bluuebunny/crossref_metadata_2025_split huggingface dataset:
Certified Basic Life Support Instructors Identify Improper Cardiopulmonary Resuscitation Skills Poorly
Authors: Hansen Camilla , Bang Camilla , Stærk Mathilde , Krogh Kristian , Løfgren Bo 
Published: September 2019

Introduction
During basic life support (BLS) training, instructors assess learners' cardiopulmonary resuscitation (CPR) skills and correct errors to ensure high-quality performance. This study aimed to investigate certified BLS instructors' assessments of CPR skills.

Methods
Data were collected at BLS courses for medical students at Aarhus University, Aarhus, Denmark. Two certified BLS instructors evaluated each learner with a cardiac arrest test scenario, where learners demonstrated CPR on a resuscitation manikin for 3.5 minutes. Instructors' assessments were compared with manikin data as reference for correct performance. The first 3 CPR cycles were analyzed. Correct chest compressions were defined as 2 or more of 3 CPR cycles with 30 ± 2 chest compressions, 50 to 60 mm depth, and 100 to 120 min−1 rate. Correct rescue breaths were defined as 50% or more efficient breaths with visible, but not excessive manikin chest inflation (for instructors) or 500 to 600mL air (manikin data).

Results
Overall, 90 CPR assessments were performed by 16 instructor pairs. Instructors passed 81 (90%) learners, whereas manikin pass rate was 2%. Instructors identified correct chest compressions with a sensitivity of 0.96 [95% confidence interval (CI) = 0.79–1) and a specificity of 0.05 (95% CI = 0.01–0.14), as well as correct rescue breaths with a sensitivity of 1 (95% CI = 0.40–1) and a specificity of 0.07 (95% CI = 0.03–0.15). Instructors mistakenly failed 1 learner with adequate chest compression depth, while passing 53 (59%) learners with improper depth. Moreover, 80 (89%) improper rescue breath performances were not identified.

Conclusions
Certified BLS instructors assess CPR skills poorly. Particularly, improper chest compression depth and rescue breaths are not identified.
Species and sex divergence in vocalizations between hybridizing role-reversed shorebirds, Northern Jacana(Jacana spinosa)and Wattled Jacana(Jacana jacana)
Authors: Buck Evan J. , Brown Toni , Zwicky Gina , Derryberry Elizabeth P. , Lipshutz Sara E. 
Published: September 2019

ABSTRACTSpecies-specific vocalizations can act as a reproductive isolating mechanism between closely related populations. We analyzed vocal divergence between two hybridizing species of sex-role reversed polyandrous shorebirds, the Northern Jacana (Jacana spinosa) and Wattled Jacana (Jacana jacana). We found thatJ. spinosacalls have higher peak frequency and fundamental frequency thanJ. jacanacalls. We also compared calls between males and females, as both jacana species are sex-role reversed and females compete for male mates. Males produce calls with a higher peak frequency, exhibit shorter note lengths and emit a greater number of notes within a calling bout than females, which could relate to mate attraction. These results suggest that vocal divergence could act as a behavioral barrier to limit hybridization between the species and vocalizations may function differently between male and female jacanas.
GISA: Using Gauss Integrals to identify rare conformations in protein structures
Authors: Grønbæk Christian , Hamelryck Thomas , Røgen Peter 
Published: September 2019

AbstractThe native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations.We here propose a general method which transforms a structure into a “fingerprint of topological-geometric values” consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is therefore not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general. To achieve this our new algorithm, GISA, as a key novelty produces the descriptors, so called Gauss integrals, not only for the full chains of a protein but for all its sub-chains, thereby allowing fingerprinting on any scale from local to global. The Gauss integrals are known to be effective descriptors of global protein folds.Applying GISA to a set of about 8000 high resolution structures (top8000), we first show how it enables swift identification of predefined geometries such as pokes and links. We then apply GISA with no restrictions on geometry, to show how it allows identifying rare conformations by finding rare invariant values only. In this unrestricted search, pokes and links are still found, but also knotted conformations, as well as more highly entangled configurations not previously described. Thus, applying the basic scan method in GISA’s tool-box to the top8000 set, 10 known cases of knots are ranked as the top positive Gauss number cases, while placing at the top of the negative Gauss numbers 14 cases in cis-trans isomerases sharing a spatial motif of little secondary structure content, which possibly has gone unnoticed.Potential applications of the GISA tools include finding errors in protein models and identifying unusual conformations that might be important for protein folding and function. By its broad potential, we believe that GISA will be of general benefit to the structural bioinformatics community.GISA is coded in C and comes as a command line tool. Source and compiled code for GISA plus read-me and examples are publicly available at GitHub (https://github.com).
High-throughput fluorescence-based screen identifies the neuronal microRNA miR-124 as a positive regulator of alphavirus infection
Authors: López Paula , Girardi Erika , Mounce Bryan C. , Weiss Amélie , Chane-Woon-Ming Béatrice , Messmer Mélanie , Kaukinen Pasi , Kopp Arnaud , Bortolamiol-Becet Diane , Fendri Ali , Vignuzzi Marco , Brino Laurent , Pfeffer Sébastien 
Published: September 2019

ABSTRACTMicro (mi)RNAs are small regulatory RNAs, which act as guide for the RISC complex to modulate the expression of target genes. In addition to their role in maintaining essential physiological functions in the cell, miRNAs can also regulate viral infections. They can do so directly by targeting RNAs of viral origin or indirectly by targeting RNAs from the host and this can result in a positive or negative outcome for the virus. Here, we performed a miRNA genome-wide screen in order to identify cellular miRNAs involved in the regulation of arbovirus infection in human cells. We identified sixteen miRNAs showing a positive effect on the virus, among which a number of neuron-specific ones such as miR-124. We confirmed that overexpression of miR-124 increases Sindbis virus (SINV) viral production and that this effect is mediated by its seed sequence. We further demonstrated that the SINV genome possesses a binding site for miR-124-3p. Both inhibition of miR-124-3p or silent mutations to disrupt this binding site in the viral RNA abolished the positive regulation. We also proved that miR-124 inhibition reduces SINV infection in human differentiated neuronal cells. Finally, we showed that the proviral effect of miR-124 is conserved for other medically relevant alphaviruses. Indeed, inhibition of miR-124 expression reduces chikungunya virus (CHIKV) viral production in human cells. Altogether, our work expands the panel of positive regulation of the viral cycle by direct binding of host miRNAs to the viral RNA and provides new insights into the role of cellular miRNAs as regulators of alphavirus infection.SIGNIFICANCE STATEMENTArthropod-borne (arbo) viruses are part of a class of pathogens that are transmitted to their final hosts by insects. Because of climate change, the habitat of some of these insects, such as mosquitoes, is shifting, thereby facilitating the emergence of viral epidemics. Among the pathologies associated with arboviruses infection, neurological diseases like meningitis or encephalitis represent a significant health burden. Using a genome-wide miRNA screen, we identified the neuronal miR-124 as a positive regulator of the Sindbis and chikungunya alphaviruses. We also showed that this effect was in part direct, thereby opening novel avenues to treat alphaviruses infection.
Positive and negative intra-molecular modulation in a dual-cassette RNA helicase
Authors: Vester Karen , Santos Karine F. , Kuropka Benno , Weise Christoph , Wahl Markus C. 
Published: September 2019

ABSTRACTRNA helicase Brr2 is required for the activation of the spliceosome prior to the first catalytic step of splicing. Brr2 represents a distinct subgroup of Ski2-like nucleic acid helicases whose members comprise tandem helicase cassettes. Only the N-terminal cassette of Brr2 is an active ATPase and can unwind substrate RNAs. The C-terminal cassette represents a pseudo-enzyme that can stimulate RNA-related activities of the N-terminal cassette. However, the molecular mechanisms, by which the C-terminal cassette modulates the activities of the N-terminal unit remain elusive. Here, we show that N- and C-terminal cassettes adopt vastly different relative orientations in a crystal structure of Brr2 in complex with an activating domain of the spliceosomal Prp8 protein as compared to the crystal structure of isolated Brr2. Likewise, the cassettes occupy different relative positions and engage in different inter-cassette contacts during different stages of splicing. Engineered disulfide bridges that lock the cassettes in two different relative orientations have opposite effects on RNA-related activities of the N-terminal cassette compared to the unrestrained protein. Moreover, different relative positioning of the cassettes strongly influences ATP hydrolysis by the N-terminal cassette. Our results demonstrate that the inactive C-terminal cassette of Brr2 can exert both positive and negative influence on the active N-terminal helicase unit from a distance.
Comparative genomics unravels mechanisms of genetic adaptation for the catabolism of the phenylurea herbicide linuron inVariovorax
Authors: Öztürk Başak , Werner Johannes , Meier-Kolthoff Jan P. , Bunk Boyke , Spröer Cathrin , Springael Dirk 
Published: September 2019

AbstractBiodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of theVariovoraxgenus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full genome sequences of six linuron degradingVariovoraxstrains isolated from geographically distant locations were analyzed to acquire insight in the mechanisms of genetic adaptation towards linuron metabolism inVariovorax. Whole genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade withinVariovoraxand indicated their unlikely origin from a common ancestral linuron degrader. The linuron degraders differentiated from non-degraders by the presence of multiple plasmids of 20 to 839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed (i) high conservation and synteny and (ii) strain-dependent distribution among the different plasmids. All were bordered by IS1071elements forming composite transposon structures appointing IS1071as key for catabolic gene recruitment. Most of the strain carried at least one broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1Variovoraxstrains, despite their different geographical origin, made use of a limited genetic repertoire to acquire linuron biodegradation.ImportanceThe genusVariovoraxand especially a clade of strains that phylogenetically separates from the majority ofVariovoraxspecies, appears to be a specialist in the biodegradation of the phenyl urea herbicide linuron. Horizontal gene transfer (HGT) likely played an essential role in the genetic adaptation of those strain to acquire the linuron catabolic genotype. However, we do not know the genetic repertoire involved in this adaptation both regarding catabolic gene functions as well as gene functions that promote HGT neither do we know how this varies between the different strains. These questions are addressed in this paper by analyzing the full genome sequences of six linuron degradingVariovoraxstrains. This knowledge is important for understanding the mechanisms that steer world-wide genetic adaptation in a particular species and this for a particular phenotypic trait as linuron biodegradation.
Ultra-low frequency neural entrainment to pain
Authors: Guo Y , Bufacchi RJ , Novembre G , Kilintari M , Moayedi M , Hu L , Iannetti GD 
Published: September 2019

AbstractNervous systems exploit regularities in the sensory environment to predict sensory input and adjust behavior, and thereby maximize fitness. Entrainment of neural oscillations allows retaining temporal regularities of sensory information, a prerequisite for prediction. Entrainment has been extensively described at the frequencies of periodic inputs most commonly present in visual and auditory landscapes (e.g. >1 Hz). An open question is whether neural entrainment also occurs for regularities at much longer timescales. Here we exploited the fact that the temporal dynamics of thermal stimuli in natural environment can unfold very slowly. We show that ultra-low frequency neural oscillations preserved a long-lasting trace of sensory information through neural entrainment to periodic thermo-nociceptive input as low as 0.1 Hz. Importantly, revealing the functional significance of this phenomenon, both power and phase of the entrainment predicted individual pain sensitivity. In contrast, periodic auditory input at the same ultra-low frequency did not entrain ultra-low frequency oscillations. These results demonstrate that a functionally-significant neural entrainment can occur at temporal scales far longer than those commonly explored. The non-supramodal nature of our results suggests that ultra-low frequency entrainment might be tuned to the temporal scale of the statistical regularities characteristic of different sensory modalities.
A Systematic Review of the Biomechanical Effects of Harness and Head-Collar use in Dogs
Authors: Blake S , Williams R , Ferro de Godoy R 
Published: September 2019

AbstractThe number of dogs in the UK is on the rise, as are canine sports involving the use of a harness to allow the dog to pull against an interface in the same way as a husky might pull a sled. Service dogs and those involved in essential work commonly wear a harness throughout their working lives, yet little is understood regarding the biomechanical impact of their use. This systematic review was conducted to review reported evidence of the biomechanical effects of harness and head collar (Halti) use in dogs.Searches were applied covering 1910 to 2018 on the following databases: PubMed, Web of Science and Writtle Discovery.Three publications were identified as suitable which were then critically evaluated using predefined criteria and ARRIVE based guidelines for bias assessment. Only one was considered to provide the most reliable data regarding the influence of harnesses on gait, whilst the remainder were considered to suffer a variety of issues including poor sample size, repeatability and study execution. The most appropriate study found that wearing a chest strap harness reduced shoulder extension in both walk and trot by up to 8° of movement, whilst a Y-shaped harness commonly marketed as non-restrictive reduced shoulder extension by up to 10° of movement, suggesting that the use of harness type restraints can affect canine gait, whereas no studies were found relating to the biomechanical effects of head-collar usage.
The expression of cannabinoid-related genes in multiple disease cell lines
Authors: Arlen Philip A. , Wu Xingzhu 
Published: September 2019

AbstractThe endocannabinoid system comprises a series of ligands and receptors that have putative roles in regulating physiological and cognitive processes such as pre- and post-natal development, appetite, pain sensation, mood, and memory. Besides the endocannabinoids, these endogenous receptors are also capable of mediating the pharmacological effects of phytocannabinoids, which are derived from the cannabis plant. We sought to interrogate a panel of cell lines, representative of multiple human diseases, to characterize their cannabinoid-mediating gene expression. We found all lines expressed one or more gene product that rendered the cell potentially responsive to cannabinoids. Moreover, the expression profiles differed between normal and cancerous cells, as well as between cells derived from the brain, pancreas, and skin. Taken together, given the presence of one or more of these mediating gene products, our findings suggest a potential therapeutic role for phytocannabinoids.
Effects of anesthetic tricaine on stress and reproductive aspects of South American silver catfish (Rhamdia quelen) male
Authors: dos Santos Teixeira Nathalia , Marques Lis Santos , Rodrigues Rômulo Batista , Gusso Darlan , Nunes Fossati Ana Amélia , Streit Danilo Pedro 
Published: September 2019

AbstractAnesthesia is a common practice used in fish research and aquaculture. For both applications, it is important to understand anesthetics effects on the animal and tissues of interest to ensure the validity of data and to improve animal welfare. Captive fish production is only possible with artificial reproduction, and it is known that manipulation is a stressor stimulus in fish. The most common method of determining fish stress responses is measuring the circulating level of cortisol. Therefore, the purpose of this study was to evaluate the effects of different concentrations (100, 200, and 300 mg L-1) of the anesthetic tricaine methanesulfonate (MS-222) on cortisol levels and their influence on the sperm quality maintenance in Rhamdia quelen. After hormonal induction, 28 sexually mature males (average weight = 363.00 ± 71.24 g) were randomly distributed among treatments, and their semen and blood samples were collected. Anesthesia induction time, motility rate, sperm concentration and morphology, plasma cortisol levels, and reproductive hormones concentrations (testosterone, 17-α-hydroxyprogesterone, and estradiol) were evaluated. Anesthesia with 100 mg L-1 MS-222 presented a longer induction time than that with 200 and 300 mg L-1 MS-222. Sperm motility rate was significantly higher in the control than in the 300 mg L-1 treatment but did not differ among the control, 100, and 200 mg L-1 treatments. Estradiol level was significantly higher in non-anesthetized than in anesthetized fish, but plasma cortisol levels did not differ significantly between treatments (182.50 ± 42.03 ng mL-1). MS-222 anesthetizes fish by blocking the sodium channels, preventing the development of nerve action potentials. However, MS222 at concentrations of 100, 200, and 300 mg L-1 did not prevent stress in South American silver catfish males. In addition, its use did not maintain sperm quality, as it impaired motility and decreased levels of plasma estradiol.
Low concordance of short-term and long-term selection responses in experimentalDrosophilapopulations
Authors: Langmüller Anna Maria , Schlötterer Christian 
Published: September 2019

AbstractExperimental evolution is becoming a popular approach to study the genomic selection response of evolving populations. Computer simulation studies suggest that the accuracy of the signature increases with the duration of the experiment. Since some assumptions of the computer simulations may be violated, it is important to scrutinize the influence of the experimental duration with real data. Here, we use a highly replicated Evolve and Resequence study inDrosophila simulansto compare the selection targets inferred at different time points. At each time point, approximately the same number of SNPs deviates from neutral expectations, but only 10 % of the selected haplotype blocks identified from the full data set can be detected after 20 generations. Those haplotype blocks that emerge already after 20 generations differ from the others by being strongly selected at the beginning of the experiment and display a more parallel selection response. Consistent with previous computer simulations, our results demonstrate that only Evolve and Resequence experiments with a sufficient number of generations can characterize complex adaptive architectures.
Novel Universal Primers for Metabarcoding eDNA Surveys of Marine Mammals and Other Marine Vertebrates
Authors: Valsecchi Elena , Bylemans Jonas , Goodman Simon J. , Lombardi Roberto , Carr Ian , Castellano Laura , Galimberti Andrea , Galli Paolo 
Published: September 2019

ABSTRACTMetabarcoding studies using environmental DNA (eDNA) and high throughput sequencing (HTS) are rapidly becoming an important tool for assessing and monitoring marine biodiversity, detecting invasive species, and supporting basic ecological research. Several barcode loci targeting teleost fish and elasmobranchs have previously been developed, but to date primer sets focusing on other marine megafauna, such as marine mammals have received less attention. Similarly, there have been few attempts to identify potentially ‘universal’ barcode loci which may be informative across multiple marine vertebrate Orders. Here we describe the design and validation of four new sets of primers targeting hypervariable regions of the vertebrate mitochondrial 12S and 16S rRNA genes, which have conserved priming sites across virtually all cetaceans, pinnipeds, elasmobranchs, boney fish, sea turtles and birds, and amplify fragments with consistently high levels of taxonomically diagnostic sequence variation. ‘In silico’ validation using the OBITOOLS software showed our new barcode loci outperformed most existing vertebrate barcode loci for taxon detection and resolution. We also evaluated sequence diversity and taxonomic resolution of the new barcode loci in 680 complete marine mammal mitochondrial genomes demonstrating that they are effective at resolving amplicons for most taxa to the species level. Finally, we evaluated the performance of the primer sets with eDNA samples from aquarium communities with known species composition. These new primers will potentially allow surveys of complete marine vertebrate communities in single HTS metabarcoding assessments, simplifying workflows, reducing costs, and increasing accessibility to a wider range of investigators.