Comparison of visual and passive acoustic estimates of beaked whale density off El Hierro, Canary Islands

Passive acoustic monitoring (PAM) offers considerable potential for density estimation of cryptic cetaceans, such as beaked whales. However, comparative studies on the accuracy of PAM density estimates from these species are lacking. Concurrent, low-cost drifting PAM, with SoundTraps suspended at 200 m depth, and land-based sightings, were conducted off the Canary Islands. Beaked whale density was estimated using a cue-count method, with click production rate and the probability of click detection derived from digital acoustic recording tags (DTags), and distance sampling techniques, adapted to fixed-point visual surveys. Of 32 870 detections obtained throughout 206 h of PAM recordings, 68% were classified as "certain" beaked whale clicks. Acoustic detection probability was 0.15 [coefficient variation (CV) 0.24] and click production rate was 0.46 clicks s - 1 (CV 0.05). PAM density estimates were in the range of 21.5 or 48.6 whales per 1000 km2 [CV 0.50 or 0.44, 95% confidence interval (CI) 20.7-22.4 or 47-50.9), depending on whether "uncertain" clicks were considered. Density estimates from concurrent sightings resulted in 33.7 whales per 1000 km2 (CV 0.77, 95% CI 8.9-50.5). Cue-count PAM methods under application provide reliable estimates of beaked whale density, over relatively long time periods and in realistic scenarios, as these match the concurrent density estimates obtained from visual observations.

Clinical experience and management of adverse events in patients with advanced ALK-positive non-small-cell lung cancer receiving alectinib

Alectinib is a preferred first-line therapy for patients with advanced anaplastic lymphoma kinase (ALK)-positive non-small-cell lung cancer (NSCLC) in several national clinical practice guidelines. The randomized, global, phase III ALEX study has demonstrated significant improvement in progression-free survival for alectinib over crizotinib in treatment-naive ALK-positive NSCLC. It was also the first study to show clinically meaningful improvement in overall survival for a next-generation ALK tyrosine kinase inhibitor relative to crizotinib. The J-ALEX and ALESIA phase III studies confirmed the clinical benefit of alectinib relative to crizotinib in the first-line ALK-positive NSCLC treatment setting in Japanese and Asian patients, respectively. Across these pivotal phase III trials, alectinib had a manageable, well-characterized safety profile. Here, we review the safety and tolerability of long-term alectinib treatment in patients with advanced ALK-positive NSCLC and provide guidance for physicians, based on clinical experience, on the management of the most frequently reported adverse events (AEs). Most AEs associated with alectinib can be managed by dose reduction. Some alectinib-related AEs are not yet fully characterized, including myalgia and peripheral oedema and deciphering their underlying mechanism of action could enhance their management. With longer-term follow-up, the safety profile of alectinib continues to remain consistent in the ALEX study, with no new safety signals observed. Safety and tolerability data from the first-line phase III alectinib trials are also consistent with those observed in clinical trials of alectinib in later-line settings. These results add to the weight of evidence recommending alectinib as a preferred therapy for treatment-naive advanced ALK-positive NSCLC.

A distinctive epigenetic ageing profile in human granulosa cells

STUDY QUESTION

Does women’s age affect the DNA methylation (DNAm) profile differently in mural granulosa cells (MGCs) from other somatic cells?

SUMMARY ANSWER

Accumulation of epimutations by age and a higher number of age-related differentially methylated regions (DMR) in MGCs were found compared to leukocytes from the same woman, suggesting that the MGCs have a distinctive epigenetic profile.

WHAT IS KNOWN ALREADY

The mechanisms underlying the decline in women’s fertility from the mid-30s remain to be fully elucidated. The DNAm age of many healthy tissues changes predictably with and follows chronological age, but DNAm age in some reproductive tissues has been shown to depart from chronological age (older: endometrium; younger: cumulus cells, spermatozoa).

STUDY DESIGN, SIZE, DURATION

This study is a multicenter cohort study based on retrospective analysis of prospectively collected data and material derived from healthy women undergoing IVF or ICSI treatment following ovarian stimulation with antagonist protocol. One hundred and nineteen women were included from September 2016 to June 2018 from four clinics in Denmark and Sweden.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Blood samples were obtained from 118 healthy women with varying ovarian reserve status. MGCs were collected from 63 of the 119 women by isolation from pooled follicles immediately after oocyte retrieval. DNA from leukocytes and MGCs was extracted and analysed with a genome-wide methylation array. Data from the methylation array were processed using the ENmix package. Subsequently, DNAm age was calculated using established and tailored age predictors and DMRs were analysed with the DMRcate package.

MAIN RESULTS AND ROLE OF CHANCE

Using established age predictors, DNAm age in MGCs was found to be considerable younger and constant (average: 2.7 years) compared to chronological age (average: 33.9 years). A Granulosa Cell clock able to predict the age of both MGCs (average: 32.4 years) and leukocytes (average: 38.8 years) was successfully developed. MGCs differed from leukocytes in having a higher number of epimutations (P = 0.003) but predicted telomere lengths unaffected by age (Pearson’s correlation coefficient = −0.1, P = 0.47). DMRs associated with age (age-DMRs) were identified in MGCs (n = 335) and in leukocytes (n = 1) with a significant enrichment in MGCs for genes involved in RNA processing (45 genes, P = 3.96 × 10−08) and gene expression (152 genes, P = 2.3 × 10−06). The top age-DMRs included the metastable epiallele VTRNA2-1, the DNAm regulator ZFP57 and the anti-Müllerian hormone (AMH) gene. The apparent discordance between different epigenetic measures of age in MGCs suggests that they reflect difference stages in the MGC life cycle.

LARGE SCALE DATA

N/A.

LIMITATIONS, REASONS FOR CAUTION

No gene expression data were available to associate with the epigenetic findings. The MGCs are collected during ovarian stimulation, which may influence DNAm; however, no correlation between FSH dose and number of epimutations was found.

WIDER IMPLICATIONS OF THE FINDINGS

Our findings underline that the somatic compartment of the follicle follows a different methylation trajectory with age than other somatic cells. The higher number of epimutations and age-DMRs in MGCs suggest that their function is affected by age.

STUDY FUNDING/COMPETING INTEREST(S)

This project is part of ReproUnion collaborative study, co-financed by the European Union, Interreg V ÖKS, the Danish National Research Foundation and the European Research Council. The authors declare no conflict of interest.

Efficacy of chemotherapy and atezolizumab in patients with non-small-cell lung cancer receiving antibiotics and proton pump inhibitors: pooled post hoc analyses of the OAK and POPLAR trials

BACKGROUND

Preclinical data have shown that proton pump inhibitors (PPI) can modulate the microbiome, and single-arm studies suggested that antibiotics (ATB) may decrease the efficacy of immune checkpoint inhibitors (ICI), but randomized controlled trial data are lacking. This pooled analysis evaluated the effect of ATB and PPI on outcome in patients randomized between ICI and chemotherapy.

PATIENTS AND METHODS

This retrospective analysis used pooled data from the phase II POPLAR (NCT01903993) and phase III OAK (NCT02008227) trials, which included 1512 patients with previously treated non-small-cell lung cancer (NSCLC) randomly assigned to receive atezolizumab (n = 757) or docetaxel (n = 755). The main objective of this analysis was to assess the impact of ATB and PPI use on overall survival (OS) and progression-free survival (PFS).

RESULTS

A total of 169 (22.3%) patients in the atezolizumab group and 202 (26.8%) in the docetaxel group received ATB, and 234 (30.9%) and 260 (34.4%), respectively, received PPI. Multivariate analysis in all patients revealed that ATB were associated with shorter OS [hazard ratio (HR) 1.20, 95% confidence interval (CI) 1.04-1.39], as was PPI (HR 1.26, 95% CI 1.10-1.44). Within the atezolizumab population, OS was significantly shorter in patients who received ATB (8.5 versus 14.1 months, HR 1.32, 95% CI 1.06-1.63, P = 0.01) or PPI (9.6 versus 14.5 months, HR 1.45, 95% CI 1.20-1.75, P = 0.0001). PPI use was associated with shorter PFS in the atezolizumab population (1.9 versus 2.8 months, HR 1.30, 95% CI 1.10-1.53, P = 0.001). There was no association between ATB and PPI use and PFS or OS within the docetaxel population.

CONCLUSION

In this unplanned analysis from two randomized trials, data suggest that ATB or PPI use in patients with metastatic NSCLC is associated with poor outcome and may influence the efficacy of ICI.

Alectinib versus chemotherapy in crizotinib-pretreated anaplastic lymphoma kinase (ALK)-positive non-small-cell lung cancer: results from the phase III ALUR study

Background

This is the first trial to directly compare efficacy and safety of alectinib versus standard chemotherapy in advanced/metastatic anaplastic lymphoma kinase (ALK)-positive non-small-cell lung cancer (NSCLC) patients who have progressed on, or were intolerant to, crizotinib.

Patients and methods

ALUR (MO29750; NCT02604342) was a randomized, multicenter, open-label, phase III trial of alectinib versus chemotherapy in advanced/metastatic ALK-positive NSCLC patients previously treated with platinum-based doublet chemotherapy and crizotinib. Patients were randomized 2 : 1 to receive alectinib 600 mg twice daily or chemotherapy (pemetrexed 500 mg/m² or docetaxel 75 mg/m², both every 3 weeks) until disease progression, death, or withdrawal. Primary end point was investigator-assessed progression-free survival (PFS).

Results

Altogether, 107 patients were randomized (alectinib, n = 72; chemotherapy, n = 35) in 13 countries across Europe and Asia. Median investigator-assessed PFS was 9.6 months [95% confidence interval (CI): 6.9–12.2] with alectinib and 1.4 months (95% CI: 1.3–1.6) with chemotherapy [hazard ratio (HR) 0.15 (95% CI: 0.08–0.29); P < 0.001]. Independent Review Committee-assessed PFS was also significantly longer with alectinib [HR 0.32 (95% CI: 0.17–0.59); median PFS was 7.1 months (95% CI: 6.3–10.8) with alectinib and 1.6 months (95% CI: 1.3–4.1) with chemotherapy]. In patients with measurable baseline central nervous system (CNS) disease (alectinib, n = 24; chemotherapy, n = 16), CNS objective response rate was significantly higher with alectinib (54.2%) versus chemotherapy (0%; P < 0.001). Grade ≥3 adverse events were more common with chemotherapy (41.2%) than alectinib (27.1%). Incidence of AEs leading to study-drug discontinuation was lower with alectinib (5.7%) than chemotherapy (8.8%), despite alectinib treatment duration being longer (20.1 weeks versus 6.0 weeks).

Conclusion

Alectinib significantly improved systemic and CNS efficacy versus chemotherapy for crizotinib-pretreated ALK-positive NSCLC patients, with a favorable safety profile.

Trial registration

ClinicalTrials.gov NCT02604342; Roche study MO29750

Titanium dioxide modified with silver by two methods for bactericidal applications

“Titanium dioxide (TiO₂) is a semiconductor material that exhibits antibacterial activity due to its photocatalytic properties under ultraviolet light. On the other hand, silver also exhibits strong antibacterial activity towards a wide range of microorganisms and TiO₂ with silver addition exhibits more efficient photocatalytic properties than unmodified TiO₂. In this work, TiO₂ nanoparticles were synthesized by the hydrothermal method and modified with silver by two different methods: wet impregnation (Ex situ) and In situ incorporation. The antimicrobial activity of TiO₂ nanoparticles synthesized and modified by both methods was evaluated against Escherichia coli and Staphylococcus aureus. The results showed that TiO₂ nanoparticles have anatase phase. Also, spherical morphology with a mean particle size around 10.6 nm was obtained. The presence of silver in the modified TiO₂ nanoparticles was confirmed by EDS and XPS. TiO₂ particles modified by the Ex situ method, showed a better bactericidal activity compared to the particles modified by In situ incorporation method and TiO₂ unmodified nanoparticles. This study demonstrated that both methods used to modify the titanium dioxide nanoparticles are effective as bactericidal materials and better results were found for the Ex situ method.”

Delay in starting radiotherapy due to neoadjuvant therapy does not worsen survival in unresected glioblastoma patients

PURPOSE

We retrospectively examined the potential effect on overall survival (OS) of delaying radiotherapy to administer neoadjuvant therapy in unresected glioblastoma patients.

PATIENTS AND METHODS

We compared OS in 119 patients receiving neoadjuvant therapy followed by standard treatment (NA group) and 96 patients receiving standard treatment without neoadjuvant therapy (NoNA group). The MaxStat package of R identified the optimal cut-off point for waiting time to radiotherapy.

RESULTS

OS was similar in the NA and NoNA groups. Median waiting time to radiotherapy after surgery was 13 weeks for the NA group and 4.2 weeks for the NoNA group. The longest OS was attained by patients who started radiotherapy after 12 weeks and the shortest by patients who started radiotherapy within 4 weeks (12.3 vs 6.6 months) (P = 0.05). OS was 6.6 months for patients who started radiotherapy before the optimal cutoff of 6.43 weeks and 19.1 months for those who started after this time (P = 0.005). Patients who completed radiotherapy had longer OS than those who did not, in all 215 patients and in the NA and NoNA groups (P = 0.000). In several multivariate analyses, completing radiotherapy was a universally favorable prognostic factor, while neoadjuvant therapy was never identified as a negative prognostic factor.

CONCLUSION

In our series of unresected patients receiving neoadjuvant treatment, in spite of the delay in starting radiotherapy, OS was not inferior to that of a similar group of patients with no delay in starting radiotherapy.

Optimal design of monitoring networks for multiple groundwater quality parameters using a Kalman filter: application to the Irapuato-Valle aquifer

A new method for the optimal design of groundwater quality monitoring networks is introduced in this paper. Various indicator parameters were considered simultaneously and tested for the Irapuato-Valle aquifer in Mexico. The steps followed in the design were (1) establishment of the monitoring network objectives, (2) definition of a groundwater quality conceptual model for the study area, (3) selection of the parameters to be sampled, and (4) selection of a monitoring network by choosing the well positions that minimize the estimate error variance of the selected indicator parameters. Equal weight for each parameter was given to most of the aquifer positions and a higher weight to priority zones. The objective for the monitoring network in the specific application was to obtain a general reconnaissance of the water quality, including water types, water origin, and first indications of contamination. Water quality indicator parameters were chosen in accordance with this objective, and for the selection of the optimal monitoring sites, it was sought to obtain a low-uncertainty estimate of these parameters for the entire aquifer and with more certainty in priority zones. The optimal monitoring network was selected using a combination of geostatistical methods, a Kalman filter and a heuristic optimization method. Results show that when monitoring the 69 locations with higher priority order (the optimal monitoring network), the joint average standard error in the study area for all the groundwater quality parameters was approximately 90 % of the obtained with the 140 available sampling locations (the set of pilot wells). This demonstrates that an optimal design can help to reduce monitoring costs, by avoiding redundancy in data acquisition.

A meta-analysis of published studies of endothelial dysfunction does not support its routine clinical use

BACKGROUND

Endothelial dysfunction is a marker of future cardiovascular disease (CVD) risk, yet epidemiological studies have yielded inconsistent results. We therefore studied the association between endothelial dysfunction and CVD under diverse circumstances.

METHODS AND RESULTS

Literature-based meta-analysis of prospective observational studies with ≥ 12 months of follow-up published in Medline and having information on endothelial function and CVD outcomes. Tabular data on participant characteristics, endothelial function assessments and incident CVD outcomes were abstracted from individual studies. Random-effects meta-analysis was used to quantify pooled associations, and I(2) statistic to evaluate between-study heterogeneity. Potential sources of heterogeneity were explored by subgroup analyses and meta-regression. Thirty five studies involving 17,206 participants met the inclusion criteria. During more than 80,000 person-years of observation, up to 2755 CVD events were accrued, yielding a pooled relative risk (RR) of 1.25 (95% confidence interval 1.15-1.35) for CVD comparing top (i.e. more severe) vs. bottom (less severe) third of endothelial dysfunction. There was significant between-study heterogeneity and evidence of publication bias. RRs varied importantly according to the method used to ascertain endothelial function, and were higher among older individuals and among participants with risk factors for CVD or established CVD at baseline.

CONCLUSIONS

Although endothelial dysfunction is an important determinant of cardiovascular outcomes in people with pre-existing CVD, current evidence base does not support its use as a potentially useful measurement for risk stratification in people at lower risk of CVD.

Middle Miocene closure of the Central American Seaway

Uranium-lead geochronology in detrital zircons and provenance analyses in eight boreholes and two surface stratigraphic sections in the northern Andes provide insight into the time of closure of the Central American Seaway. The timing of this closure has been correlated with Plio-Pleistocene global oceanographic, atmospheric, and biotic events. We found that a uniquely Panamanian Eocene detrital zircon fingerprint is pronounced in middle Miocene fluvial and shallow marine strata cropping out in the northern Andes but is absent in underlying lower Miocene and Oligocene strata. We contend that this fingerprint demonstrates a fluvial connection, and therefore the absence of an intervening seaway, between the Panama arc and South America in middle Miocene times; the Central American Seaway had vanished by that time.

Evaluation of hydrochemical changes due to intensive aquifer exploitation: case studies from Mexico

The impact of intensive aquifer exploitation has been observed in numerous places around the world. Mexico is a representative example of this problem. In 2010, 101 out of the 653 aquifers recognized in the country, showed negative social, economic, and environmental effects related to intensive exploitation. The environmental effects include, among others, groundwater level decline, subsidence, attenuation, and drying up of springs, decreased river flow, and deterioration of water quality. This study aimed at determining the hydrochemical changes produced by intensive aquifer exploitation and highlighting water quality modifications, taking as example the Valle de Toluca, Salamanca, and San Luis Potosi aquifers in Mexico's highlands. There, elements such as fluoride, arsenic, iron, and manganese have been detected, resulting from the introduction of older groundwater with longer residence times and distinctive chemical composition (regional flows). High concentrations of other elements such as chloride, sulfate, nitrate, and vanadium, as well as pathogens, all related to anthropogenic pollution sources (wastewater infiltration, irrigation return flow, and atmospheric pollutants, among others) were also observed. Some of these elements (nitrate, fluoride, arsenic, iron, and manganese) have shown concentrations above Mexican and World Health Organization drinking water standards.