bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of American Indians and Alaska Natives in Public Health Data Sets: A Comparison Using Linkage-Corrected Washington State Death Certificates
Authors: Joshi Sujata , Warren-Mears Victoria 
Published: April 2019

Context:
Efforts to address disparities experienced by American Indians/Alaska Natives (AI/ANs) have been hampered by a lack of accurate and timely health data. One challenge to obtaining accurate data is determining who “counts” as AI/AN in health and administrative data sets.

Objective:
To compare the effects of definition and misclassification of AI/AN on estimates of all-cause and cause-specific mortality for AI/AN in Washington during 2015-2016.

Design:
Secondary analysis of death certificate data from Washington State. Data were corrected for AI/AN racial misclassification through probabilistic linkage with the Northwest Tribal Registry. Counts and age-adjusted rates were calculated and compared for 6 definitions of AI/AN. Comparisons were made with the non-Hispanic white population to identify disparities.

Setting:
Washington State.

Participants:
AI/AN and non-Hispanic white residents of Washington State who died in 2015 and 2016.

Main Outcome Measures:
Counts and age-adjusted rates for all-cause mortality and mortality from cardiovascular diseases, cancer, and unintentional injuries.

Results:
The most conservative single-race definition of AI/AN identified 1502 AI/AN deaths in Washington State during 2015-2016. The least conservative multiple-race definition of AI/AN identified 2473 AI/AN deaths, with an age-adjusted mortality rate that was 48% higher than the most conservative definition. Correcting misclassified AI/AN records through probabilistic linkage significantly increased mortality rate estimates by 11%. Regardless of definition used, AI/AN in Washington had significantly higher all-cause mortality rates than non-Hispanic whites in the state.

Conclusions:
Reporting single-race versus multiple-race AI/AN had the most consequential effect on mortality counts and rates. Correction of misclassified AI/AN records resulted in small but statistically significant increases in AI/AN mortality rates. Researchers and practitioners should consult with AI/AN communities on the complex issues surrounding AI/AN identity to obtain the best method for identifying AI/AN in health data sets.
Modulating dream experience: Noninvasive brain stimulation over the sensorimotor cortex reduces dream movement
Authors: Noreika Valdas , Windt Jennifer M. , Kern Markus , Valli Katja , Salonen Tiina , Parkkola Riitta , Revonsuo Antti , Karim Ahmed A. , Ball Tonio , Lenggenhager Bigna 
Published: April 2019

AbstractRecently, cortical correlates of specific dream contents have been reported, such as the activation of the sensorimotor cortex during dreamed hand clenching. Yet, the causal mechanisms underlying specific dream content remain largely elusive. Here, we investigated how alterations in the excitability of sensorimotor areas through transcranial direct current stimulation (tDCS) might alter dream content. Following bihemispheric tDCS or sham stimulation, participants who were awakened from REM sleep filled out a questionnaire on bodily sensations in dreams. tDCS, compared to sham stimulation, significantly decreased reports of dream movement, especially repetitive actions. Contrary to this, other types of bodily experiences, such as tactile or vestibular sensations, were not affected by tDCS, confirming the specificity of stimulation effects. In addition, tDCS reduced interhemispheric coherence in parietal areas and altered the phasic electromyography correlation between the two arms. These findings reveal that a complex reorganization of the motor network co-occurred with the reduction of dream movement, confirming spatial specificity of the stimulation site. We conclude that tDCS over the sensorimotor cortex causally interferes with dream movement during REM sleep.
The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations
Authors: Tett Adrian , Huang Kun D. , Asnicar Francesco , Fehlner-Peach Hannah , Pasolli Edoardo , Karcher Nicolai , Armanini Federica , Manghi Paolo , Bonham Kevin , Zolfo Moreno , De Filippis Francesca , Magnabosco Cara , Bonneau Richard , Lusingu John , Amuasi John , Reinhard Karl , Rattei Thomas , Boulund Fredrik , Engstrand Lars , Zink Albert , Collado Maria Carmen , Littman Dan R. , Eibach Daniel , Ercolini Danilo , Rota-Stabelli Omar , Huttenhower Curtis , Maixner Frank , Segata Nicola 
Published: April 2019

AbstractPrevotella copri is a common inhabitant of the human gut. Interest in P. copri has gathered pace due to conflicting reports on whether it is beneficial or detrimental to health. In a cross-continent meta-analysis exploiting >6,500 available metagenomes supported by new isolate sequencing and recovery of high-quality genomes from metagenomes, we obtained >1,000 P. copri genomes. This 100-fold increase over existing isolate genomes allowed the genetic and global population structure of P. copri to be explored at an unprecedented depth. We demonstrate P. copri is not a monotypic species, but encompasses four distinct clades (>10% inter-clade vs. <4% intra-clade average single nucleotide variants) for which we propose the name P. copri complex, comprising clades A, B, C and D. We show the complex is near ubiquitous in non-Westernised populations (95.4% versus 29.6% in Westernised populations), where all four clades are typically co-present within an individual (61.6% of the cases), in contrast to Westernised populations (4.6%). Genomic analysis of the complex reveals substantial and complementary functional diversity, including the potential for utilisation of complex carbohydrates, suggestive that multi-generational dietary modifications may be a driver for the reduced P. copri prevalence in Westernised populations. Analysis of ancient stool microbiomes highlights a similar pattern of P. copri presence consistent with modern non-Westernised populations, allowing us to estimate the time of clade delineation to pre-date human migratory waves out of Africa. Our analysis reveals P. copri to be far more diverse than previously appreciated and this diversity appears to be underrepresented in Western-lifestyle populations.
Ribo-seQC: comprehensive analysis of cytoplasmic and organellar ribosome profiling data
Authors: Calviello Lorenzo , Sydow Dominique , Harnett Dermot , Ohler Uwe 
Published: April 2019

AbstractSummaryRibosome profiling enables genome-wide analysis of translation with unprecedented resolution. We present Ribo-seQC, a versatile tool for the comprehensive analysis of Ribo-seq data, providing in-depth insights on data quality and translational profiles for cytoplasmic and organelle ribosomes. Ribo-seQC automatically generates platform-independent HTML reports, offering a detailed and easy-to-share basis for collaborative Ribo-seq projects.AvailabilityRibo-seQC is available at https://github.com/ohlerlab/RiboseQC and submitted to Bioconductor.Contactuwe.ohler@mdc-berlin.de
Myelin Basic Protein dynamics from out-of-equilibrium functional state to degraded state in myelin
Authors: Di Gioacchino M. , Bianconi A. , Burghammer M. , Ciasca G. , Bruni F. , Campi G. 
Published: April 2019

ABSTRACTLiving matter is a quasi-stationary out-of-equilibrium system; in this physical condition, structural fluctuations at nano- and meso-scales are needed to understand the physics behind its biological functionality. Myelin has a simple ultrastructure whose fluctuations show correlated disorder in its functional out-of-equilibrium state. However, there is no information on the relationship between this correlated disorder and the dynamics of the intrinsically disordered Myelin Basic Protein (MBP) which is expected to influence the membrane structure and overall functionality. In this work, we have investigated the role of this protein structural dynamics in the myelin ultrastructure fluctuations in and out-of-equilibrium conditions, by using synchrotron Scanning micro X Ray Diffraction and Small Angle X ray Scattering. We have induced the crossover from out-of-equilibrium functional state to in-equilibrium degeneration changing the pH far away from physiological condition. While the observed compression of the cytosolic layer thickness probes the unfolding of the P2 protein and of the cytoplasmic P0 domain (P0cyt), the intrinsic large MBP fluctuations preserve the cytosol structure also in the degraded state. Thus, the transition of myelin ultrastructure from correlated to uncorrelated disordered state, is significantly affected by the unfolding of the P2 and P0 proteins, which in this latter state do not act in synergistic manner with MBP to determine the membrane functionality.STATEMENT OF SIGNIFICANCEA better comprehension of myelin degenerative process and the role of protein dynamics in this biological membrane is a topic issue in today’s scientific community. The myelin ultrastructural fluctuations exhibit correlated disorder in its functional state, that becomes uncorrelated as it degenerates. In this work we elucidate the interplay of protein structural dynamics and myelin ultrastructure in the transition from its functional state to the degraded state. The results highlight that the intrinsically disordered Myelin Basic Protein (MBP) allows to preserve the myelin structure following both the small correlated fluctuations in physiological state and the large disordered fluctuations in degraded conditions, where the myelin functionality is close to being lost and the MBP remains the single active protein.
Citizen scientists highlight conservation value of a small subtropical reef, Flinders Reef, southeast Queensland, Australia
Authors: Grol Monique G.G. , Vercelloni Julie , Kenyon Tania M. , Bayraktarov Elisa , van den Berg Cedric P. , Haris Daniel , Loder Jennifer A. , Mihaljević Morana , Rowland Phebe I. , Roelfsema Chris M. 
Published: April 2019

AbstractSubtropical reefs are unique ecosystems that require effective management – informed by regular ecological monitoring – to foster resilience to environmental changes. Resources to conduct monitoring are limited, and citizen science can complement data from local management agencies. Here, citizen science efforts document the ecological status of a subtropical reef, Flinders Reef, Moreton Bay Marine Park, Australia. Ecological surveys, following Reef Check Australia and CoralWatch protocols, were conducted by 44 trained volunteers. Ten sites at Flinders Reef were surveyed at 5-10 m depth in autumn and spring. Additionally, underwater photos and depth surveys were integrated with satellite imagery to create a detailed habitat map. Coral cover across sites ranged between 14% and 67%. Branching corals dominated the site with 67% cover and showed 89% dissimilarity in coral community composition compared to other sites. Coral community composition was mostly explained by spatial variation, of which 16% was influenced by wave exposure. Observed reef impacts including physical damage, unknown scars and coral disease were three times lower than studies on more accessible reefs in Moreton Bay Marine Park. Invertebrate abundance was relatively low (6.65 individuals per 100 m2), with the most abundant groups observed being sea urchins (Diademaspp.), gastropods (Drupellaspp.) and anemones. Butterflyfish were recorded at every site and were the most abundant fish group surveyed. Findings highlight the healthy condition of Flinders Reef, likely influenced by its offshore location and protection status as a ‘no-take’ zone. This study demonstrates that increasing the current 500m radius protection zone by a further 500m could double the protected area of coral, offering potential further conservation benefits. The findings resulting from the ecological data analysis and created benthic habitat map, provide an example of how citizen science based projects can assist marine park authorities and the public in ongoing conservation efforts.
Intestinal peroxisomal fatty acid β-oxidation regulates neural serotonin signaling through a feedback mechanism
Authors: Bouagnon Aude , Srivastava Shubhi , Panda Oishika , Schroeder Frank C. , Srinivasan Supriya , Ashrafi Kaveh 
Published: April 2019

AbstractThe ability to coordinate behavioral responses with metabolic status is fundamental to the maintenance of energy homeostasis. In numerous species includingC. elegansand mammals, neural serotonin signaling regulates a range of food-related behaviors. However, the mechanisms that integrate metabolic information with serotonergic circuits are poorly characterized. Here, we identify metabolic, molecular, and cellular components of a circuit that links peripheral metabolic state to serotonin-regulated behaviors inC. elegans. We find that blocking the entry of fatty acyl-CoAs into peroxisomal β-oxidation in the intestine results in blunting of the effects of neural serotonin signaling on feeding and egg-laying behaviors. Comparative genomics and metabolomics revealed that interfering with intestinal peroxisomal β-oxidation results in a modest global transcriptional change but significant changes to the metabolome, including a large number of changes in ascaroside and phospholipid species, some of which affect feeding behavior. We also identify body cavity neurons and an ether-a-go-go related (EAG) potassium channel that functions in these neurons as key cellular components of the circuitry linking peripheral metabolic signals to regulation of neural serotonin signaling. These data raise the possibility that the effects of serotonin on satiety may have their origins in feedback, homeostatic metabolic responses from the periphery.
In Search of Consciousness: Examining the Temporal Dynamics of Conscious Visual Perception using MEG time-series data
Authors: Mai Anh-Thu , Grootswagers Tijl , Carlson Thomas A. 
Published: April 2019

AbstractThe mere presence of information in the brain does not always mean that this information is available to consciousness (de-Wit, Alexander, Ekroll, & Wagemans, 2016). Experiments using paradigms such as binocular rivalry, visual masking, and the attentional blink have shown that visual information can be processed and represented by the visual system without reaching consciousness. Using multivariate pattern analysis (MVPA) and magneto-encephalography (MEG), we investigated the temporal dynamics of information processing for unconscious and conscious stimuli. We decoded stimulus information from the brain recordings while manipulating visual consciousness by presenting stimuli at threshold contrast in a backward masking paradigm. Participants’ consciousness was measured using both a forced-choice categorisation task and self-report. We show that brain activity during both conscious and non-conscious trials contained stimulus information, and that this information was enhanced in conscious trials. Overall, our results indicate that visual consciousness is characterised by enhanced neural activity representing the visual stimulus, and that this effect arises as early as 180 ms post-stimulus onset.
RhoG and Cdc42 can contribute to Rac-dependent lamellipodia formation through WAVE Regulatory Complex-binding
Authors: Schaks Matthias , Döring Hermann , Kage Frieda , Steffen Anika , Klünemann Thomas , Blankenfeldt Wulf , Stradal Theresia , Rottner Klemens 
Published: April 2019

ABSTRACTCell migration frequently involves the formation of lamellipodial protrusions, the initiation of which requires Rac GTPases signalling to heteropentameric WAVE regulatory complex (WRC). While Rac-related RhoG and Cdc42 can potently stimulate lamellipodium formation, so far presumed to occur by upstream signalling to Rac activation, we show here that the latter can be bypassed by RhoG and Cdc42 given that WRC has been artificially activated. This evidence arises from generation of B16-F1 cells simultaneously lacking both Rac GTPases and WRC, followed by reconstitution of lamellipodia formation with specific Rho-GTPase and differentially active WRC variant combinations. We conclude that formation of canonical lamellipodia requires WRC activation through Rac, but can possibly be tuned, in addition, by WRC interactions with RhoG and Cdc42.
Nanopore sequencing and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization
Authors: Salazar Alex N. , Gorter de Vries Arthur R. , van den Broek Marcel , Brouwers Nick , de la Torre Cortès Pilar , Kuijpers Niels G. A , Daran Jean-Marc G. , Abeel Thomas 
Published: April 2019

AbstractBackgroundThe lager brewing yeast,S. pastorianus, is a hybrid betweenS. cerevisiaeandS. eubayanuswith extensive chromosome aneuploidy.S. pastorianusis subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity forS. cerevisiaechromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies ofS. pastorianusstrains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history.ResultsTo fill this gap, we generated a chromosome-level genome assembly of theS. pastorianusstrain CBS 1483 using MinION sequencing and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history ofS. pastorianusstrains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between theS. cerevisiaesubgenomes of Group 1 and 2 strains, and marked differences from sequencedS. cerevisiae strains.ConclusionsOur findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygousS. cerevisiaestrain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.
Subcellular compartments interplay for carbon and nitrogen allocation in Chromera velia and Vitrella brassicaformis
Authors: Füssy Zoltán , Faitová Tereza , Oborník Miroslav 
Published: April 2019

ABSTRACTEndosymbioses necessitate functional cooperation of cellular compartments to avoid pathway redundancy and streamline the control of biological processes. To gain insight into the metabolic compartmentation in chromerids, phototrophic relatives to apicomplexan parasites, we prepared a reference set of proteins probably localized to mitochondria, cytosol and the plastid, taking advantage of available genomic and transcriptomic data. Training of prediction algorithms with the reference set now allows a genome-wide analysis of protein localization in C. velia and V. brassicaformis. We confirm that the chromerid plastids house enzymatic pathways needed for their maintenance and photosynthetic activity, but for carbon and nitrogen allocation, metabolite exchange is necessary with the cytosol and mitochondria. This indeed suggests that the regulatory mechanisms operate in the cytosol to control carbon metabolism based on the availability of both light and nutrients. We discuss that this arrangement is largely shared with apicomplexans and dinoflagellates, possibly stemming from a common ancestral metabolic architecture, and supports the mixotrophy of the chromerid algae.
Inflation shocks and income inequality
Authors: Gonzales Rolando , Rojas-Hosse Andrea 
Published: April 2019

Purpose
The purpose of this paper is to analyze the effects of inflationary shocks on inequality, using data of selected countries of the Middle East and North Africa (MENA).

Design/methodology/approach
Inflationary shocks were measured as deviations from core inflation, based on a genetic algorithm. Bayesian quantile regression was used to estimate the impact of inflationary shocks in different levels of inequality.

Findings
The results showed that inflationary shocks substantially affect countries with higher levels of inequality, thus suggesting that the detrimental impact of inflation is exacerbated by the high division of classes in a country.

Originality/value
The study contributes to the literature about the relationship between inflation and inequality by proposing that not only the sustained increase in prices but also the inflationary shocks – the deviations from core inflation – contribute to the generation of inequality. Also, to the best of the authors knowledge, the relationship between inflation shocks and inequality in the MENA region has never been analyzed before, thus creating a research gap to provide additional empirical evidence about the sources of inequality. Additionally, the authors contribute with a methodological approach to measure inflationary shocks, based on a semelparous genetic algorithm.
Innovations in intellectual property rights management
Authors: Modic Dolores , Hafner Ana , Damij Nadja , Cehovin Zajc Luka 
Published: April 2019

Purpose
The purpose of this paper is to evaluate innovations in intellectual property rights (IPR) databases, techniques and software tools, with an emphasis on selected new developments and their contribution towards achieving advantages for IPR management (IPRM) and wider social benefits. Several industry buzzwords are addressed, such as IPR-linked open data (IPR LOD) databases, blockchain and IPR-related techniques, acknowledged for their contribution in moving towards artificial intelligence (AI) in IPRM.

Design/methodology/approach
The evaluation, following an original framework developed by the authors, is based on a literature review, web analysis and interviews carried out with some of the top experts from IPR-savvy multinational companies.

Findings
The paper presents the patent databases landscape, classifying patent offices according to the format of data provided and depicting the state-of-art in the IPR LOD. An examination of existing IPR tools shows that they are not yet fully developed, with limited usability for IPRM. After reviewing the techniques, it is clear that the current state-of-the-art is insufficient to fully address AI in IPR. Uses of blockchain in IPR show that they are yet to be fully exploited on a larger scale.

Originality/value
A critical analysis of IPR tools, techniques and blockchain allows for the state-of-art to be assessed, and for their current and potential value with regard to the development of the economy and wider society to be considered. The paper also provides a novel classification of patent offices and an original IPR-linked open data landscape.