bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract

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

AbstractBackgroundPlasmodium 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.MethodsWe 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.ResultsAntibodies 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.ConclusionsGrowth 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

Abstract12-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

Abstract
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

AbstractBackgroundMetatranscriptomics 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.ResultsCoMW 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.ConclusionsWe 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

AbstractThe 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.HighlightsThe 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

AbstractThe 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

AbstractThe 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

ABSTRACTGenetic 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

AbstractNatural 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

AbstractBackgroundVariation 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.ResultsWe 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.ConclusionsThese 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

AbstractWhile 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

AbstractHow 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.