptors. Hence the name. Previously described for a panel of 728 biochemical and cellular kinase assays, we have now built an enormous pQSAR from 11,805 diverse Novartis IC50and EC50assays. This large number of assays, and hence of compound descriptors for PLS, dictated reducing the profile by only including RFR models whose predictions correlate with the assay being modeled. The RFR and pQSAR models were evaluated with our “realistically novel” held-out test set whose median average similarity to the nearest training set member across the 11,805 assays was only 0.34, thus testing a realistically large applicability domain. For the 11,805 single-assay RFR models, the median correlation of prediction with experiment was onlyR2ext=0.05, virtually random, and only 8% of the models achieved our standard success threshold ofR2ext=0.30. For pQSAR, the median correlation wasR2ext=0.53, comparable to 4-concentration experimental IC50s, and 72% of the models met ourR2ext>0.30 standard, totaling 8558 successful models. The successful models included assays from all of the 51 annotated target sub-classes, as well as 4196 phenotypic assays, indicating that pQSAR can be applied to virtually any disease area. Every month, all models are updated to include new measurements, and predictions are made for 5.5 million Novartis compounds, totaling 50 billion predictions. Common uses have included virtual screening, selectivity design, toxicity and promiscuity prediction, mechanism-of-action prediction, and others.
Preparation and pharmacokinetics of genistein MePEG-PLGA copolymer micelles
Authors: Swartz Mina , Smith John 
Published: April 2019

AbstractIn this report, we demonstrated a novel technique to prepare genistein (GEN) MePEG-PLGA copolymer micelles. Initial stability and pharmacokinetic behavior in rats after intravenous administration were investigated. The micelles were prepared by modified self-emulsifying solvent evaporation method. The morphology, encapsulation efficiency, drug loading, particle size and Zeta potential were investigated. The release behavior was investigated by dynamic membrane dialysis technique. The micelles were stored in a refrigerator at 4 °C, and samples were taken after 1 d, 10 d, 1 month, 3 months, and 6 months, and the encapsulation efficiency and drug loading were examined. The GEN micelles were injected into the tail vein of healthy rats. The blood concentration of GEN in rats was determined by HPLC. The plasma concentration data was processed by DAS 2.0 software. The main pharmacokinetic parameters were statistically analyzed by SPSS 17.0 software. Results The encapsulation efficiency of the prepared micelles was (84.43+/-2.93) %, the drug loading was (2.63+/-0.91) %, and the particle size was (63.75+/-4.12) nm. The release behavior of GEN micelles was in line with the Weibull model. The 6-month leakage rate of GEN micelles was 2.45%, and the drug loading decreased by 0.18%. The main pharmacokinetic parameters AUC0-t after GEN micelles and GEN emulsion 40 mg·kg-1 were injected into the tail vein of rats. They were (99.46+/- 4.77) mg · L-1 ·h and (57.51+/-1.37) mg·L-1 ·h, and t1/2 were (7.48+/-1.15)h and (4.95+/- 1.15)h, respectively, and Cmax was (16.03+/-1.20) mg·L-1 and (16.73+/-1.10) mg·L-1, CL are (0.36+/-0.02) L·h-1 ·kg-1 and (0.67+/-0.02)L·h-1 ·kg-1.
Weak passports and bad behavior:
Authors: SHERIDAN DEREK 
Published: April 2019

ABSTRACTChinese migrants in Tanzania regularly face inspections by street‐level bureaucrats, inspections that are often resolved by paying “tips.” These encounters make the Chinese feel vulnerable in Africa, although they disagree about why this is so. Some claim they are vulnerable because China lacks a colonial history in Africa, while others put the blame on some migrants’ illicit practices, which have made all Chinese targets for extortion. These contending etiologies reveal competing vernacular theories regarding the relationship between power, ethics, and status. The performance of petty corruption encounters reveals the ambiguities of economic and political power that characterize South‐South exchanges. How to act is therefore a space for experimenting with different possible forms of global Chinese citizenship. [empire, ethics, inequality, migration, corruption, South‐South relations, global China, Tanzania]
“Father released me”:
Authors: HARDIN JESSICA 
Published: April 2019

ABSTRACTIn Samoan Pentecostal churches, ritualized friendships among women are an informal but essential relationship through which churches grow. The mentorship that women provide when a new convert is introduced to church life creates escalating forms of care and obligation, as well as an experience of urgency and acceleration. Converts learn how to construct rupture in their narratives and spiritual practices, which are modeled in peer socialization practices. This period of intense yet temporary mentorship creates a temporality of “repair”—embodied, linguistic, and social practices that restore the convert's identity, which has been disrupted by conversion. This care work compels us to consider the temporalization of care as a future‐making endeavor. [temporality, care, gender, conversion, Pentecostalism, Christianity, Samoa]
Impossible occultists:
Authors: DOOSTDAR ALIREZA 
Published: April 2019

ABSTRACTSince the turn of the 21st century, many middle‐class Iranians have turned to the Islamic tradition of occult sciences to find solutions to difficult life problems. Despite the intensity of their engagements, these Iranians often consider occult practice impossible. Their struggles elucidate differences between practicing a tradition and participating in it: In practice, one's purposes (healing a friend, cursing an enemy, winning a love interest, acquiring wealth) are aligned with internal goods like esoteric insight and realizing connections between the microcosm and macrocosm of God's universe. In participation, purposes and internal goods exist in tension and remain unreconciled. Participation may thus appear as a negation of practice, but it can also emerge as a possibility for learning or creating something new. [occult, tradition, practice, Islam, Iran]
Experts beyond discourse:
Authors: KLOOS DAVID 
Published: April 2019

ABSTRACTIn Malaysia women exercise authority as they combine professional expertise with Islamic knowledge to engage with contentious religious debates. In the context of transformations caused by mass education and mass mediatization, professional experts without Islamic (seminary) education—such as doctors, lawyers, and psychologists—can successfully claim religious authority and establish themselves as part of the Islamic public sphere. This creates possibilities for women. Contemporary cultures of professionalism enable them to challenge long‐standing configurations of religious authority, including the perception that this authority is (primarily or necessarily) male. Their performances, although not without constraints, require an analysis that moves anthropological debates about women's roles and autonomies beyond a Foucauldian concern with discourse and the modes of (self‐)disciplining and resistance associated with it. [religious authority, professionalism, expertise, women, gender, Islam, Malaysia]
Conflictual collaboration:
Authors: POLLERI MAXIME 
Published: April 2019

ABSTRACTIn the aftermath of the 2011 Fukushima nuclear disaster, citizen scientists collectively tracked and monitored residual radioactivity in Japan, legitimizing alternative views to an official assessment of the radioactive contamination. But initial practices of resistance have evolved in collaboration with the official Japanese politics of radioactive governance, supporting hegemonic understandings of radiation danger and normative visions of postdisaster recovery. Civic resources used to resist and reinterpret official narratives of contamination end up reinforcing a state‐sponsored normalization of this disaster. Meanwhile, they become crucial techniques of neoliberal governmentality designed to govern the conduct of populations amid contaminated environments. [nuclear disaster, radioactive contamination, citizen science, governance, neoliberalism, Fukushima, Japan]
REMARKS ON A PROCEDURAL CONDITION FOR THE VOTING PARADOX
Authors: Cato Susumu 
Published: April 2019

ABSTRACTSchwartz [A Procedural Condition Necessary and Sufficient for Cyclic Social Preference, J. Econ. Theory 137 (2007), 688–695] provides a generalization of the voting paradox by using the impotence‐partition condition. This paper aims to clarify his result by providing several remarks. We show that a main result of Schwartz can be strengthened by replacing strong Pareto by weak Pareto. We also discuss how the impotence partition is related to the standard concept of decisiveness, which is widely employed in the literature on social choice.
Mothers' well‐being, parenting attitudes, and home environment: Cumulative risk and parity in early motherhood
Authors: Hickey Grainne , McGilloway Sinead , Leckey Yvonne , Furlong Mairead , Leavy Shane , Stokes Ann , O'Connor Siobhan , Bywater Tracey , Donnelly Michael 
Published: April 2019

AbstractBackgroundThis study explores mothers' wellbeing, experiences, and attitudes and the impact of cumulative demographic and antenatal risks and parity on parenting outcomes. A secondary aim was to assess mother and infant service utilisation.MethodThis study involved an assessment of the baseline characteristics of a sample of mothers (N = 190; Mean age = 31.6 years, SD = 5.4) with young infants (average age = 10.13 weeks, SD = 0.8) living in disadvantaged communities in Ireland.ResultsMothers with more risk factors (e.g., lone and/or teenage parenthood, socioeconomic disadvantage, and low social support) reported significantly higher levels of depression and lower parental self‐efficacy. Observations of the home environment indicated that at‐risk parents engaged in less cognitive stimulation and lower levels of emotional support for their child. The impact of these risk factors differed for primiparous and multiparous mothers.ConclusionsAt‐risk mothers are more susceptible to mental health difficulties and poorer parenting outcomes during the transition to parenthood. This study also provides important comparative insights into experiences of primiparous and multiparous parents. These findings have important implications for practitioners and policy makers, particularly the provision of universal and proportionate supports to prevent and/or interrupt poor parent–child relationships and negative developmental outcomes.
Type 2 diabetes remission: economic evaluation of the DiRECT/Counterweight‐Plus weight management programme within a primary care randomized controlled trial
Authors: Xin Y. , Davies A. , McCombie L. , Briggs A. , Messow C.‐M. , Grieve E. , Leslie W. S. , Taylor R. , Lean M. E. J. 
Published: April 2019

AbstractAimThe Counterweight‐Plus weight management programme achieved 46% remission of Type 2 diabetes at 1 year in the DiRECT trial. We estimated the implementation costs of the Counterweight‐Plus programme and its 1‐year cost‐effectiveness in terms of diabetes remission, compared with usual care, from the UK National Health Service (NHS) perspective.MethodsWithin‐trial total costs included programme set‐up and running costs (practitioner appointment visits, low‐energy formula diet sachets and training), oral anti‐diabetes and anti‐hypertensive medications, and healthcare contacts. Total costs were calculated for aggregated resource use for each participant and 95% confidence intervals (CI) were based on 1000 non‐parametric bootstrap iterations.ResultsOne‐year programme costs under trial conditions were estimated at £1137 per participant (95% CI £1071, £1205). The intervention led to a significant cost‐saving of £120 (95% CI £78, £163) for the oral anti‐diabetes drugs and £14 (95% CI £7.9, £22) for anti‐hypertensive medications compared with the control. Deducting the cost‐savings of all healthcare contacts from the intervention cost resulted an incremental cost of £982 (95% CI £732, £1258). Cost per 1 year of diabetes remission was £2359 (95% CI £1668, £3250).ConclusionsRemission of Type 2 diabetes within 1‐year can be achieved at a cost below the annual cost of diabetes (including complications). Providing a reasonable proportion of remissions can be maintained over time, with multiple medical gains expected, as well as immediate social benefits, there is a case for shifting resources within diabetes care budgets to offer support for people with Type 2 diabetes to attempt remission. (Clinical Trial Registry No.: ISRCTN03267836)
Measured and modelled effect of land‐use change from temperate grassland to Miscanthus on soil carbon stocks after 12 years
Authors: Holder Amanda J. , Clifton‐Brown John , Rowe Rebecca , Robson Paul , Elias Dafydd , Dondini Marta , McNamara Niall P. , Donnison Iain S. , McCalmont Jon P. 
Published: April 2019

AbstractSoil organic carbon (SOC) is an important carbon pool susceptible to land‐use change (LUC). There are concerns that converting grasslands into the C4 bioenergy crop Miscanthus (to meet demands for renewable energy) could negatively impact SOC, resulting in reductions of greenhouse gas mitigation benefits gained from using Miscanthus as a fuel. This work addresses these concerns by sampling soils (0–30 cm) from a site 12 years (T12) after conversion from marginal agricultural grassland into Miscanthus x giganteus and four other novel Miscanthus hybrids. Soil samples were analysed for changes in below‐ground biomass, SOC and Miscanthus contribution to SOC (using a 13C natural abundance approach). Findings are compared to ECOSSE soil carbon model results (run for a LUC from grassland to Miscanthus scenario and continued grassland counterfactual), and wider implications are considered in the context of life cycle assessments based on the heating value of the dry matter (DM) feedstock. The mean T12 SOC stock at the site was 8 (±1 standard error) Mg C/ha lower than baseline time zero stocks (T0), with assessment of the five individual hybrids showing that while all had lower SOC stock than at T0 the difference was only significant for a single hybrid. Over the longer term, new Miscanthus C4 carbon replaces pre‐existing C3 carbon, though not at a high enough rate to completely offset losses by the end of year 12. At the end of simulated crop lifetime (15 years), the difference in SOC stocks between the two scenarios was 4 Mg C/ha (5 g CO2‐eq/MJ). Including modelled LUC‐induced SOC loss, along with carbon costs relating to soil nitrous oxide emissions, doubled the greenhouse gas intensity of Miscanthus to give a total global warming potential of 10 g CO2‐eq/MJ (180 kg CO2‐eq/Mg DM).
Protective effect of sodium–glucose cotransporter 2 inhibitors in patients with rapid renal function decline, stage G3 or G4 chronic kidney disease and type 2 diabetes
Authors: Miyoshi Hideaki , Kameda Hiraku , Yamashita Kumiko , Nakamura Akinobu , Kurihara Yoshio 
Published: April 2019

AbstractAims/IntroductionThe risk of end‐stage kidney disease increases in proportion to the decline in the estimated glomerular filtration rate (eGFR). Although protective effects of sodium–glucose cotransporter 2 inhibitors (SGLT2i) on the eGFR decline were shown in several large‐scale clinical trials, there are no studies investigating patients with a high risk of end‐stage kidney disease. We investigated the efficacy and safety of SGLT2i in advanced renal dysfunction patients (stage G3 or G4 of chronic kidney disease) with a rapid decline in eGFR.Materials and MethodsThis retrospective, longitudinal study enrolled patients with type 2 diabetes who were treated with SGLT2i, and whose eGFR was <60 mL/min/1.73 m2 and had declined >20% over 2 years (%ΔeGFR−2y) before initiating SGLT2i. The primary end‐point was the change in eGFR 2 years after initiation (%ΔeGFR+2y) compared with %ΔeGFR−2y.ResultsA total of 17 patients among 553 patients treated with SGLT2i for ≥2 years were included in the study. The average age, glycated hemoglobin and eGFR at SGLT2i initiation were 68.5 years, 7.3% and 38.3 mL/min/1.73 m2, respectively. %ΔeGFR+2y in patients who were treated with SGLT2i was significantly increased compared with the patients not treated with SGLT2i (2.3 and −21.7%, respectively; P < 0.0001). A multiple regression analysis showed that only the proportion of the rate of eGFR decline was the independent factor associated with improvement of %ΔeGFR+2y. There was no increase in serious adverse events including acute kidney injury.ConclusionsSGLT2i was safe, and prevented further eGFR decline in patients with type 2 diabetes and advanced renal dysfunction.