bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computed tomography scans prior to transfer to a pediatric trauma center: Transfer time effects, neurosurgical interventions, and practice variability
Authors: Snyder Christopher W. , Danielson Paul D. , Gonzalez Raquel , Chandler Nicole M. 
Published: March 2019

BACKGROUND
Many nontrauma centers perform computed tomography (CT) on injured children prior to transfer to a pediatric trauma center (PTC), but the institutional variability and clinical impact of this practice is unclear. This study evaluated the association of pretransfer CT with transfer delays, the likelihood of emergent neurosurgical intervention among patients who underwent pretransfer head CT, and the effects of transfer distance on prevalence and regional variability of pretransfer CT.

METHODS
All injured children transferred from outlying nontrauma centers to a single freestanding PTC from 2009 to 2017 were included. Patients were categorized by undergoing pretransfer CT head alone, CT of multiple/other areas, or no CT. Transfer time (referring hospital arrival to PTC arrival) was compared between CT groups, using multivariable modeling to adjust for covariates. Neurosurgical interventions were compared between patients with normal and abnormal Glasgow Coma Scale (GCS) scores. The prevalence of pretransfer CT among referring centers was compared, with stratification by transfer distance.

RESULTS
Of 2,947 transfer patients, 1,225 (42%) underwent pretransfer CT (29%, head CT alone; 13%, other/multiple CT). Transfer times were significantly longer for patients who underwent pretransfer head CT or multiple CT (287 or 298 minutes vs. 260 minutes, p < 0.0001) after adjustment for baseline characteristics, injury severity, and transfer distance. Among patients with normal pretransfer GCS who received a pretransfer head CT, the likelihood of urgent neurosurgical intervention was 1.3%. Prevalence rates of pretransfer CT by referring center varied from 15% to 94%; prevalence increased with increasing transfer distance but demonstrated wide variability among centers of similar distance.

CONCLUSION
Pretransfer CT, whether of the head alone or multiple areas, is associated with delays in transfer to definitive care. Among patients with pretransfer GCS 15, the risk of urgent neurosurgical intervention is very low. Wide variability in pretransfer CT use between referring centers suggests opportunity for development of standardized protocols.

LEVEL OF EVIDENCE
Economic/decision, level III.
The endocannabinoid system in migraine: from bench to pharmacy and back
Authors: Tassorelli Cristina , Greco Rosaria , Silberstein Stephen D. 
Published: March 2019

Purpose of review
Migraine is a common, highly disabling disorder. Its treatment involves acute and preventive therapy. Many of available preventive medications are not well tolerated, which results in poor compliance and limited effectiveness. Cannabinoids have been proposed for the treatment of migraine but their efficacy and tolerability are controversial.

Recent findings
Cannabinoids modulate functions and activity of signaling pathways that have a key role in pain control. Growing preclinical evidence and initial clinical findings suggest that modulation of the endocannabinoid system, via endogenous or exogenous cannabinoids may be relevant for migraine via multiple mechanisms.

Summary
The endocannabinoid system qualifies as an interesting area of research worth exploration in the quest for therapeutic targets for the treatment of migraine.
Ian Read Gibbons. 30 October 1931—30 January 2018
Authors: Gibbons Wendy E. , Vale Ronald D. , Sale Winfield S. 
Published: March 2019

Ian Read Gibbons is best known for discovering dynein, a molecular motor that powers the motion of cilia and flagella, is involved in assembling the mitotic spindle and moves chromosomes as well as other cargoes inside cells. Gibbons devoted his career in the lab of more than 50 years to understanding the mechanism of how dynein works in driving motility. In doing so, he built a life-long reputation as a creative, collaborative and tenacious researcher with an unusual gift for crafting innovative solutions to tricky experimental problems. His experimental methods spanned electron as well as light microscopy, biochemistry, molecular biology, crystallography and molecular modelling. He perceived the right set of experimental moves that would allow him to dissect and observe the physical underpinnings of minute biological processes such as the delicate movements of dynein. Gibbons traced his success to the ability to envision how pieces of a scientific puzzle might fit together to make a coherent story: ‘My own approach to research has always emphasized intuition over logic. Perhaps for that reason, I get attracted to questions with aesthetic appeal.’ Even though dynein holds much promise for helping to engineer ways to fight disease, Gibbons' focus was always on the intrinsic grace of understanding nature's workings.Gibbons’ marriage to his biochemist wife Barbara played a particularly vital role in his life. Barbara and Ian worked frequently together as she built her own scientific career through their partnership in the study of dynein. Ian's many scientific accomplishments as well as his dedication to his friends and family represent enduring gifts to us all.
On the forces that cable webs under tension can support and how to design cable webs to channel stresses
Authors: Bouchitté Guy , Mattei Ornella , Milton Graeme W. , Seppecher Pierre 
Published: March 2019

In many applications of structural engineering, the following question arises: given a set of forces

f

1
,

f

2
, …,

f

N

applied at prescribed points

x

1
,

x

2
, …,

x

N

, under what constraints on the forces does there exist a truss structure (or wire web) with all elements under tension that supports these forces? Here we provide answer to such a question for any configuration of the terminal points

x

1
,

x

2
, …,

x

N

in the two- and three-dimensional cases. Specifically, the existence of a web is guaranteed by a necessary and sufficient condition on the loading which corresponds to a finite dimensional linear programming problem. In two dimensions, we show that any such web can be replaced by one in which there are at most
P
elementary loops, where elementary means that the loop cannot be subdivided into subloops, and where
P
is the number of forces

f

1
,

f

2
, …,

f

N

applied at points strictly within the convex hull of

x

1
,

x

2
, …,

x

N

. In three dimensions, we show that, by slightly perturbing

f

1
,

f

2
, …,

f

N

, there exists a uniloadable web supporting this loading. Uniloadable means it supports this loading and all positive multiples of it, but not any other loading. Uniloadable webs provide a mechanism for channelling stress in desired ways.
Phage-Encoded LuxR-Type Receptors Responsive to Host-Produced Bacterial Quorum-Sensing Autoinducers
Authors: Silpe Justin E. , Bassler Bonnie L. 
Published: March 2019

AbstractQuorum sensing (QS) is a process of cell-to-cell communication that bacteria use to orchestrate collective behaviors. QS relies on the cell-density-dependent production, accumulation, and receptor-mediated detection of extracellular signaling molecules called autoinducers (AIs). Gram-negative bacteria commonly use N-acyl homoserine lactones (AHLs) as their AIs and they are detected by LuxR-type receptors. Often, LuxR-type receptors are insoluble when not bound to a cognate AI. In this report, we show that LuxR-type receptors are encoded on phage genomes and, in the cases we tested, the phage LuxR-type receptors bind to and are solubilized specifically by the AHL AI produced by the host bacterium. We do not yet know the viral activities that are controlled by these phage QS receptors, however, our observations, coupled with recent reports, suggest that their occurrence is more widespread than previously appreciated. Using receptor-mediated detection of QS AIs could enable phages to garner information concerning the population density status of their bacterial hosts. We speculate that such information can be exploited by phages to optimize the timing of execution of particular steps in viral infection.ImportanceBacteria communicate with chemical signal molecules to regulate group behaviors in a process called quorum sensing (QS). In this report, we find that genes encoding receptors for Gram-negative bacterial QS communication molecules are present on genomes of viruses that infect these bacteria. These viruses are called phages. We show that two phage-encoded receptors, like their bacterial counterparts, bind to the communication molecule produced by the host bacterium, suggesting that phages can “listen in” on their bacterial hosts. Interfering with bacterial QS and using phages to kill pathogenic bacteria represent attractive possibilities for development of new antimicrobials to combat pathogens that are resistant to traditional antibiotics. Our findings of interactions between phages and QS bacteria need consideration as new antimicrobial therapies are developed.
‘Normal’ hearing thresholds and fundamental auditory grouping processes predict difficulties with speech-in-noise perception
Authors: Holmes Emma , Griffiths Timothy D. 
Published: March 2019

AbstractUnderstanding speech when background noise is present is a critical everyday task that varies widely among people. A key challenge is to understand why some people struggle with speech-in-noise perception, despite having clinically normal hearing. Here, we developed new figure-ground tests that require participants to extract a coherent tone pattern from a stochastic background of tones. These tests dissociated variability in speech-in-noise perception related to mechanisms for detecting static (same-frequency) patterns and those for tracking patterns that change frequency over time. In addition, elevated hearing thresholds that are widely considered to be ‘normal’ explained significant variance in speech-in-noise perception, independent of figure-ground perception. Overall, our results demonstrate that successful speech-in-noise perception is related to audiometric thresholds, fundamental grouping of static acoustic patterns, and tracking of acoustic sources that change in frequency. Crucially, measuring both peripheral (audiometric thresholds) and central (grouping) processes is required to adequately assess speech-in-noise deficits.
REM negatively predicts statistical learning but not other forms of gist
Authors: Matorina Nelly , Poppenk Jordan 
Published: March 2019

AbstractHuman memory for recent events is believed to undergo reactivation during sleep. This process is thought to be relevant for the consolidation of both individual episodic memories and gist extraction, the formation of generalized memory representations from multiple, related memories. Which kinds of gist are actually enhanced, however, is the subject of less consensus. To address this question, we focused our design on four types of gist: inferential gist (relations extracted across non-contiguous events), statistical learning (regularities extracted from a series), summary gist (a theme abstracted from a temporally contiguous series of items), and category gist (characterization of a stimulus at a higher level in the semantic hierarchy). Sixty-nine participants (30 men, 38 women, and 1 other) completed memory encoding tasks addressing these types of gist and corresponding retrieval tasks the same evening, the morning after, and one week later. Inferential gist was retained over a week, whereas memory for category gist, summary gist, and statistical learning decayed. Higher proportions of REM were associated with worse performance in a statistical learning task controlling for time. Our results support that REM sleep is involved in schema disintegration, which works against participants’ ability to identify regularities within temporal series.SIGNIFICANCE STATEMENTTo gain the most from our experiences, we extract from them the most important elements, or “gist”, with sleep believed to facilitate this process. However, what is referred to as gist varies considerably across studies. We report categorically different mnemonic trajectories of two classes of gist. In particular, we show that gist involving synthesis across relational memories is retained over time, whereas other gists were subject to substantial decay. Moreover, our evidence supports the idea that REM works to discretize, rather than synthesize experiences. Future research should test similar constructs in different tasks to determine whether these findings are generalizable. Our research suggests that patients with reduced REM sleep may experience more interference between similar memories.
Complete genome sequence and evolution analysis of Psychrobacter sp. YP14 from Gammaridea Gastrointestinal Microbiota of Yap Trench
Authors: Jiaqiang Wei , Zhiyuan Gao , Whenfeng Liu , Hao Chen 
Published: March 2019

AbstractPsychrobacter sp. YP14, a moderately psychrophilic bacterium belonging to the class Gammaproteobacteria, was isolated from Gammaridea Gastrointestinal Microbiota of Yap Trench. The strain has one circular chromosome of 2,895,311 bp with a 44.66% GC content, consisting of 2333 protein-coding genes, 53 tRNA genes and 9 rRNA genes. Four plasmids were completely assembled and their sizes were 13,712 bp, 19711 bp, 36270 bp, 8194 bp, respectively. In particular, a putative open reading frame (ORF) for dienelactone hydrolase (DLH) related to degradation of chlorinated aromatic hydrocarbons. To get an better understanding of the evolution of Psychrobacter sp. YP14 in this genus, six Psychrobacter strains (G, PRwf-1, DAB_AL43B, AntiMn-1,P11G5, P2G3), with publicly available complete genome, were selected and comparative genomics analysis were performed among them. The closest phylogenetic relationship was identified between strains G and K5 based on 16s gene and ANI (average nucleotide identity) values. Analysis of the pan-genome structure found that YP14 has fewer COG clusters associated with transposons and prophage which indicates fewer sequence rearrangements compared with PRwf-1. Besides, stress response-related genes of strain YP14 demonstrates that it has less strategies to cope with extreme environment, which is consistent with its intestinal habitat. The difference of metabolism and strategies coped with stress response of YP14 are more conducive to the study of microbial survival and metabolic mechanisms in deep sea environment.
PlotsOfDifferences – a web app for the quantitative comparison of unpaired data
Authors: Goedhart Joachim 
Published: March 2019

AbstractThe quantitative comparison of data acquired under different conditions is an important aspect of experimental science. The most widely used statistic for quantitative comparisons is the p-value. However, p-values suffer from several shortcomings. The most prominent shortcoming that is relevant for quantitative comparisons is that p-values fail to convey the magnitude of differences. The differences between conditions are best quantified by the determination of effect size. To democratize the calculation of effect size, we have developed a web-based tool. The tool uses bootstrapping to resample mean or median values for each of the conditions and these values are used to calculate the effect size and their compatibility interval. The web tool generates a graphical output, showing the bootstrap distribution of the difference next to the actual data for optimal interpretation. A tabular output with statistics and effect sizes is also generated and the table can be supplemented with p-values that are calculated with a randomization test. The app that we report here is dubbed PlotsOfDifferences and is available at: https://huygens.science.uva.nl/PlotsOfDifferences
Embodiment is related to better performance on an immersive brain computer interface in head-mounted virtual reality: A pilot study
Authors: Juliano Julia M , Spicer Ryan P , Vourvopoulos Athanasios , Lefebvre Stephanie , Jann Kay , Ard Tyler , Santarnecchi Emiliano , Krum David M , Liew Sook-Lei 
Published: March 2019

AbstractBrain computer interfaces (BCI) can be used to provide individuals with neurofeedback of their own brain activity and train them to learn how to control their brain activity. Neurofeedback-based BCIs used for motor rehabilitation aim to ‘close the loop’ between attempted motor commands and sensory feedback by providing supplemental sensory information when individuals successfully establish specific brain patterns. Existing neurofeedback-based BCIs have used a variety of displays to provide feedback, ranging from devices that provide a more immersive and compelling experience (e.g., head-mounted virtual reality (HMD-VR) or CAVE systems) to devices that are considered less immersive (e.g., computer screens). However, it is not clear whether more immersive systems (i.e., HMD-VR) improve neurofeedback performance compared to computer screens, and whether there are individual performance differences in HMD-VR versus screen-based neurofeedback. In this pilot experiment, we compared neurofeedback performance in HMD-VR versus on a computer screen in twelve healthy individuals. We also examined whether individual differences in presence or embodiment correlated with neurofeedback performance in either environment. Participants were asked to control a virtual right arm by imagining right hand movements. Real-time brain activity indicating motor imagery, which was measured via electroencephalography (EEG) as desynchronized sensorimotor rhythms (SMR; 8-24 Hz) in the left motor cortex, drove the movement of the virtual arm towards (increased SMR desynchronization) or away from (decreased SMR desynchronization) targets. Participants performed two blocks of 30 trials, one for each condition (Screen, HMD-VR), with the order of conditions counterbalanced across participants. After completing each block, participants were asked questions relating to their sense of presence and embodiment in each environment. We found that, while participants’ performance on the neurofeedback-based BCI task was similar between conditions, the participants’ reported levels of embodiment was significantly different between conditions. Specifically, participants experienced higher levels of embodiment in HMD-VR compared to the computer screen. We further found that reported levels of embodiment positively correlated with neurofeedback performance only in the HMD-VR condition. Overall, these preliminary results suggest that embodiment may improve performance on a neurofeedback-based BCI and that HMD-VR may increase embodiment during a neurofeedback-based BCI task compared to a standard computer screen.
Two ecotype-related long non-coding RNAs in the environmental control of root growth
Authors: Blein Thomas , Balzergue Coline , Roulé Thomas , Gabriel Marc , Scalisi Laetitia , Sorin Céline , Christ Aurélie , Delannoy Etienne , Martin-Magniette Marie-Laure , Nussaume Laurent , Hartmann Caroline , Gautheret Daniel , Desnos Thierry , Crespi Martin 
Published: March 2019

AbstractBackgroundRoot architecture varies widely between species and even between ecotypes of the same species despite the strong conservation of the protein-coding portion of their genomes. In contrast, non-coding RNAs evolved rapidly between ecotypes and may control their differential responses to the environment as several long non-coding RNAs (lncRNAs) can quantitatively regulate gene expression.ResultsRoots from Columbia (Col) and Landsbergerecta(Ler) ecotypes respond differently to phosphate starvation. We compared complete transcriptomes (mRNAs, lncRNAs and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of new lncRNAs categorized as intergenic or antisense RNAs that were largely conserved at DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independently of the phosphate condition. These ecotype-related lncRNAs were characterized by analyzing their sequence variability among plants and their link with siRNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes including specific antisense RNAs targeting key regulators of root growth responses. Mis-regulation of several intergenic lncRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in Col.ConclusionsThe in depth exploration of the non-coding transcriptome of two ecotypes identified thousands of new lncRNAs showing specific expression in root apexes. De-regulation of two ecotype-related lncRNAs revealed a new pathway involved in the regulation of primary root growth. The non-coding genome may reveal novel mechanisms involved in ecotype adaptation of roots to different soil environments.
Evidence of extensive intraspecific noncoding reshuffling in a 169-kb mitochondrial genome of a basidiomycetous fungus
Authors: Lee Hsin-Han , Ke Huei-Mien , Lin Chan-Yi Ivy , Lee Tracy J. , Chung Chia-Lin , Tsai Isheng J. 
Published: March 2019

AbstractComparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern of rearrangement between and within major phyla owing to horizontal gene transfer (HGT) and recombination. The role of recombination was exemplified at a finer evolutionary time scale in basidiomycetes group of fungi as they display a diversity of mitochondrial DNA (mtDNA) inheritance patterns. Here, we assembled mitogenomes of six species from the Hymenochaetales order of basidiomycetes and examined 59 mitogenomes from two genetic lineages ofPyrrhoderma noxium. Gene order is largely colinear while intergene regions are major determinants of mitogenome size variation. Substantial sequence divergence was found in shared introns consistent with high HGT frequency observed in yeasts, but we also identified a rare case where an intron was retained in five species since speciation. In contrast to the hyperdiversity observed in nuclear genomes ofP. noxium, mitogenomes’ intraspecific polymorphisms at protein coding sequences are extremely low. Phylogeny based on introns revealed turnover as well as exchange of introns between two lineages. Strikingly, some strains harbor a mosaic origin of introns from both lineages. Analysis of intergenic sequence indicated substantial differences between and within lineages, and an expansion may be ongoing as a result of exchange between distal intergenes. These findings suggest that the evolution in mtDNAs is usually lineage specific but chimeric mitotypes are frequently observed, thus capturing the possible evolutionary processes shaping mitogenomes in a basidiomycete. The large mitogenome sizes reported in various basidiomycetes appear to be a result of interspecific reshuffling of intergenes.