Qualitative Research as a Hero’s Journey: Six Archetypes to Draw on

Is the research process similar to a hero’s journey? Just as a hero draws on different archetypes during the journey, a researcher moves through phases and must draw upon different strengths. In this article, the six archetypes that Pearson (1998) links to the hero’s journey are described. Then, each phase of a qualitative research study is described, followed by reflection on which of Pearson’s six archetypes were active. Discussion focuses on how other archetypes could have been helpful in each phase, as well as how other researchers could use this process of archetypal reflectivity to make their work more authentic and intentional

Molecular identification and first demographic insights of sharks based on artisanal fisheries bycatch in the Pacific Coast of Colombia: implications for conservation

The Pacific coast of Colombia is characterized by mangrove ecosystems which play a crucial role as possible nurseries for juvenile sharks. However, trophic food webs from coastal ecosystems are heavily disturbed by increased fishing pressure, which affects numerous shark species. In this region of the Eastern Tropical Pacific (ETP), fisheries’ data from coastal areas are scarce and unspecific, as most sharks from artisanal fisheries are landed decapitated and finless, making their morphological identification difficult. For the establishment and implementation of effective regional conservation and management policies, information on the diversity and population dynamics of shark species is crucial. We therefore sequenced the mitochondrial NADH2 gene of 696 samples taken from fishermen’s landings of shark’s bycatch along the Colombian north Pacific coast. We were able to identify 14 species of sharks, two of the most abundant species were Sphyrna lewini and Carcharhinus falciformis, both evaluated on IUCN the Red List of Threatened species (Critically Endangered and Vulnerable) and CITES regulated. We found low genetic diversity in the sampled area increasing the concern for both species in the region, even more considering that the majority of individuals were juveniles. Our results showed the importance of genetic markers for first population genetic insights as a complementary tool during the decision-making process in management plans. For this specific region, strategies such as the delimitation of conservation priority areas or the regulation of fishing gears could help improve the sustainability of shark populations in the Colombian Pacific.publishedVersio

Adaptive simulation of unsteady flow past the submerged part of a floating wind turbine platform

Offshore floating platforms for wind turbines represent challenging concepts for designers trying to combine an optimal compromise between cost effectiveness and performance. Modelling of the hydrodynamic behaviour of the structure is still the subject of wide debate in the technical communities. The assessment of the hydrodynamics of the support structure is not an easy task as the floaters consist of an assembly of columns, braces and pontoons, commonly also with heave plates: Each of these components corresponds to a different hydrodynamic model and it further interacts with the other elements. This results in very complex non-linear modeling, which makes it necessary to resort to computational fluid dynamics (CFD) methods for the evaluation of the combined hydrodynamics. In the framework of the collaboration between the Basque Centre for Applied Mathematics (BCAM) and Tecnalia R&I, the interaction of the sea flow with a semisubmersible floating offshore wind platform have been calculated by using the open source solver Unicorn in the FEniCS-HPC framework when subject to a steady inflow. The prototype of the platform consists in a semi-submersible 4-columns column stabilized platform - NAUTILUS Floating Solutions concept-; columns are connected by a rigid ring pontoon provided with heave damping plates at the bottom. The novelty of the approach in FEniCS-HPC hinges upon an implicit formulation for the turbulence, a cheap free slip model of the boundary layer and goal-oriented mesh adaptivity [8, 6, 9, 20, 1]. We find that the results are consistent with experimental results for cylinders at high Reynolds number

Phylogeography of the vector nematode Xiphinema index using mitochondrial and microsatellite markers highlights its Eastern origin closely linked to grapevine domestication.

The economic impact of the dagger nematode Xiphinema index is high in Western vineyards by transmitting the damaging Grapevine fanleaf virus. Our phylogeographical study based on mitochondrial sequences and microsatellite loci used more than 80 X. index representative samples collected from the Middle- and Near East, the Eastern-, Central- and Western Mediterranean, and the Western countries (Europe and the Americas). In this mainly (meiotic) parthenogenetic species, the mitochondrial marker CytB was first considered for comparison of X. index with the related amphimictic vector species X. diversicaudatum. Xiphinema index exhibits a significantly lower intraspecific molecular variability than X. diversicaudatum, in agreement with the respective reproduction modes of both nematodes. We then showed that CytB, concatenated with additional mitochondrial genes ATP6, ND4 and COI, display a robust phylogeographical pattern consisting in three clades grouping Eastern Mediterranean, Nearand Middle Eastern samples and a single clade grouping samples from Western Mediterranean, Europe and the Americas. The highest mitochondrial polymorphism is observed in one clade of Middle- and Near-East samples that overlaps the Transcaucasia and Southern Caspian Sea region from where grapevine has been presumably domesticated and that likely overlaps the nematode native area. East-to-west nematode dissemination appears to match that of its domesticated grapevine host during the Antiquity mainly by the Greeks and then the Romans. In Western Mediterranean, Europe and the Americas, two close and almost exclusive mitochondrial haplotypes were detected. The first haplotype, found in vineyards from the Southern Iberian Peninsula, Bordeaux and Provence, exhibits a high microsatellite polymorphism. By contrast, the second haplotype contains a single predominant microsatellite genotype surprisingly widespread in most Western countries. This is almost certainly due to its recent dispersal during the massive grapevine replants following the 19th century phylloxera crisis. Our data provide an improved knowledge of X. index diversity for future pest control strategies

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase is a distant IPK member with a singular inositide binding site for axial 2-OH recognition

Inositol phosphates (InsPs) are signaling molecules with multiple roles in cells. In particular Graphic (InsP6) is involved in mRNA export and editing or chromatin remodeling among other events. InsP6 accumulates as mixed salts (phytate) in storage tissues of plants and plays a key role in their physiology. Human diets that are exclusively grain-based provide an excess of InsP6 that, through chelation of metal ions, may have a detrimental effect on human health. Ins(1,3,4,5,6)P5 2-kinase (InsP5 2-kinase or Ipk1) catalyses the synthesis of InsP6 from InsP5 and ATP, and is the only enzyme that transfers a phosphate group to the axial 2-OH of the myo-inositide. We present the first structure for an InsP5 2-kinase in complex with both substrates and products. This enzyme presents a singular structural region for inositide binding that encompasses almost half of the protein. The key residues in substrate binding are identified, with Asp368 being responsible for recognition of the axial 2-OH. This study sheds light on the unique molecular mechanism for the synthesis of the precursor of inositol pyrophosphates

f [N pi N]: from quarks to the pion derivative coupling

We study the N pi N coupling, in the framework of a QCD-inspired confining Nambu-Jona-Lasinio model. A simple relativistic confining and instantaneous quark model is reviewed. The Salpeter equation for the nucleon and the boosted pion is solved. The f [n pi n] and f[n pi Delta] couplings are calculated and they turn out to be reasonably good. The sensibility of f[n pi n] and f[n pi Delta] to confinement, chiral symmetry breaking and Lorentz invariance is briefly discussed.Comment: 30 pages in LaTex RevTex, 6 postscript figure

RLCYC 75: A 2 kW electrically calibrated laser calorimeter designed for Laser MegaJoule diagnostics calibration

RLCYC 75 is a new electrically calibrated laser calorimeter specially manufactured by Laser Metrology to calibrate energy diagnostics within the Laser MegaJoule (LMJ) facility. It consists of an optical cavity cooled by a hydraulic system. The system is designed to provide 1 m wavelength power laser measurements with uncertainty less than 1% at 2 kW and traceability to the International System of Units (SI). In this paper, the accuracy of RLCYC 75 measurements is studied. More precisely, three points are detailed: instrumentation uncertainty estimation, equivalence between optical and electrical supply and light absorption. To this end, electrical calibration campaigns and power laser measurement campaigns are conducted. Moreover, thermal and optical models are developed. Results show that RLCYC 75 design and instrumentation are efficient enough to reach the goal of relative uncertainty of about 1% at 2 kW. RLCYC 75 will become the 2 kW laser power primary standard for LMJ applications

Non-alcoholic fatty liver in hereditary fructose intolerance

Background: Non-alcoholic fatty liver disease (NAFLD) is characterized by fat accumulation affecting >5% of the liver volume that is not explained by alcohol abuse. It is known that fructose gives rise to NAFLD and it has been recently described that the ingestion of fructose in low amounts in aldolase B deficient mice is associated with the development of fatty liver. Therefore, it is reasonable that patients with HFI (Hereditary Fructose Intolerance) present fatty liver at diagnosis, but its prevalence in patients treated and with adequate follow-up is not well documented in the literature. The aim of this study is to analyze the association between HFI and NAFLD in treated patients. Methods: A cross-sectional observational study was conducted. The population comprised 16 genetically diagnosed HFI patients aged from 3 years to 48 and in dietary treatment of fructose, sorbitol and sacarose exclusion at least for two years. Blood samples were obtained for analytical studies and anthropometric measurements of each patient were performed. Results: Patients presented a Body Mass Index (BMI) of 17.9 ± 2.9 kg/m 2 . The HOMA index and Quick index were in normal range for our population. The S-adenosyl-methionine (SAM)/S-adenosyl-L-homocysteine (SAH) ratio was increased in the patients in whom this analysis was performed. By imaging techniques it was observed that 9 of the 16 patients presented fatty liver (7 by hepatic MRI). Of these 9 patients, only 3 presented hepatomegaly. 7 of 9 patients affected by the c.448G > C mutation had fatty infiltration, of which three of them presented in addition hepatomegaly. Conclusions: There is a high prevalence of fatty liver in HFI patients and it is not related to obesity and insulin resistance. The diagnosis of fatty liver in HFI patients and, above all, the identification of new therapeutic approaches, can positively impact the quality of life of these patients

Truncation-Driven Lateral Association of α-Synuclein Hinders Amyloid Clearance by the Hsp70-Based Disaggregase

The aggregation of α-synuclein is the hallmark of a collective of neurodegenerative disorders known as synucleinopathies. The tendency to aggregate of this protein, the toxicity of its aggregation intermediates and the ability of the cellular protein quality control system to clear these intermediates seems to be regulated, among other factors, by post-translational modifications (PTMs). Among these modifications, we consider herein proteolysis at both the N- and C-terminal regions of α-synuclein as a factor that could modulate disassembly of toxic amyloids by the human disaggregase, a combination of the chaperones Hsc70, DnaJB1 and Apg2. We find that, in contrast to aggregates of the protein lacking the N-terminus, which can be solubilized as efficiently as those of the WT protein, the deletion of the C-terminal domain, either in a recombinant context or as a consequence of calpain treatment, impaired Hsc70-mediated amyloid disassembly. Progressive removal of the negative charges at the C-terminal region induces lateral association of fibrils and type B* oligomers, precluding chaperone action. We propose that truncation-driven aggregate clumping impairs the mechanical action of chaperones, which includes fast protofilament unzipping coupled to depolymerization. Inhibition of the chaperone-mediated clearance of C-truncated species could explain their exacerbated toxicity and higher propensity to deposit found in vivo.This work was supported by grants PID2019-111068GB-I00 (to A.M.) (AEI/FEDER, UE) and PID2019-105872GB-I00 (to J.M.V.) (AEI/FEDER, UE) from the Ministry of Science and Innovation and by the Basque Government (grant IT1201-19 to AM). The Centro Nacional de Biotecnología (CNB) is a Severo Ochoa Center of Excellence (MINECO award SEV 2017-0712). N.O. holds a contract funded by Fundacion Biofisika Bizkaia. Acknowledgment

Early respiratory viral infections in infants with cystic fibrosis

This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Background Viral infections contribute to morbidity in cystic fibrosis (CF), but the impact of respiratory viruses on the development of airway disease is poorly understood. Methods Infants with CF identified by newborn screening were enrolled prior to 4 months of age to participate in a prospective observational study at 4 centers. Clinical data were collected at clinic visits and weekly phone calls. Multiplex PCR assays were performed on nasopharyngeal swabs to detect respiratory viruses during routine visits and when symptomatic. Participants underwent bronchoscopy with bronchoalveolar lavage (BAL) and a subset underwent pulmonary function testing. We present findings through 8.5 months of life. Results Seventy infants were enrolled, mean age 3.1 ± 0.8 months. Rhinovirus was the most prevalent virus (66%), followed by parainfluenza (19%), and coronavirus (16%). Participants had a median of 1.5 viral positive swabs (range 0–10). Past viral infection was associated with elevated neutrophil concentrations and bacterial isolates in BAL fluid, including recovery of classic CF bacterial pathogens. When antibiotics were prescribed for respiratory-related indications, viruses were identified in 52% of those instances. Conclusions Early viral infections were associated with greater neutrophilic inflammation and bacterial pathogens. Early viral infections appear to contribute to initiation of lower airway inflammation in infants with CF. Antibiotics were commonly prescribed in the setting of a viral infection. Future investigations examining longitudinal relationships between viral infections, airway microbiome, and antibiotic use will allow us to elucidate the interplay between these factors in young children with CF