bluuebunny/crossref_metadata_2025 huggingface dataset:
Australia, the utility of force and the society-centric battlespace
Authors: Kelton Maryanne , Sullivan Michael , Bienvenue Emily , Rogers Zac
Published: May 2019

Greater uncertainty characterizes Australia's strategic environment. Power transitions in the Indo-Pacific test US primacy at a time when Australia as a major US alliance partner is encountering new asymmetric, society-centric threats from state and non-state actors in what is called the ‘cognitive battlespace’. This is a different kind of warfare, utilizing information as military force. Threats take the form of direct manipulation of interconnected, information-rich environments. Securing the national interest from society-centric threats involving the ‘weaponization of information’, especially of social media and the global corporate platforms upon which they operate, poses considerable strategic, conceptual and technological challenges for Australia's civilian and military cyber-defence agencies. We begin by briefly reviewing the evolution of the strategic culture underpinning Australia's understanding and use of military force, arguing that it is shaped largely by historical insecurity borne from a deeply embedded social sense of isolation and an unquestioned strategic imperative to rely on alliances with ‘great and powerful friends’. We give a brief account of Australia's ‘last wars’ which saw it deploy to Afghanistan, Iraq and Syria and note the evolving cyber-enabled changes to the battlefield. We then argue that the new cyber-threats target the domestic fabric of liberal democracies and market economies, posing risks to all military and civilian institutions as well as weakening citizens' belief in the values which underpin them. Finally, we examine Australia's evolving integration with US networked cyber capabilities, and legislative and bureaucratic reforms to counter foreign political interference campaigns, asking whether they are sufficient.
Start-ups, job creation, and founder characteristics
Authors: Brown J David , Earle John S , Kim Mee Jung , Lee Kyung Min
Published: May 2019

Analyzing data on all US employers in a cohort of entering firms, we document a highly skewed size distribution, such that the largest 5% account for over half of cohort employment at firm birth and more than two-thirds at firm age 7. Analyzing linked survey-administrative data, we find that female, African–American, and younger founders are initially less likely to start large firms. The gender gap persists through firm age 7, while racial and age gaps do not. Education is positively associated with start-up size, except for graduate degrees. Prior entrepreneurship and founding team size are positively associated, but team diversity is not. Specifications with capital and industry controls illuminate roles of financial constraints and sectoral choice.
Prevalence of voriconazole-resistant invasive aspergillosis and its impact on mortality in haematology patients
Authors: Resendiz-Sharpe Agustin , Mercier Toine , Lestrade Pieter P A , van der Beek Martha T , von dem Borne Peter A , Cornelissen Jan J , De Kort Elizabeth , Rijnders Bart J A , Schauwvlieghe Alexander F A D , Verweij Paul E , Maertens Johan , Lagrou Katrien
Published: May 2019

Background

Increasing resistance of Aspergillus fumigatus to triazoles in high-risk populations is a concern. Its impact on mortality is not well understood, but rates from 50% to 100% have been reported.

Objectives

To determine the prevalence of voriconazole-resistant A. fumigatus invasive aspergillosis (IA) and its associated mortality in a large multicentre cohort of haematology patients with culture-positive IA.

Methods

We performed a multicentre retrospective study, in which outcomes of culture-positive haematology patients with proven/probable IA were analysed. Patients were stratified based on the voriconazole susceptibility of their isolates (EUCAST broth microdilution test). Mycological and clinical data were compared, along with survival at 6 and 12 weeks.

Results

We identified 129 A. fumigatus culture-positive proven or probable IA cases; 103 were voriconazole susceptible (79.8%) and 26 were voriconazole resistant (20.2%). All but one resistant case harboured environment-associated resistance mutations in the cyp51A gene: TR34/L98H (13 cases) and TR46/Y121F/T289A (12 cases). Triazole monotherapy was started in 75.0% (97/129) of patients. Mortality at 6 and 12 weeks was higher in voriconazole-resistant cases in all patients (42.3% versus 28.2%, P = 0.20; and 57.7% versus 36.9%, P = 0.064) and in non-ICU patients (36.4% versus 21.6%, P = 0.16; and 54.4% versus 30.7%; P = 0.035), compared with susceptible ones. ICU patient mortality at 6 and 12 weeks was very high regardless of triazole susceptibility (75.0% versus 66.7%, P = 0.99; and 75.0% versus 73.3%, P = 0.99).

Conclusions

A very high prevalence of voriconazole resistance among culture-positive IA haematology patients was observed. The overall mortality at 12 weeks was significantly higher in non-ICU patients with voriconazole-resistant IA compared with voriconazole-susceptible IA.
Online health community experiences of sexual minority women with cancer
Authors: Lee Young Ji , Kamen Charles , Margolies Liz , Boehmer Ulrike
Published: May 2019

Objective

The study sought to explore online health communities (OHCs) for sexual minority women (SMW) with cancer by conducting computational text analysis on posts.

Materials and Methods

Eight moderated OHCs were hosted by the National LGBT Cancer Network from 2013 to 2015. Forty-six SMW wrote a total of 885 posts across the OHCs, which were analyzed using Linguistic Inquiry and Word Count and latent Dirichlet allocation. Pearson correlation was calculated between Linguistic Inquiry and Word Count word categories and participant engagement in the OHCs. Latent Dirichlet allocation was used to derive main topics.

Results

Participants (average age 46 years; 89% white/non-Hispanic) who used more sadness, female-reference, drives, and religion-related words were more likely to post in the OHCs. Ten topics emerged: coping, holidays and vacation, cancer diagnosis and treatment, structure of day-to-day life, self-care, loved ones, physical recovery, support systems, body image, and symptom management. Coping was the most common topic; symptom management was the least common topic.

Discussion

Highly engaged SMW in the OHCs connected to others via their shared female gender identity. Topics discussed in these OHCs were similar to OHCs for heterosexual women, and sexual identity was not a dominant topic. The presence of OHC moderators may have driven participation. Formal comparison between sexual minority and heterosexual women’s OHCs are needed.

Conclusions

Our findings contribute to a better understanding of the experiences of SMW cancer survivors and can inform the development of tailored OHC-based interventions for SMW who are survivors of cancer.
Screening Sugars Can Benefit the Parasitoid Cotesia chilonis (Hymenoptera: Braconidae) Without Benefiting Its Host, Chilo suppressalis (Lepidoptera: Crambidae)
Authors: Tian Jun-Ce , Chen Yang , Shelton Anthony M , Zheng Xu-Song , Xu Hong-Xing , Lu Zhong-Xian
Published: May 2019

Most adult parasitoids depend on carbohydrate-rich food as an energy source for longevity, fecundity, and mobility. Thus, providing sugars has been proposed as a technique to maximize the biological control efficacy of parasitoids. However, the sugars provided for parasitoids need to be carefully selected because herbivore hosts might also benefit. Here we explore the effects of 12 naturally occurring sugars on the longevity and fecundity of the rice pest, Chilo suppressalis, and the longevity of its parasitoid, Cotesia chilonis, as well as the effect of sugars on sugar consumption of C. chilonis. Results showed that none of the tested sugars significantly impacted the longevity of C. suppressalis, but fructose, glucose, maltose, and sucrose significantly increased its fecundity. The longevity of C. chilonis was significantly increased when fed fructose, glucose, sucrose, maltose, trehalose, and melezitose. Our data suggest that C. chilonis consumed larger quantities of glucose, fructose, and sucrose followed by maltose, melezitose, and trehalose and the longevity of C. chilonis was positively correlated to sugar consumption. Our data also suggest that the herbivore C. suppressalis and its parasitoid C. chilonis responded differently to trehalose and melezitose. Although additional studies are needed, our data suggest that these sugars could be considered as candidate components for sugar sprays to enhance the activity and efficacy of C. chilonis, but without benefiting its pest host.
In the mood for learning? How the thought collectives of designers and engineers co-create innovations
Authors: Punstein Anna Mateja , Glückler Johannes
Published: May 2019

In this article, we argue that learning across fields depends on the social construction of (in)commensurability rather than on the ‘distance’ between bodies of knowledge. Building on Fleck’s (1935) original concept of thought collectives, we examine how two professions, engineers and industrial designers, often fail yet sometimes succeed to make their knowledge commensurable and co-create innovation. Empirically, we draw on qualitative fieldwork in Baden-Württemberg to identify three types of relations between industrial design and technical innovation: separation (design without designers), sequential collaboration (shallow and aesthetic design), and co-creation (pervasive design). We extend the concept of inter-collective learning geographically and explore how place and various scales of space affect local thought styles, the retention of thought solidarity and the emergence of new temporary thought collectives.
Sodium Ascorbate as a Potential Toxicant in Attractive Sugar Baits for Control of Adult Mosquitoes (Diptera: Culicidae) and Sand Flies (Diptera: Psychodidae)
Authors: McDermott Emily G , Morris Erin K , Garver Lindsey S
Published: May 2019

Attractive toxic sugar baits (ATSBs) can be an effective vector control tool, especially in areas where aerial or aquatic applications of pesticides are undesirable or impractical. In general, there is a need to develop novel or alternative insecticides for vector control, and there is a demand from consumers for more ‘natural’ pest control products. Sodium ascorbate (SA) is a naturally occurring antioxidant compound, found in fruits and vegetables, and is available commercially in the United States as a food additive and supplement. In this study, we continuously exposed groups of adult Aedes aegypti (L.), Anopheles stephensi Liston (Diptera: Culicidae), Phlebotomus papatasi Scopoli, and Lutzomyia longipalpis (Lutz & Neiva; Diptera: Psychodidae) to ATSBs containing SA in concentrations of 6, 8, 10, and 20%, and tracked their mortality over 10 d. We also exposed insects to a 20% SA–ATSB on a single day to determine the effect of a single exposure to the bait on mortality. Concentrations of ≥8% SA significantly reduced survival of both mosquito species over 10 d compared with sugar-fed controls. Sand fly mortality was inconsistent. A single exposure to 20% SA significantly reduced the survival of An. stephensi. Mosquitoes exposed to SA exhibited elevated catalase levels and cell death. The use of SA in ATSBs may be most effective in areas where sugar sources are scarce, and where mosquito species frequently sugar-feed. SA sugar baits may be a particularly attractive option for the general public looking to control mosquito populations using ‘natural’ alternatives to synthetic insecticides.
Distances and parallax bias in Gaia DR2
Authors: Schönrich Ralph , McMillan Paul , Eyer Laurent
Published: May 2019

We derive Bayesian distances for all stars in the radial velocity sample of Gaia DR2, and use the statistical method of Schönrich, Binney & Asplund to validate the distances and test the Gaia parallaxes. In contrast to other methods, which rely on special sources, our method directly tests the distances to all stars in our sample. We find clear evidence for a near-linear trend of distance bias f with distance s, proving a parallax offset δp. On average, we find ${\delta _{\rm p}}= -0.054 \, {\rm mas}$ (parallaxes in Gaia DR2 need to be increased) when accounting for the parallax uncertainty underestimate in the Gaia set (compared to ${\delta _{\rm p}}= -0.048 \, {\rm mas}$ on the raw parallax errors), with negligible formal error and a systematic uncertainty of about $0.006 \, {\rm mas}$. The value is in concordance with results from asteroseismic measurements, but differs from the much lower bias found on quasar samples. We further use our method to compile a comprehensive set of quality cuts in colour, apparent magnitude, and astrometric parameters. Lastly, we find that for this sample δp appears to strongly depend on σp (when including the additional $0.043 \, {\rm mas}$) with a statistical confidence far in excess of 10σ and a proportionality factor close to 1, though the dependence varies somewhat with σp. Correcting for the σp dependence also resolves otherwise unexplained correlations of the offset with the number of observation periods ${n_{\rm vis}}$ and ecliptic latitude. Every study using Gaia DR2 parallaxes/distances should investigate the sensitivity of its results on the parallax biases described here and – for fainter samples – in the DR2 astrometry paper.
Painting with baryons: augmenting N-body simulations with gas using deep generative models
Authors: Tröster Tilman , Ferguson Cameron , Harnois-Déraps Joachim , McCarthy Ian G
Published: May 2019

Running hydrodynamical simulations to produce mock data of large-scale structure and baryonic probes, such as the thermal Sunyaev–Zeldovich (tSZ) effect, at cosmological scales is computationally challenging. We propose to leverage the expressive power of deep generative models to find an effective description of the large-scale gas distribution and temperature. We train two deep generative models, a variational auto-encoder and a generative adversarial network, on pairs of matter density and pressure slices from the BAHAMAS hydrodynamical simulation. The trained models are able to successfully map matter density to the corresponding gas pressure. We then apply the trained models on 100 lines of sight from SLICS, a suite of N-body simulations optimized for weak lensing covariance estimation, to generate maps of the tSZ effect. The generated tSZ maps are found to be statistically consistent with those from BAHAMAS. We conclude by considering a specific observable, the angular cross-power spectrum between the weak lensing convergence and the tSZ effect and its variance, where we find excellent agreement between the predictions from BAHAMAS and SLICS, thus enabling the use of SLICS for tSZ covariance estimation.
Fluorescent C ii* 1335Å emission spectroscopically resolved in a galaxy at z = 5.754
Authors: Bosman Sarah E I , Laporte Nicolas , Ellis Richard S , Ouchi Masami , Harikane Yuichi
Published: May 2019

We report the discovery of the first spectroscopically resolved C ii/C ii* 1334, 1335 doublet in the Lyman-break galaxy J0215–0555 at zLyα = 5.754. The separation of the resonant and fluorescent emission channels was possible thanks to the large redshift of the source and long integration time, as well as the small velocity width of the feature, 0.6 ± 0.2Å. We model this emission and find that at least two components are required to reproduce the combination of morphologies of C ii* emission, C ii absorption and emission, and Lyman-α emission from the object. We suggest that the close alignment between the fluorescence and Lyman-α emission could indicate an ionization escape channel within the object. While the faintness of such a C ii/C ii* doublet makes it prohibitively difficult to pursue for similar systems with current facilities, we suggest it can become a valuable porosity diagnostic in the era of JWST and the upcoming generations of ELTs.
Profiling the genome-wide landscape of tandem repeat expansions
Authors: Mousavi Nima , Shleizer-Burko Sharona , Yanicky Richard , Gymrek Melissa
Published: May 2019

Tandem repeat (TR) expansions have been implicated in dozens of genetic diseases, including Huntington’s Disease, Fragile X Syndrome, and hereditary ataxias. Furthermore, TRs have recently been implicated in a range of complex traits, including gene expression and cancer risk. While the human genome harbors hundreds of thousands of TRs, analysis of TR expansions has been mainly limited to known pathogenic loci. A major challenge is that expanded repeats are beyond the read length of most next-generation sequencing (NGS) datasets and are not profiled by existing genome-wide tools. We present GangSTR, a novel algorithm for genome-wide genotyping of both short and expanded TRs. GangSTR extracts information from paired-end reads into a unified model to estimate maximum likelihood TR lengths. We validate GangSTR on real and simulated data and show that GangSTR outperforms alternative methods in both accuracy and speed. We apply GangSTR to a deeply sequenced trio to profile the landscape of TR expansions in a healthy family and validate novel expansions using orthogonal technologies. Our analysis reveals that healthy individuals harbor dozens of long TR alleles not captured by current genome-wide methods. GangSTR will likely enable discovery of novel disease-associated variants not currently accessible from NGS.
High-protein diet with renal hyperfiltration is associated with rapid decline rate of renal function: a community-based prospective cohort study
Authors: Jhee Jong Hyun , Kee Youn Kyung , Park Seohyun , Kim Hyoungnae , Park Jung Tak , Han Seung Hyeok , Kang Shin-Wook , Yoo Tae-Hyun
Published: May 2019

Background

The effect of a high-protein diet with renal hyperfiltration (RHF) on decline of kidney function has rarely been explored. We investigated the association between a high-protein diet, RHF and declining kidney function.

Methods

A total of 9226 subjects from the Korean Genome and Epidemiology Study, a community-based prospective study (2001–14), were enrolled and classified into quartiles according to daily amount of protein intake based on food frequency questionnaires. RHF was defined as estimated glomerular filtration rate (eGFR) with residuals of >95th percentile after adjustment for age, sex, history of hypertension or diabetes, height and weight. Rapid decline of renal function was defined as decline rate of eGFR >3 mL/min/1.73 m2/year.

Results

The relative risk of RHF was 3.48-fold higher in the highest than in the lowest protein intake quartile after adjustment for confounding factors [95% confidence interval (CI) 1.39–8.71]. The mean eGFR decline rate was faster as quartiles of protein intake increased. Furthermore, the highest quartile was associated with 1.32-fold increased risk of rapid eGFR decline (95% CI 1.02–1.73). When subjects were divided into two groups with or without RHF, the highest quartile was associated with a rapid decline in renal function only in RHF subjects (odds ratio 3.35; 95% CI 1.07–10.51). The sensitivity analysis using the Korean National Health and Nutrition Examination Survey (2008–15) data with 40 113 subjects showed that higher quartile was associated with increased risk for RHF.

Conclusions

A high-protein diet increases the risk of RHF and a rapid renal function decline in the general population. These findings suggest that a high-protein diet has a deleterious effect on renal function in the general population.
Polysomy is associated with poor outcome in 1p/19q codeleted oligodendroglial tumors
Authors: Chen Hui , Thomas Cheddhi , Munoz Felipe Andres , Alexandrescu Sanda , Horbinski Craig M , Olar Adriana , McGuone Declan , Camelo-Piragua Sandra , Wang Lu , Pentsova Elena , Phillips Joanna , Aldape Kenneth , Chen Wen , Iafrate A John , Chi Andrew S , Zagzag David , Golfinos John G , Placantonakis Dimitris G , Rosenblum Marc , Ohman-Strickland Pamela , Hameed Meera , Snuderl Matija
Published: May 2019

Background

Chromosomal instability is associated with earlier progression in isocitrate dehydrogenase (IDH)–mutated astrocytomas. Here we evaluated the prognostic significance of polysomy in gliomas tested for 1p/19q status.

Methods

We analyzed 412 histologic oligodendroglial tumors with use of 1p/19q testing at 8 institutions from 1996 to 2013; fluorescence in situ hybridization (FISH) for 1p/19q was performed. Polysomy was defined as more than two 1q and 19p signals in cells. Tumors were divided into groups on the basis of their 1p/19q status and polysomy and were compared for progression-free survival (PFS) and overall survival (OS).

Results

In our cohort, 333 tumors (81%) had 1p/19q loss; of these, 195 (59%) had concurrent polysomy and 138 (41%) lacked polysomy, 79 (19%) had 1p/19q maintenance; of these, 30 (38%) had concurrent polysomy and 49 (62%) lacked polysomy. In agreement with prior studies, the group with 1p/19q loss had significantly better PFS and OS than did the group with 1p/19q maintenance (P < 0.0001 each). Patients with 1p/19q loss and polysomy showed significantly shorter PFS survival than patients with 1p/19q codeletion only (P < 0.0001), but longer PFS and OS than patients with 1p/19q maintenance (P < 0.01 and P < 0.0001). There was no difference in survival between tumors with >30% polysomic cells and those with <30% polysomic cells. Polysomy had no prognostic significance on PFS or OS in patients with 1p/19q maintenance.

Conclusions

The presence of polysomy in oligodendroglial tumors with codeletion of 1p/19q predicts early recurrence and short survival in patients with 1p/19q codeleted tumors.
Current status of PET imaging in neuro-oncology
Authors: Galldiks Norbert , Lohmann Philipp , Albert Nathalie L , Tonn Jörg C , Langen Karl-Josef
Published: May 2019

Over the past decades, a variety of PET tracers have been used for the evaluation of patients with brain tumors. For clinical routine, the most important clinical indications for PET imaging in patients with brain tumors are the identification of neoplastic tissue including the delineation of tumor extent for the further diagnostic and therapeutic management (ie, biopsy, resection, or radiotherapy planning), the assessment of response to a certain anticancer therapy including its (predictive) effect on the patients’ outcome and the differentiation of treatment-related changes (eg, pseudoprogression and radiation necrosis) from tumor progression at follow-up. To serve medical professionals of all disciplines involved in the diagnosis and care of patients with brain tumors, this review summarizes the value of PET imaging for the latter-mentioned 3 clinically relevant indications in patients with glioma, meningioma, and brain metastases.
Contribution of work ability and core self-evaluations to worker health
Authors: Coomer K , Houdmont J
Published: May 2019

Background

Work ability (WA) concerns the capacity to manage job demands in relation to physical and psychological resources. Core self-evaluations (CSE) refer to a composite personality construct comprising self-esteem, locus of control, self-efficacy and emotional stability traits. Studies have shown the independent contribution of WA and CSE to work outcomes, yet none has explored their additive contribution, when applied together, to identify workers at risk of impaired health and performance-related outcomes.

Aims

The aim was to explore the contribution of WA and CSE to explaining variance in psychological distress and work engagement in a sample of UK manufacturing sector workers.

Methods

A self-report questionnaire containing validated measures of WA, CSE, psychological distress and work engagement was administered to employees in four UK manufacturing organizations. Bivariate correlations were calculated to identify patterns of relationships between the variables and hierarchical linear regression analyses performed to examine the incremental contribution of WA and CSE to the target variables.

Results

Analyses were conducted on data contributed by 311 workers (21% response rate). WA accounted for around one-quarter of the variance in psychological distress and around one-fifth of the variance in work engagement. The addition of CSE explained a further 10% (psychological distress) and 7% (work engagement) of the variance.

Conclusions

These exploratory findings suggest that WA and CSE might be useful in the identification of workers at risk of poor psychological well-being and work effectiveness in UK manufacturing. Longitudinal sector-representative studies are required to establish the constructs’ predictive power.
Antibody Reactivity to Merozoite Antigens in Ghanaian Adults Correlates With Growth Inhibitory Activity Against Plasmodium falciparum in Culture
Authors: Mensah-Brown Henrietta E , Aspeling-Jones Harvey , Delimini Rupert K , Asante Kwaku Poku , Amlabu Emmanuel , Bah Saikou Y , Beeson James G , Wright Gavin J , Conway David J , Awandare Gordon A
Published: May 2019

Background

Plasmodium falciparum uses a repertoire of merozoite-stage proteins for invasion of erythrocytes. Antibodies against some of these proteins halt the replication cycle of the parasite by preventing erythrocyte invasion and are implicated as contributors to protective immunity against malaria.

Methods

We assayed antibody reactivity against a panel of 9 recombinant antigens based on erythrocyte-binding antigen (EBA) and reticulocyte-like homolog (Rh) proteins in plasma from children with malaria and healthy adults residing in 3 endemic areas in Ghana using enzyme-linked immunosorbent assay. Purified immunoglobulin (Ig)G from adult plasma samples was also tested for invasion inhibition against 7 different P falciparum culture lines, including clinical isolates.

Results

Antibodies against the antigens increased in an age-dependent manner in children. Breadth of reactivity to the different antigens was strongly associated with in vitro parasite growth inhibitory activity of IgG purified from the adults. The strongest predictors of breadth of antibody reactivity were age and transmission intensity, and a combination of reactivities to Rh2, Rh4, and Rh5 correlated strongly with invasion inhibition.

Conclusions

Growth inhibitory activity was significantly associated with breadth of antibody reactivity to merozoite antigens, encouraging the prospect of a multicomponent blood-stage vaccine.
12-Hydroxy-Jasmonoyl-l-Isoleucine Is an Active Jasmonate That Signals through CORONATINE INSENSITIVE 1 and Contributes to the Wound Response in Arabidopsis
Authors: Poudel Arati N , Holtsclaw Rebekah E , Kimberlin Athen , Sen Sidharth , Zeng Shuai , Joshi Trupti , Lei Zhentian , Sumner Lloyd W , Singh Kamlendra , Matsuura Hideyuki , Koo Abraham J
Published: May 2019

12-hydroxy-jasmonoyl-isoleucine (12OH-JA-Ile) is a metabolite in the catabolic pathway of the plant hormone jasmonate, and is synthesized by the cytochrome P450 subclade 94 enzymes. Contrary to the well-established function of jasmonoyl-isoleucine (JA-Ile) as the endogenous bioactive form of jasmonate, the function of 12OH-JA-Ile is unclear. Here, the potential role of 12OH-JA-Ile in jasmonate signaling and wound response was investigated. Exogenous application of 12OH-JA-Ile mimicked several JA-Ile effects including marker gene expression, anthocyanin accumulation and trichome induction in Arabidopsis thaliana. Genome-wide transcriptomics and untargeted metabolite analyses showed large overlaps between those affected by 12OH-JA-Ile and JA-Ile. 12OH-JA-Ile signaling was blocked by mutation in CORONATINE INSENSITIVE 1. Increased anthocyanin accumulation by 12OH-JA-Ile was additionally observed in tomato and sorghum, and was disrupted by the COI1 defect in tomato jai1 mutant. In silico ligand docking predicted that 12OH-JA-Ile can maintain many of the key interactions with COI1-JAZ1 residues identified earlier by crystal structure studies using JA-Ile as ligand. Genetic alternation of jasmonate metabolic pathways in Arabidopsis to deplete both JA-Ile and 12OH-JA-Ile displayed enhanced jasmonate deficient wound phenotypes and was more susceptible to insect herbivory than that depleted in only JA-Ile. Conversely, mutants overaccumulating 12OH-JA-Ile showed intensified wound responses compared with wild type with similar JA-Ile content. These data are indicative of 12OH-JA-Ile functioning as an active jasmonate signal and contributing to wound and defense response in higher plants.
Development of a method for measuring rare earth elements in the environment for future experiments with gadolinium-loaded detectors
Authors: Ito S , Okada T , Takaku Y , Harada M , Ikeda M , Kishimoto Y , Koshio Y , Nakahata M , Nakajima Y , Sekiya H
Published: May 2019

Demand to use gadolinium (Gd) in detectors is increasing in the field of elementary particle physics, especially in neutrino measurements and dark matter searches. Large amounts of Gd are used in these experiments. To assess the impact of Gd on the environment it is becoming important to measure the baseline concentrations of Gd. Such measurement, however, is not easy due to interference by other elements. In this paper a method for measuring the concentrations of rare earth elements, including Gd, is proposed. In the method, inductively coupled plasma-mass spectrometry is utilized after collecting the dissolved elements in chelating resin. Results of the ability to detect anomalous concentrations of rare earth elements in river water samples in the Kamioka and Toyama areas are also reported.
To assemble or not to resemble – A validated Comparative Metatranscriptomics Workflow (CoMW)
Authors: Anwar Muhammad Zohaib , Lanzen Anders , Bang-Andreasen Toke , Jacobsen Carsten Suhr
Published: May 2019

Background

Metatranscriptomics has been used widely for investigation and quantification of microbial communities’ activity in response to external stimuli. By assessing the genes expressed, metatranscriptomics provide an understanding of the interactions between different major functional guilds and the environment. Here, we presentde-novoassembly-based Comparative Metatranscriptomics Workflow (CoMW) implemented in a modular, reproducible structure, significantly improving the annotation and quantification of metatranscriptomes. Metatranscriptomics typically utilize short sequence reads, which can either be directly aligned to external reference databases (“assembly-free approach”) or first assembled into contigs before alignment (“assembly-based approach”). We also compare CoMW (assembly-based implementation) with assembly-free alternative workflow, using simulated and real-world metatranscriptomes from Arctic and Temperate terrestrial environments. We evaluate their accuracy in precision and recall using generic and specialized hierarchical protein databases.

Results

CoMW provided significantly fewer false positives resulting in more precise identification and quantification of functional genes in metatranscriptomes. Using the comprehensive database M5nr, the assembly-based approach identified genes with only 0.6% false positives at thresholds ranging from inclusive to stringent compared to the assembly-free approach yielding up to 15% false positives. Using specialized databases (Carbohydrate Active-enzyme and Nitrogen Cycle), the assembly-based approach identified and quantified genes with 3-5x less false positives. We also evaluated the impact of both approaches on real-world datasets.

Conclusions

We present an open sourcede-novoassembly-based Comparative Metatranscriptomics Workflow (CoMW). Our benchmarking findings support the argument of assembling short reads into contigs before alignment to a reference database, since this provides higher precision and minimizes false positives.
The Dream Catcher experiment: Blinded analyses disconfirm markers of dreaming consciousness in EEG spectral power
Authors: Wong William , Noreika Valdas , Móró Levente , Revonsuo Antti , Windt Jennifer , Valli Katja , Tsuchiya Naotsugu
Published: May 2019

The Dream Catcher test defines the criteria for a genuine discovery of the neural constituents of phenomenal consciousness. Passing the test implies that some patterns of purely brain-based data directly correspond to the subjective features of phenomenal experience, which would help to bridge the explanatory gap between consciousness and brain. Here, we conducted the Dream Catcher test for the first time in a graded and simplified form, capturing its core idea. The experiment involved a Data Team, who measured participants’ brain activity during sleep and collected dream reports, and a blinded Analysis Team, who was challenged to predict better than chance, based solely on brain measurements, whether or not a participant had a dream experience. Using a serial-awakening paradigm, the Data Team prepared 54 one-minute polysomnograms of NREM sleep—27 of dreamful sleep (3 from each of the 9 participants) and 27 of dreamless sleep—redacting from them all associated participant and dream information. The Analysis Team attempted to classify each recording as either dreamless or dreamful using an unsupervised machine learning classifier, based on hypothesis-driven, extracted features of EEG spectral power and electrode location. The procedure was repeated over five iterations with a gradual removal of blindness. At no level of blindness did the Analysis Team perform significantly better than chance, suggesting that EEG spectral power does not carry any signatures of phenomenal consciousness. Furthermore, we demonstrate an outright failure to replicate key findings of recently reported correlates of dreaming consciousness.

Highlights

The first reported attempt of the Dream Catcher test.

The correlates of conscious experience may not lie in EEG spectral power.

Reported markers of NREM dreaming consciousness misperformed in a blinded setting.

Those markers also could not be confirmed in an unblinded setting.
Rock the Chalk: A five-year comparative analysis of a large microbiology lecture course reveals improved outcomes of chalk-talk compared to PowerPoint
Authors: Waters Christopher M.
Published: May 2019

The rise of electronic assisted presentation programs such as PowerPoint in undergraduate large lecture biology classes has displaced more traditional hand-drawn lectures such as the blackboard or overhead projectors, referred here as “chalk-talk” approaches. But which method is more effective in a large lecture microbiology classroom is unclear. Here I present data from a large microbial genetics lecture course taken during a five-year span comparing PowerPoint to chalk-talk lecturing methods. The results indicate that the chalk-talk approach was preferred by the students and rated higher in all measured metrics including course enjoyment, learning of key concepts, and course outcomes.
Morphology and development of the Portuguese man of war,Physalia physalis
Authors: Munro Catriona , Vue Zer , Behringer Richard R. , Dunn Casey W.
Published: May 2019

The Portuguese man of war,Physalia physalis, is a siphonophore that uses a gas-filled float as a sail to catch the wind. It is one of the most conspicuous, but poorly understood members of the pleuston, a community of organisms that occupy a habitat at the sea-air interface. The development, morphology, and colony organization ofP. physalisis very different from all other siphonophores. Here, we propose a framework for homologizing the axes with other siphonophores, and also suggest that the tentacle bearing zooids should be called tentacular palpons. We also look at live and fixed larval and non-reproductively mature juvenile specimens, and use optical projection tomography to build on existing knowledge about the morphology and development of this species. Previous descriptions ofP. physalislarvae, especially descriptions of budding order, were often framed with the mature colony in mind. However, we use the simpler organization of larvae and the juvenile specimens to inform our understanding of the morphology, budding order, and colony organization in the mature specimen. Finally, we review what is known about the ecology and lifecyle ofP. physalis.
Reconstruction of networks with direct and indirect genetic effects
Authors: Kruijer Willem , Behrouzi Pariya , Bustos-Korts Daniela , Rodríguez-Álvarez María Xosé , Mahmoudi Seyed Mahdi , Yandell Brian , Wit Ernst , van Eeuwijk Fred A.
Published: May 2019

Genetic variance of a phenotypic trait can originate from direct genetic effects, or from indirect effects, i.e., through genetic effects on other traits, affecting the trait of interest. This distinction is often of great importance, for example when trying to improve crop yield and simultaneously controlling plant height. As suggested by Sewall Wright, assessing contributions of direct and indirect effects requires knowledge of (1) the presence or absence of direct genetic effects on each trait, and (2) the functional relationships between the traits. Because experimental validation of such relationships is often unfeasible, it is increasingly common to reconstruct them using causal inference methods. However, most of the current methods require all genetic variance to be explained by a small number of QTLs with fixed effects. Only few authors considered the ‘missing heritability’ case, where contributions of many undetectable QTLs are modelled with random effects. Usually, these are treated as nuisance terms, that need to be eliminated by taking residuals from a multi-trait mixed model (MTM). But fitting such MTM is challenging, and it is impossible to infer the presence of direct genetic effects. Here we propose an alternative strategy, where genetic effects are formally included in the graph. This has important advantages: (1) genetic effects can be directly incorporated in causal inference, implemented via our PCgen algorithm, which can analyze many more traits and (2) we can test the existence of direct genetic effects and improve the orientation of edges between traits. Finally, we show that reconstruction is much more accurate if individual plant or plot data are used, instead of genotypic means. We have implemented the PCgen-algorithm in the R-package pcgen.
TGFβ drives mitochondrial dysfunction in peripheral blood NK cells during metastatic breast cancer
Authors: Slattery Karen , Zaiatz-Bittencourt Vanessa , Woods Elena , Brennan Kiva , Marks Sam , Chew Sonya , Conroy Michael , Goggin Caitriona , Kennedy John , Finlay David K. , Gardiner Clair M.
Published: May 2019

Natural Killer (NK) cells provide important protection from cancer and are a key requirement for particular immunotherapies. In activated NK cells, a metabolic response towards increased glycolysis and oxidative phosphorylation is crucial for NK cell effector functions. However, there is accumulating evidence that NK cells become dysfunctional during chronic inflammatory diseases, such as human breast cancer. This dysfunction is apparent in peripheral blood NK cells and can impact on normal NK cell immune responses and their effective targeting during immunotherapy. Herein, we demonstrate that prolonged cytokine stimulation combined with metabolic restriction, through inhibition of mTORC1, is sufficient to induce persistent dysfunction in human NK cells. TGFβ, also restricted NK cell metabolism and promoted persistent NK cell dysfunction. NK cells from patients with metastatic breast cancer had profound metabolic defects in glycolysis and mitochondrial function, and clear structural differences in NK cell mitochondrial morphology. Importantly, blocking elevated TGFβ improved readouts of metabolism and restored IFNγ production in patient NK cells.
A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants
Authors: McInerney Tim W , Fulton-Howard Brian , Patterson Christopher , Paliwal Devashi , Jermiin Lars S , Patel Hardip R , Pa Judy , Swerdlow Russell H , Goate Alison , Easteal Simon , Andrews Shea J ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: May 2019

Background

Variation in mitochondrial DNA (mtDNA) identified by genotyping microarrays or by sequencing only hypervariable regions of the genome may be insufficient to reliably assign mitochondrial genomes to phylogenetic lineages or haplogroups. This lack of resolution can limit functional and clinical interpretation of a substantial body of existing mtDNA data. To address this limitation, we developed and evaluated a method for imputing missing mtDNA single nucleotide variants (mtSNVs) that uses a large reference alignment of complete mtDNA sequences. The method and reference alignment are combined into a pipeline, which we call MitoImpute.

Results

We aligned the sequences of 36,960 complete human mitochondrial genomes downloaded from GenBank, filtered and controlled for quality. These sequences were reformatted for use in imputation software, IMPUTE2. We assessed the imputation accuracy of MitoImpute by measuring haplogroup and genotype concordance in data from the 1,000 Genomes Project and the Alzheimer’s Disease Neuroimaging Initiative (ADNI). The mean improvement of haplogroup assignment in the 1,000 Genomes samples was 42.7% (Matthew’s correlation coefficient = 0.64). In the ADNI cohort, we imputed missing single nucleotide variants.

Conclusions

These results show that our reference alignment and panel can be used to impute missing mtSNVs in exiting data obtained from using microarrays, thereby broadening the scope of functional and clinical investigation of mtDNA. This improvement may be particularly useful in studies where participants have been recruited over time and mtDNA data obtained using different methods, enabling better integration of early data collected using less accurate methods with more recent sequence data.
Two different epigenetic pathways detected in wild three-spined sticklebacks are involved in salinity adaptation
Authors: Heckwolf Melanie J. , Meyer Britta S. , Häsler Robert , Höppner Marc P. , Eizaguirre Christophe , Reusch Thorsten B. H.
Published: May 2019

While environmentally inducible epigenetic marks are discussed as one mechanism of transgenerational plasticity, environmentally stable epigenetic marks emerge randomly. When resulting in variable phenotypes, stable marks can be targets of natural selection analogous to DNA sequence-based adaptation processes. We studied both postulated pathways in natural populations of three-spined sticklebacks (Gasterosteus aculeatus) and sequenced their methylomes and genomes across a salinity cline. Consistent with local adaptation, populations showed differential methylation (pop-DMS) at genes enriched for osmoregulatory processes. In a two-generation experiment, 62% of these pop-DMS were insensitive to salinity manipulation, suggesting that they could be stable targets for natural selection. Two-thirds of the remaining inducible pop-DMS became more similar to patterns detected in wild populations from the corresponding salinity, and this pattern accentuated over consecutive generations, indicating a mechanism of adaptive transgenerational plasticity. Natural DNA methylation patterns can thus be attributed to two epigenetic pathways underlying the rapid emergence of adaptive phenotypes in the face of environmental change.
Resting brain fluctuations are intrinsically coupled to visual response dynamics
Authors: Belloy Michaël E. , Billings Jacob , Abbas Anzar , Kashyap Amrit , Pan Wen-ju , Hinz Rukun , Vanreusel Verdi , Van Audekerke Johan , Van der Linden Annemie , Keilholz Shella D. , Verhoye Marleen , Keliris Georgios A.
Published: May 2019

How do intrinsic brain dynamics interact with processing of external sensory stimuli? We sought new insights using functional (f)MRI to track spatiotemporal activity patterns at the whole brain level in lightly anesthetized mice, during both resting conditions and visual stimulation trials. Our results provide evidence that quasiperiodic patterns (QPPs) govern mouse resting brain dynamics. QPPs captured the temporal alignment of global brain fluctuations, anti-correlation of the Default Mode (DMN)- and Task Positive (TPN)-like networks, and activity in neuromodulatory nuclei of the reticular formation. While visual stimulation could trigger a transient spatiotemporal pattern highly similar to intrinsic QPPs, global signal fluctuations and QPPs during rest periods could explain variance in the following visual responses. QPPs and the global signal thus appeared to capture a common arousal-related brain-state fluctuation, orchestrated through neuromodulation. Our findings provide new frontiers to understand the neural processes that shape functional brain states and modulate sensory input processing.
A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: Probing the binding pathway of dasatinib to Src-kinase
Authors: Sohraby Farzin , Moghadam Mostafa Javaheri , Aliyar Masoud , Aryapour Hassan
Published: May 2019

Small molecules such as metabolites and drugs play essential roles in biological processes and pharmaceutical industry. Knowing their interactions with biomacromolecular targets demands a deep understanding of binding mechanisms. Dozens of papers have suggested that discovering of the binding event by means of conventional unbiased molecular dynamics (MD) simulation urges considerable amount of computational resources, therefore, only one who holds a cluster or a supercomputer can afford such extensive simulations. Thus, many researchers who do not own such resources are reluctant to take the benefits of running unbiased molecular dynamics simulation, in full atomistic details, when studying a ligand binding pathway. Many researchers are impelled to be content with biased molecular dynamics simulations which seek its validation due to its intrinsic preconceived framework. In this work, we have presented a workable stratagem to encourage everyone to perform unbiased (unguided) molecular dynamics simulations, in this case a protein-ligand binding process, by typical desktop computers and so achieve valuable results in nanosecond time scale. Here, we have described a dynamical binding’s process of an anticancer drug, the dasatinib, to the c-Src kinase in full atomistic details for the first time, without applying any biasing force or potential which may lead the drug to artificial interactions with the protein. We have attained multiple independent binding events which occurred in the nano-second timescales, surprisingly as little as ∼30 ns. Both the protonated and deprotonated forms of the dasatinib reached the crystallographic binding mode without having any major intermediate state during induction.