Richer than Gold: the fungal biodiversity of Reserva Los Cedros, a threatened Andean cloud forest

BACKGROUND

Globally, many undescribed fungal taxa reside in the hyperdiverse, yet undersampled, tropics. These species are under increasing threat from habitat destruction by expanding extractive industry, in addition to global climate change and other threats. Reserva Los Cedros is a primary cloud forest reserve of ~ 5256 ha, and is among the last unlogged watersheds on the western slope of the Ecuadorian Andes. No major fungal survey has been done there, presenting an opportunity to document fungi in primary forest in an underrepresented habitat and location. Above-ground surveys from 2008 to 2019 resulted in 1760 vouchered collections, cataloged and deposited at QCNE in Ecuador, mostly Agaricales sensu lato and Xylariales. We document diversity using a combination of ITS barcode sequencing and digital photography, and share the information via public repositories (GenBank & iNaturalist).

RESULTS

Preliminary identifications indicate the presence of at least 727 unique fungal species within the Reserve, representing 4 phyla, 17 classes, 40 orders, 101 families, and 229 genera. Two taxa at Los Cedros have recently been recommended to the IUCN Fungal Red List Initiative (Thamnomyces chocöensis Læssøe and "Lactocollybia" aurantiaca Singer), and we add occurrence data for two others already under consideration (Hygrocybe aphylla Læssøe & Boertm. and Lamelloporus americanus Ryvarden).

CONCLUSIONS

Plants and animals are known to exhibit exceptionally high diversity and endemism in the Chocó bioregion, as the fungi do as well. Our collections contribute to understanding this important driver of biodiversity in the Neotropics, as well as illustrating the importance and utility of such data to conservation efforts.

RESUMEN

Antecedentes: A nivel mundial muchos taxones fúngicos no descritos residen en los trópicos hiper diversos aunque continúan submuestreados. Estas especies están cada vez más amenazadas por la destrucción del hábitat debido a la expansión de la industria extractivista además del cambio climático global y otras amenazas. Los Cedros es una reserva de bosque nublado primario de ~ 5256 ha y se encuentra entre las últimas cuencas hidrográficas no explotadas en la vertiente occidental de los Andes ecuatorianos. Nunca antes se ha realizado un estudio de diversidad micológica en el sitio, lo que significa una oportunidad para documentar hongos en el bosque primario, en hábitat y ubicación subrepresentatadas. El presente estudio recopila información entre el 2008 y 2019 muestreando material sobre todos los sustratos, reportando 1760 colecciones catalogadas y depositadas en el Fungario del QCNE de Ecuador, en su mayoría Agaricales sensu lato y Xylariales; además se documenta la diversidad mediante secuenciación de códigos de barras ITS y fotografía digital, la información está disponible en repositorios públicos digitales (GenBank e iNaturalist).

RESULTADOS

La identificación preliminar indica la presencia de al menos 727 especies únicas de hongos dentro de la Reserva, que representan 4 filos, 17 clases, 40 órdenes, 101 familias y 229 géneros. Recientemente dos taxones en Los Cedros se recomendaron a la Iniciativa de Lista Roja de Hongos de la UICN (Thamnomyces chocöensis Læssøe y "Lactocollybia" aurantiaca Singer) y agregamos datos de presencia de otros dos que ya estaban bajo consideración (Hygrocybe aphylla Læssøe & Boertm. y Lamelloporus americanus Ryvarden).

CONCLUSIONES

Se sabe que plantas y animales exhiben una diversidad y endemismo excepcionalmente altos en la bioregión del Chocó y los hongos no son la excepción. Nuestras colecciones contribuyen a comprender este importante promotor de la biodiversidad en el Neotrópico además de ilustrar la importancia y utilidad de dichos datos para los esfuerzos de conservación.

Genome-wide gene expression responses to experimental manipulation of Saccharomyces cerevisiae repressor activator protein 1 (Rap1) expression level

Precise regulation of transcription in gene expression is critical for all aspects of normal organism form, fitness, and function and even minor alterations in the level, location, and timing of gene expression can result in phenotypic variation within and between species including evolutionary innovations and human disease states. Eukaryotic transcription is regulated by a complex interplay of multiple factors working both at a physical and molecular levels influencing this process. In Saccharomyces cerevisiae, the TF with the greatest number of putative regulatory targets is the essential gene Repressor Activator Protein 1 (RAP1). While much is known about the roles of Rap1 in gene regulation and numerous cellular processes, the response of Rap1 target genes to systematic titration of RAP1 expression level remains unknown. To fill this knowledge gap, we used a strain with a tetracycline-titratable promoter replacing wild-type regulatory sequences of RAP1 to systematically reduce the expression level of RAP1 and followed this with RNA sequencing (RNA-seq) to measure genome-wide gene expression responses. Previous research indicated that Rap1 plays a significant regulatory role in particular groups of genes including telomere-proximal genes, homothallic mating (HM) loci, glycolytic genes, DNA repair genes, and ribosomal protein genes; therefore, we focused our analyses on these groups and downstream targets to determine how they respond to reductions in RAP1 expression level. Overall, despite being known as both an activator and as a repressor of its target genes, we found that Rap1 acts as an activator for more target genes than as a repressor. Additionally, we found that Rap1 functions as an activator of ribosomal protein genes and a repressor of the silent mating locus genes consistent with predictions from the literature. Unexpectedly, we found that Rap1 functions as a repressor of glycolytic enzyme genes contrary to prior reports of it having the opposite effect. We also compared the expression of RAP1 to five different genes related to DNA repair pathway and found that decreasing RAP1 downregulated four of those five genes. Finally, we found no effect of RAP1 depletion on telomere-proximal genes despite its functioning to silence telomeric repeat-containing RNAs. Together our results enrich our understanding of this important transcriptional regulator. The graphical abstract is provided as a supplementary fig. (S-Fig 1).

Vaccine distrust: Investigation of the views and attitudes of parents in regard to vaccination of their children

BACKGROUND

In France, many parents have lost confidence in vaccinations, which has a direct impact on immunization coverage. Pharmacists, like other health professionals, often encounter parents exhibiting vaccine distrust.

METHODS

Using a survey distributed in a school and in a number of volunteering pharmacies, the objective of this study was to gain a better understanding of the views and the attitude of parents in regard to vaccination of their children.

RESULTS

Our results show that the main concerns were in regard to vaccine adjuvants, the risk of short- and long-term adverse effects, and the risk of developing a disease or a disability as a result of vaccination. The parents, although they tended to express a degree of reluctance and apprehension, in general, they were not opposed to vaccination, and they sought objective scientific information and full transparency regarding all aspects of vaccine composition, adverse effects, and effectiveness. Cooperation of all the parties involved in the health system on this subject is essential for a seamless chain of care and to improve vaccination coverage.

CONCLUSION

The information collected, combined with a review of the international literature, allow avenues for dialogue adapted to parents' opinions to be established and thus assist health professionals to communicate effectively regarding vaccines, which is a bona fide public health issue.

Micromagnetic study of the vortex state in sub-micron iron discs

Magnetic nanostructures have been widely studied due to its poten¬tial applicability into several research fields such as data storage, sensing and biomedical applications. In this work, micromagnetic simulations (mumax3) of sub-micron iron discs are performed for different normalized inter-dot distance (distance/diameter), to better understand the magnetic behaviour of these nanos-tructures. Two sets of samples were studied: ideal circular discs and disc-shaped nanostructures (based on images of real samples). By analyzing the nucleation and annihilation fields and the magnetic susceptibility, it was found that the (ideal) discs could be considered as isolated for inter-dot distances greater than twice the raidus of the disc (2R). The difference in the shape of the disc-shaped nanostructures resulted in an in-plane anisotropy, noticeable on the hysteresis loops for different directions.

Linezolid versus vancomycin cost in the treatment of staphylococcal pneumonia

OBJECTIVE

Staphylococcusaureus is involved in around 20% of nosocomial pneumonia cases. Vancomycin used to be the reference antibiotic in this indication, but new molecules have been commercialized, such as linezolid. Previous studies comparing vancomycin and linezolid were based on models. Comparing their real costs from a hospital perspective was needed.

METHODS

We performed a bicentric retrospective analysis with a cost-minimization analysis. The hospital antibiotic acquisition costs were used, as well as the laboratory test and administration costs from the health insurance cost scale. The cost of each hospital stay was evaluated using the national cost scale per diagnosis related group (DRG), and was then weighted by the stay duration.

RESULTS

Fifty-eight patients were included. All bacteria identified in pulmonary samples were S. aureus. The cost of nursing care per stay with linezolid was €234.10 (SD=91.50) vs. €381.70 (SD=184.70) with vancomycin (P=0.0029). The cost of laboratory tests for linezolid was €172.30 (SD=128.90) per stay vs. €330.70 (SD=198.40) for vancomycin (P=0.0005). The acquisition cost of linezolid per stay was not different from vancomycin based on the price of the generic drug (€54.92 [SD=20.54] vs. €40.30 [SD=22.70]). After weighting by the duration of stay observed, the mean cost per hospital stay was €47,411.50 for linezolid and €57,694.0 for vancomycin (NSD).

CONCLUSION

These results, in favor of linezolid, support other former pharmacoeconomic study based on models. The mean cost per hospitalization stay was not statistically different between the two study groups, but a trend in favor of linezolid is emerging.

A prospective observational study of medication errors in a pediatric emergency department

We present a prospective, observational study evaluating the incidence of medication errors (ME) in a university hospital pediatric emergency department and describe their characteristics and determinants. A systematic analysis of the handwritten prescriptions was conducted by a clinician and pharmacist. Of 11,573 consecutively studied prescriptions in children under 15 years of age, the ME incidence was 0.9% (n=102). The incidence of errors found was statistically significantly higher in children older than 5 years (OR=2.05; P=0.026). There was no significant difference regarding the time of admission (P=0.544), the day of the week (P=0.940), or the affluence of people in attendance at the emergency department. The errors observed were all prescription errors. Most errors were related to analgesic (51%) and antibiotic (30%) treatments. No serious errors were reported.

CONCLUSION

We found a low incidence of medication errors in this study. The validation of prescriptions by a senior multidisciplinary staff could contribute to limited medication errors. Measures should be continued to further reduce the incidence of drug errors by calling the attention of prescribers to the most common situations at risk of ME.

Gram-negative prosthetic joint infections managed according to a multidisciplinary standardized approach: risk factors for failure and outcome with and without fluoroquinolones

OBJECTIVES

To describe the outcome and risk factors for treatment failure of 76 Gram-negative bacilli (GNB) prosthetic joint infections (PJIs) managed with a curative intent according to a standardized protocol derived from published guidelines.

METHODS

We analysed data from all the cases of GNB-PJI treated surgically over an 8 year period. Treatment failure was defined as persistence or recurrence of PJI signs during follow-up, resulting in additional surgery and/or antibiotic administration or death.

RESULTS

Treatment failure within the follow-up period (median = 2.6 years) was observed in 16 of 76 (21.1%) patients. The failure rate was similar whether the patients were treated with fluoroquinolones in the whole cohort (22.4% versus 16.7%, P = 0.75) and after stratification according to the surgical procedure. The low failure rate observed in patients not receiving fluoroquinolones might be explained by the standardized attitude of maintaining intravenous β-lactams throughout treatment duration (median = 90 days). In multivariate analysis, C-reactive protein level ≥175 mg/L was significantly associated with treatment failure (adjusted HR = 7.75, 95% CI = 2.66-22.59, P < 0.0001).

CONCLUSIONS

Management according to standardized procedures may improve the prognosis of GNB-PJI. Intravenous β-lactams, continued for 3 months, should be considered an effective alternative to fluoroquinolones.

Levofloxacin at the usual dosage to treat bone and joint infections: a cohort analysis

Fluoroquinolones are recommended for the treatment of bone and joint infections (BJIs), and levofloxacin is commonly used in this setting. However, no pre-marketing clinical study has supported its use, especially its dosage, for treating BJIs. This study aimed to assess the benefit-risk ratio of levofloxacin administered orally at a standard dosage of 500 mg once daily (OD) in a cohort of patients with BJIs. The medical records of patients admitted to a large French teaching hospital for BJI over a 1-year period and managed by a multidisciplinary team were reviewed. Patient data were recorded on a standardised form and the outcome was assessed at the end of antibiotic treatment and after 1-year of follow-up. A total of 230 patients were included, of whom 79 were treated with an antibiotic regimen including levofloxacin (34%). Most BJIs (97%) were surgically treated by wound debridement and/or removal or replacement of the infected device. Adverse drug reactions to levofloxacin leading to treatment discontinuation occurred in three patients (4%). The antibiotic treatment duration was significantly longer in patients treated with levofloxacin compared with other antibiotic regimens (median, 13 weeks vs. 6 weeks). Post-treatment outcomes were considered favourable (total or partial recovery, including orthopaedics aftermath) in 89-93% of patients, with no significant difference between treatment groups. In conclusion, oral levofloxacin at 500 mg OD is a well-tolerated and efficacious antibiotic treatment for BJIs. Our approach of following-up all treated patients is a useful way to validate specific clinical practices.

Exchange-bias phenomenon: the role of the ferromagnetic spin structure

The exchange bias of antiferromagnetic-ferromagnetic (AFM-FM) bilayers is found to be strongly dependent on the ferromagnetic spin configuration. The widely accepted inverse proportionality of the exchange bias field with the ferromagnetic thickness is broken in FM layers thinner than the FM correlation length. Moreover, an anomalous thermal dependence of both exchange bias field and coercivity is also found. A model based on springlike domain walls parallel to the AFM-FM interface quantitatively accounts for the experimental results and, in particular, for the deviation from the inverse proportionality law. These results reveal the active role the ferromagnetic spin structure plays in AFM-FM hybrids which leads to a new paradigm of the exchange bias phenomenon.

Deconvolution of the EPR spectra of vanadium oxide nanotubes

In this work we report results of continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy of vanadium oxide nanotubes. The observed EPR spectra are composed of a weak well-resolved spectrum of isolated V(4+) ions on top of an intense and broad structure-less line shape, attributed to spin-spin exchanged V(4+) clusters. With the purpose to deconvolute the structured weak spectrum from the composed broad line, a new approach based on the Krylov basis diagonalization method (KBDM) is introduced. It is based on the discrimination between broad and sharp components with respect to a selectable threshold and can be executed with few adjustable parameters, without the need of a priori information on the shape and structure of the lines. This makes the method advantageous with respect to other procedures and suitable for fast and routine spectral analysis, which, in conjunction with simulation techniques based on the spin Hamiltonian parameters, can provide a full characterization of the EPR spectrum. Results demonstrate and characterize the coexistence of two V(4+) species in the nanotubes and show good progress toward the goal of obtaining high fidelity deconvoluted spectra from complex signals with overlapping broader line shapes.

CoCrPt/Ti perpendicular media onto nanostructured polymer templates

The fabrication and the study of the magnetic properties of CoCrPt/Ti nanostructures produced by sputtering onto ordered polymer templates are reported here. Samples exhibit a significant out-of-plane component of the magnetization higher than for planar films, and it is stronger for the thicker CoCrPt films, and for nanostructured films with the shorter period ordering. The shape of the polymeric templates plays an important role for the determination of magnetic easy-axis. Magnetic Force Microscopy images of the samples show a single magnetic domain structure with high out-of-plane anisotropy for the samples with longer ordering (480 nm period).

Preparation and magnetic properties of cylindrical NiFe films and antidot arrays

Continuous NiFe (Permalloy) cylindrical films and arrays of cylindrical NiFe antidots 7 nm thick have been prepared by sputtering onto cylindrical aluminum wires and onto wires anodized to form a porous anodic alumina layer. The antidots are arranged in a close-packed pattern determined by the hexagonal pore arrangement in the porous alumina, with period 103 nm and diameter 42 nm. Hysteresis loops were measured at different angles with respect to the cylinder axis and indicate an easy plane normal to the radius of the wire. The antidots enhance the coercivity compared to the continuous cylindrical film.

Self-organized magnetic nanowire arrays based on alumina and titania templates

Densely packed arrays of magnetic nanowires have been synthesized by electrodeposition filling of nanopores in alumina and titania membranes formed by self-assembling during anodization process. Emphasis is made on the control of the production parameters leading to ordering degree and lattice parameter of the array as well as nanowires diameter and length. Structural, morphological and magnetic properties exhibited by nanowire arrays have been studied for several nanowire compositions, different ordering degree and for different nanowire aspect ratios. The magnetic behaviour of nanowires array is governed by the balance between different energy contributions: shape anisotropy of individual nanowires, the magnetostatic interaction of dipolar origin among nanowires, and magnetocrystalline and magnetoelastic anisotropies induced by the pattern templates. These novel nanocomposites, based on ferromagnetic nanowires embedded in anodic nanoporous templates, are becoming promising candidates for technological applications such as functionalised arrays for magnetic sensing, ultrahigh density magnetic storage media or spin-based electronic devices.

[Difficulty of epidural puncture for obstetric analgesia: risk factors]

INTRODUCTION

Predicting technical difficulties in performing an epidural block can affect the anesthesiologist's choice of technique or decisions about who should carry it out. Our aim was to determine patient characteristics associated with difficulty in performing an epidural block for obstetric analgesia.

MATERIAL AND METHODS

We designed a prospective observational study in 540 pregnant women who requested epidural analgesia for obstetric labor. Patient characteristics (age, weight, height), anatomical features (body constitution, visible and/or palpable spinal apophyses, structural anomalies), technical features (number of attempts, repositioning of the needle), anesthesiologist's experience (resident or staff), block success, time taken to accomplish the procedure, and obstetrical variables (parity, gestational age, cervical dilatation).

RESULTS

The factor that best correlates with puncture difficulty in the obstetric patient is the presence of visible or palpable spinal apophyses and palpation prior to carrying out the block. Factors like weight, body constitution, or anesthesiologist's experience seem to influence the rate of success or failure of the epidural block for obstetric analgesia, although to a lesser degree.

CONCLUSIONS

The most important factor for predicting success of an epidural block for obstetric analgesia in our practice is the presence of palpable spinal apophyses.

Bon usage des antibiotiques à l’hôpital

INTRODUCTION

The rationalization of medical practices for antibiotic use in hospitals is necessary to improve both the cost-efficiency and effectiveness of health care. This study sought to investigate the impact of implementation of local management guidelines for inpatient community-acquired pneumonia (CAP).

METHODS

This retrospective, comparative study measured the quality of antibiotic prescriptions with the 10-item Medication Appropriateness Index (MAI). Clinical and demographic characteristics, as well as process-of-care and outcome indicators, were recorded for all patients with CAP admitted to a medical ward at the Nantes university hospital during two 12-month periods: before (Period A, 39 patients) and after (Period B, 50 patients) implementation of local guidelines.

RESULTS

The MAI was significantly higher during period B than period A (5.1 points compared with 2.2, p=0.0001). Guideline implementation shortened the mean duration of antibiotic treatment (13.1 versus 16.0 days, p=0.0003) and of intravenous treatment (3.4 versus 4.7 days, p=0.04). The mean duration of hospital stay also fell substantially (7.4 versus 15.0 days, p=0.0001), as did the mean cost of antibiotics (35.4 versus 64.1 euros, p=0.003).

DISCUSSION

The MAI confirmed that antimicrobial practices varied significantly and that appropriate local guidelines improved the quality of antibiotic prescriptions and saved hospitalization costs.

CONCLUSION

The MAI, which assesses the appropriateness of antibiotic use in hospitals, could be an interesting tool for prospective use as an indicator of quality-of-care improvement and for more efficient use of available health care resources.

In vivo efficacy of continuous infusion versus intermittent dosing of ceftazidime alone or in combination with amikacin relative to human kinetic profiles in a Pseudomonas aeruginosa rabbit endocarditis model

Ceftazidime and amikacin were administered in a Pseudomonas aeruginosa rabbit endocarditis model using computer-controlled intravenous (iv) infusion pumps to simulate human serum concentrations for the following regimens: continuous (constant rate) infusion of 4, 6 or 8 g of ceftazidime over 24 h or intermittent dosing of 2 g every 8 h either alone or in combination with amikacin (15 mg/kg once daily). The in vivo activities of these regimens were tested on four Pseudomonas aeruginosa strains. Animals were killed 24 h after the beginning of treatment. Efficacy was assessed by comparing the effects of the different groups on bacterial counts in vegetations for each strain tested. For a susceptible reference strain (ATCC 27853; MICs of ceftazidime and amikacin 1 and 2 mg/L, respectively), continuous infusion of 4 g alone or with amikacin was as effective as intermittent dosing with amikacin. For a clinical isolate producing an oxacillinase (MICs of ceftazidime and amikacin 8 and 32 mg/L, respectively), continuous infusion of 6 g was equivalent to intermittent dosing. For a clinical isolate producing a TEM-2 penicillinase (MIC of ceftazidime and amikacin 4 mg/L), continuous infusion of 6 g, but not intermittent dosing, had a significant in vivo effect. For a clinical isolate producing an inducible, chromosomally encoded cephalosporinase (MIC of ceftazidime and amikacin 8 and 4 mg/L, respectively), neither continuous infusion nor intermittent dosing proved effective. Determination of ceftazidime concentrations in vegetations showed that continuous infusion produced tissue concentrations at the infection site far greater than the MIC throughout the treatment. It is concluded that continuous infusion of the same total daily dose provides significant activity as compared with fractionated infusion. This study confirms that a concentration of 4-5 x MIC is a reasonable therapeutic target in most clinical settings of severe P. aeruginosa infection.

Bactericidal effect of pefloxacin and fosfomycin against Pseudomonas aeruginosa in a rabbit endocarditis model with pharmacokinetics of pefloxacin in humans simulated in vivo

The bactericidal activity of pefloxacin and fosfomycin alone and in combination against Pseudomonas aeruginosa was evaluated in an experimental rabbit endocarditis model after 24 h of treatment. Two strains with intermediate susceptibility to pefloxacin and good susceptibility to fosfomycin were tested. The serum kinetics obtained during administration of 400 mg every 12 h in humans were simulated in the animals using computer-controlled variable-flow infusion. Fosfomycin was administered as a continuous infusion at a constant flow, allowing a steady-state concentration of 47.4 +/- 11.9 mg/ml to be reached in serum. In valvular vegetations, pefloxacin was less bactericidal than fosfomycin, and in combination treatment, it reduced (but did not abolish) the bactericidal effect of fosfomycin. The duration of the pretreatment interval (12-48 h) had a negative effect on the bactericidal activity of both drugs, especially that of fosfomycin.