Topical Insulin for Ocular Surface Disease

Background: Insulin and insulin-like growth factor (IGF)-1 receptors are present in ocular tissues such as corneal epithelium, keratocytes, and conjunctival cells. Insulin plays a crucial role in the growth, differentiation, and proliferation of corneal epithelial cells, as well as in wound healing processes in various tissues. Purpose: This review explores the potential role of topical insulin in the treatment of ocular surface diseases. Specifically, it examines its impact on corneal nerve regeneration, sub-basal plexus corneal nerves, and its application in conditions like corneal epithelial defects, dry eye disease, and diabetic keratopathy. Methods: The review analyzes studies conducted over the past decade that have investigated the use of topical insulin in ocular surface diseases. It focuses on indications, drug preparation methods, side effects, efficacy outcomes, and variations in insulin concentrations and dosages used. Results: While off-label use of topical insulin has shown promising results in refractory corneal epithelial defects, its efficacy in dry eye disease is yet to be demonstrated. Variations in concentrations, dilutions, and dosing guidelines have been reported. However, limited data on ocular penetration, ocular toxicity, and systemic side effects pose challenges to its widespread utility. Conclusion: This review synthesizes findings from ocular investigations on topical insulin to assess its potential applicability in treating ocular surface and corneal diseases. By highlighting indications, preparation methods, side effects, and efficacy outcomes, it aims to provide insights into the current status and future prospects of using topical insulin in ophthalmic practice.

Baseline Circulating Blood Cell Counts and Ratios and Changes Therein for Predicting Immune-Related Adverse Events during Immune Checkpoint Inhibitor Therapy: A Multicenter, Prospective, Observational, Pan-Cancer Cohort Study with a Gender Perspective

Several factors have been associated with the occurrence of immune-related adverse events (irAEs) induced by immune checkpoint inhibitor (ICI) therapy. Despite their availability, the predictive value of circulating blood cell parameters remains underexplored. Our aim was to investigate whether baseline values of and early changes in absolute neutrophil count (ANC), absolute lymphocyte count (ALC), other blood cell counts, and lymphocyte-related ratios can predict irAEs and whether sex may differentially influence this potential predictive ability. Of the 145 patients included, 52 patients (35.8%) experienced at least one irAE, with a 1-year cumulative incidence of 41.6%. Using Fine and Gray competing risk models, we identified female sex (hazard ratio (HR) = 2.17, 95% confidence interval (CI) = 1.20-3.85), high ALC before ICI initiation (HR = 1.63, 95% CI = 1.09-2.45), and low ANC after ICI initiation (HR = 0.81, 95% CI = 0.69-0.96) as predictors of irAEs. However, ALC and ANC may only have an impact on the risk of irAEs in women (stratified for female sex, ALC-related HR = 2.61, 95% CI = 1.40-4.86 and ANC-related HR = 0.57, 95% CI = 0.41-0.81). Priority should be given to developing models to predict ICI-related toxicity and their validation in various settings, and such models should assess the impact of patient sex on the risk of toxicity.

Molecular responses to ocean acidification in an Antarctic bivalve and an ascidian

Southern Ocean organisms are considered particularly vulnerable to Ocean acidification (OA), as they inhabit cold waters where calcite-aragonite saturation states are naturally low. It is also generally assumed that OA would affect calcifying animals more than non-calcifying animals. In this context, we aimed to study the impact of reduced pH on both types of species: the ascidian Cnemidocarpa verrucosa sp. A, and the bivalve Aequiyoldia eightsii, from an Antarctic fjord. We used gene expression profiling and enzyme activity to study the responses of these two Antarctic benthic species to OA. We report the results of an experiment lasting 66 days, comparing the molecular mechanisms underlying responses under two pCO2 treatments (ambient and elevated pCO2). We observed 224 up-regulated and 111 down-regulated genes (FC ≥ 2; p-value ≤ 0.05) in the ascidian. In particular, the decrease in pH caused an upregulation of genes involved in the immune system and antioxidant response. While fewer differentially expressed (DE) genes were observed in the infaunal bivalve, 34 genes were up-regulated, and 69 genes were downregulated (FC ≥ 2; p-value ≤ 0.05) in response to OA. We found downregulated genes involved in the oxidoreductase pathway (such as glucose dehydrogenase and trimethyl lysine dioxygenase), while the heat shock protein 70 was up-regulated. This work addresses the effect of OA in two common, widely distributed Antarctic species, showing striking results. Our major finding highlights the impact of OA on the non-calcifying species, a result that differ from the general trend, which describes a higher impact on calcifying species. This calls for discussion of potential effects on non-calcifying species, such as ascidians, a diverse and abundant group that form extended three-dimensional clusters in shallow waters and shelf areas in the Southern Ocean.

Significant differences in efficiency between two commonly used ionophore solutions for assisted oocyte activation (AOA): a prospective comparison of ionomycin and A23187

PURPOSE

Despite the success of ICSI in treating severe male factor infertile patients, total fertilization failure (FF) still occurs in around 1-3% of ICSI cycles. To overcome FF, the use of calcium ionophores has been proposed to induce oocyte activation and restore fertilization rates. However, assisted oocyte activation (AOA) protocols and ionophores vary between laboratories, and the morphokinetic development underlying AOA remains understudied.

METHODS

A prospective single-center cohort study involving 81 in vitro matured metaphase-II oocytes from 66 oocyte donation cycles artificially activated by A23187 (GM508 CultActive, Gynemed) (n=42) or ionomycin (n=39). Parthenogenesis was induced, and morphokinetic parameters (tPNa, tPNf, t2-t8, tSB, and tB) were compared between the 2 study groups and a control group comprising 39 2PN-zygotes from standard ICSI cycles.

RESULTS

Ionomycin treatment resulted in higher activation rates compared to A23187 (38.5% vs 23.8%, p=0.15). Importantly, none of the A23187-activated parthenotes formed blastocysts. When evaluating the morphokinetic dynamics between the two ionophores, we found that tPNa and tPNf were significantly delayed in the group treated by A23187 (11.84 vs 5.31, p=0.002 and 50.15 vs 29.69, p=0.005, respectively). t2 was significantly delayed in A23187-activated parthenotes when compared to the double heterologous control embryo group. In contrast, the morphokinetic development of ionomycin-activated parthenotes was comparable to control embryos (p>0.05).

CONCLUSION

Our results suggest that A23187 leads to lower oocyte activation rates and profoundly affects morphokinetic timings and preimplantation development in parthenotes. Despite our limited sample size and low parthenote competence, standardization and further optimization of AOA protocols may allow wider use and improved outcomes for FF cycles.

Predictive Biomarkers for Checkpoint Inhibitor Immune-Related Adverse Events

Immune-checkpoint inhibitors (ICIs) are antagonists of inhibitory receptors in the immune system, such as the cytotoxic T-lymphocyte-associated antigen-4, the programmed cell death protein-1 and its ligand PD-L1, and they are increasingly used in cancer treatment. By blocking certain suppressive pathways, ICIs promote T-cell activation and antitumor activity but may induce so-called immune-related adverse events (irAEs), which mimic traditional autoimmune disorders. With the approval of more ICIs, irAE prediction has become a key factor in improving patient survival and quality of life. Several biomarkers have been described as potential irAE predictors, some of them are already available for clinical use and others are under development; examples include circulating blood cell counts and ratios, T-cell expansion and diversification, cytokines, autoantibodies and autoantigens, serum and other biological fluid proteins, human leucocyte antigen genotypes, genetic variations and gene profiles, microRNAs, and the gastrointestinal microbiome. Nevertheless, it is difficult to generalize the application of irAE biomarkers based on the current evidence because most studies have been retrospective, time-limited and restricted to a specific type of cancer, irAE or ICI. Long-term prospective cohorts and real-life studies are needed to assess the predictive capacity of different potential irAE biomarkers, regardless of the ICI type, organ involved or cancer site.

Stochastic simulation of successive waves of COVID-19 in the province of Barcelona

Analytic compartmental models are currently used in mathematical epidemiology to forecast the COVID-19 pandemic evolution and explore the impact of mitigation strategies. In general, such models treat the population as a single entity, losing the social, cultural and economical specificities. We present a network model that uses socio-demographic datasets with the highest available granularity to predict the spread of COVID-19 in the province of Barcelona. The model is flexible enough to incorporate the effect of containment policies, such as lockdowns or the use of protective masks, and can be easily adapted to future epidemics. We follow a stochastic approach that combines a compartmental model with detailed individual microdata from the population census, including social determinants and age-dependent strata, and time-dependent mobility information. We show that our model reproduces the dynamical features of the disease across two waves and demonstrates its capability to become a powerful tool for simulating epidemic events.

Search for Gamma-Ray Spectral Lines from Dark Matter Annihilation up to 100 TeV toward the Galactic Center with MAGIC

Linelike features in TeV γ rays constitute a "smoking gun" for TeV-scale particle dark matter and new physics. Probing the Galactic Center region with ground-based Cherenkov telescopes enables the search for TeV spectral features in immediate association with a dense dark matter reservoir at a sensitivity out of reach for satellite γ-ray detectors, and direct detection and collider experiments. We report on 223 hours of observations of the Galactic Center region with the MAGIC stereoscopic telescope system reaching γ-ray energies up to 100 TeV. We improved the sensitivity to spectral lines at high energies using large-zenith-angle observations and a novel background modeling method within a maximum-likelihood analysis in the energy domain. No linelike spectral feature is found in our analysis. Therefore, we constrain the cross section for dark matter annihilation into two photons to ⟨σv⟩≲5×10^{-28}  cm^{3} s^{-1} at 1 TeV and ⟨σv⟩≲1×10^{-25}  cm^{3} s^{-1} at 100 TeV, achieving the best limits to date for a dark matter mass above 20 TeV and a cuspy dark matter profile at the Galactic Center. Finally, we use the derived limits for both cuspy and cored dark matter profiles to constrain supersymmetric wino models.

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

The new developments in Cryo-EM Single Particle Analysis are helping us to understand how the macromolecular structure and function meet to drive biological processes. By capturing many states at the particle level, it is possible to address how macromolecules explore different conformations, information that is classically extracted through 3D classification. However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. To characterize the whole structural spectrum of a macromolecule, we propose an extension of our Zernike3D approach, able to extract per-image continuous flexibility information directly from a particle dataset. Also, our method can be seamlessly applied to images, maps or atomic models, opening integrative possibilities. Furthermore, we introduce the ZART reconstruction algorithm, which considers the Zernike3D deformation fields to revert particle conformational changes during the reconstruction process, thus minimizing the blurring induced by molecular motions.

Image processing tools for the validation of CryoEM maps

The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded.

Impact of hormone therapy side effects on health-related quality of life, distress, and well-being of breast cancer survivors

To explore the modulatory role of Adjuvant Hormone Therapy (AHT) on health-related quality of life (QoL), subjective well-being and distress prevalence in Breast Cancer (BC) survivors, considering the survival phase. Cross-sectional study with control group. 616 BC survivors participated. Examination of interaction effect between AHT and time since end of primary treatment showed that many of the positive changes observed through the survival phases were experienced exclusively by survivors without AHT. When AHT was not prescribed, longer time elapsed was associated with a decrease in distress prevalence and an improvement in subjective well-being and QoL. It seems there is a turning point around the fifth year after finalization of primary treatment, from which the survivors without AHT significantly improve in several areas and those with AHT do so to a lesser extent. It is expected that the improvement in QoL throughout the different survival phases will have a significant impact on the adherence and maintenance of AHT and, consequently, the likelihood of survival. Thus, AHT side-effects should be routinely assessed by health care providers to gain accurate knowledge that allows improving the QoL of BC survivors.

Interaction of methyl-jasmonate and Fusarium poae in bread wheat

Fusarium Head Blight (FHB) is a devastating disease that affects the grain yield and quality of essential crops such as wheat. In the last years, some Fusarium species have acquired particular importance as Fusarium poae. However, studies to evaluate F. poae-wheat interaction are still scarce. The interaction between F. poae and two bread wheat cultivars with different resistance levels against FHB was evaluated. Moreover, the application of methyl-jasmonate (MeJA) was evaluated as a possible tool to reduce the fungal presence. Our results showed that the MeJA treatment is isolate-dependent, reducing F. poae fungal growth. A decrease in fungal biomass was observed in the susceptible cultivar after MeJA application; however, no differences between inoculated and inoculated-MeJA treatments were observed in the resistant cultivar. Finally, the F. poae inoculation induces the expression of PR1-1 and PDF 1.2, being early in the resistant cultivar compared to the susceptible ones. The application of MeJA combined with the F. poae inoculation increased PR1-1 and PDF1.2 expressions in resistant cultivars. To our knowledge, this is the first study that evaluates the interaction between F. poae and wheat and the MeJA treatment as a possible management strategy against this important pathogen.

Prediction of Immune-Related Adverse Events Induced by Immune Checkpoint Inhibitors With a Panel of Autoantibodies: Protocol of a Multicenter, Prospective, Observational Cohort Study

Introduction: Immune checkpoint inhibitor (ICI) therapy is markedly improving the prognosis of patients with several types of cancer. On the other hand, the growth in the use of these drugs in oncology is associated with an increase in multiple immune-related adverse events (irAEs), whose optimal prevention and management remain unclear. In this context, there is a need for reliable and validated biomarkers to predict the occurrence of irAEs in patients treated with ICIs. Thus, the main objective of this study is to evaluate the diagnostic performance of a sensitive routinely available panel of autoantibodies consisting of antinuclear antibodies, rheumatoid factor, and antineutrophil cytoplasmic antibodies to identify patients at risk of developing irAEs.

Methods and Analysis: A multicenter, prospective, observational, cohort study has been designed to be conducted in patients diagnosed with cancer amenable to ICI therapy. Considering the percentage of ICI-induced irAEs to be 25% and a loss to follow-up of 5%, it has been estimated that a sample size of 294 patients is required to detect an expected sensitivity of the autoantibody panel under study of 0.90 with a confidence interval (95%) of no less than 0.75. For 48 weeks, patients will be monitored through the oncology outpatient clinics of five hospitals in Spain. Immune-related adverse events will be defined and categorized according to CTCAE v. 5.0. All the patients will undergo ordinary blood tests at specific moments predefined per protocol and extraordinary blood tests at the time of any irAE being detected. Ordinary and extraordinary samples will be frozen and stored in the biobank until analysis in the same autoimmunity laboratory when the whole cohort reaches week 48. A predictive model of irAEs will be constructed with potential risk factors of immune-related toxicity including the autoantibody panel under study.

Ethics and Dissemination: This protocol was reviewed and approved by the Ethical Committee of the Basque Country and the Spanish Agency of Medicines and Medical Devices. Informed consent will be obtained from all participants before their enrollment. The authors declare that the results will be submitted to an international peer-reviewed journal for their prompt dissemination.

On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy

Single-particle analysis (SPA) by cryo-electron microscopy comprises the estimation of many parameters along its image-processing pipeline. Overfitting observed in SPA is normally due to misestimated parameters, and the only way to identify these is by comparing the estimates of multiple algorithms or, at least, multiple executions of the same algorithm.

Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands of macromolecules that are assumed to be structurally identical are combined into a single 3D map representing the Coulomb potential of the macromolecule under study. This article discusses possible caveats along the image-processing path and how to avoid them to obtain a reliable 3D structure. Some of these problems are very well known in the community. These may be referred to as sample-related (such as specimen denaturation at interfaces or non-uniform projection geometry leading to underrepresented projection directions). The rest are related to the algorithms used. While some have been discussed in depth in the literature, such as the use of an incorrect initial volume, others have received much less attention. However, they are fundamental in any data-analysis approach. Chiefly among them, instabilities in estimating many of the key parameters that are required for a correct 3D reconstruction that occur all along the processing workflow are referred to, which may significantly affect the reliability of the whole process. In the field, the term overfitting has been coined to refer to some particular kinds of artifacts. It is argued that overfitting is a statistical bias in key parameter-estimation steps in the 3D reconstruction process, including intrinsic algorithmic bias. It is also shown that common tools (Fourier shell correlation) and strategies (gold standard) that are normally used to detect or prevent overfitting do not fully protect against it. Alternatively, it is proposed that detecting the bias that leads to overfitting is much easier when addressed at the level of parameter estimation, rather than detecting it once the particle images have been combined into a 3D map. Comparing the results from multiple algorithms (or at least, independent executions of the same algorithm) can detect parameter bias. These multiple executions could then be averaged to give a lower variance estimate of the underlying parameters.

Association of immune-related adverse events induced by nivolumab with a battery of autoantibodies

BACKGROUND

The aim of this study was to assess the diagnostic performance of an autoantibody battery in patients receiving immune checkpoint inhibitors who experienced immune-related adverse events (irAEs).

METHODS

We retrospectively analyzed several variables potentially related to irAEs, namely, demographic, clinical, and laboratory characteristics, including an autoantibody battery (antinuclear, anti-neutrophil cytoplasmic, anti-thyroid antibodies and rheumatoid factor).

RESULTS

Sixty-nine patients (48 men; 61.8 ± 10.9 years at baseline) diagnosed with stage-4 solid-organ cancer and treated with nivolumab were followed up for 12 ± 10.3 months. Thirty-two irAEs were detected in 26 patients (37.5%). Adverse events occurred more commonly in women (62% vs. 27%, p = .006), and younger patients (irAEs: 58.1 ± 9.8, no irAEs: 64.1 ± 10.9 years, p = .024). Autoantibody battery results were available for 26 patients and were more frequently positive in patients with irAEs (87% vs. 30%, p = .009). The positive predictive value, negative predictive value, and diagnostic accuracy of the battery were 82.3%, 77.8%, and 80.8%, respectively. Among the 64 patients with an evaluable response, 23 (38.5%) experienced tumour progression, this being less frequent in patients with irAEs (19% vs. 48.5%, p = .03). Overall survival was higher in patients developing irAEs (HR = 1.88, p = .05).

CONCLUSION

Positivity in a readily available autoantibody battery may be associated with the occurrence of irAEs.KEY MESSAGESPositivity in an accessible and inexpensive autoantibody battery including antinuclear, anti-neutrophil cytoplasmic, anti-thyroid antibodies and rheumatoid factor may be associated with the occurrence of immune-related adverse events.Patients with cancer on immune checkpoint inhibitors experiencing immune-related adverse events showed a lower risk of progression and better overall survival than patients not experiencing this type of adverse effect.

Clinical risk factors for early mortality in patients with community-acquired septic shock. The importance of adequate source control

OBJECTIVE

To evaluate the incidence and risk factors for early mortality (EM) in the ICU in patients with community-acquired septic shock (CASS).

DESIGN

A retrospective cohort study of patients with CASS admitted to the ICU (2003-2016).

SETTING

ICU at a University Hospital in Spain.

PATIENTS

All consecutive patients admitted to the ICU with CASS.

INTERVENTIONS

None.

MAIN VARIABLES OF INTEREST

CASS was defined according to the Sepsis-3 definitions. EM were defined as occurring within of 72h following ICU admission. A multinomial logistic regression analysis was performed to identify the risk factors associated with early deaths.

RESULTS

During the study period, 625 patients met the Sepsis-3 criteria and admitted with CASS. 14.4% of all patients died within the first 72h. Of 161 patients who died in the ICU, 90 (55.9%) died within the first 72h. The percentage of early and late mortality did not vary significantly during the study period. The need and adequacy of source control were significantly lower in patients with EM. In the multivariate analysis, ARDS, non-respiratory infections, bacteremia and severity at admission were variables independently associated with EM. The only factor that decreased EM was adequate source control in patients with infections amenable to source control.

CONCLUSIONS

The incidence of EM has remained stable over time, which means that more than half of the patients who die from CASS do so within the first 72h. Infections where adequate source control can be performed have lower EM.

P–137 Male embryos take longer to develop to the blastocysts stage

Study question

Are there any differences in developmental timings between male and female preimplantation embryos?

Summary answer

There is a tendency for statistical difference in the time to reach blastocyst stage for male embryos compared to female embryos

What is known already

Differences in gene expression and metabolic uptake between male and female preimplantation embryos have been found in animal models and humans. These differences could affect the developmental timings of embryos resulting in differences in either sex. Morphokinetic parameters can precisely assess developmental timings. Only a few studies have analyzed morphokinetic parameters between male and female preimplantation embryos and no consensus has been reached on whether there is any sex-specific difference. The objective of this study is to compare morphokinetic parameters between male and female preimplantation embryos to determine any sex-specific developmental differences.

Study design, size, duration

This is a retrospective study including 102 preimplantation embryos from February 2018 to February 2020. The morphokinetic parameters obtained from time-lapse records of each embryo were: time to pronuclear fading (tPNf), times to 2–8 cells (t2, t3, t4, t5, t6, t7, t8), time to start of blastulation (tSB) and time to full blastocyst stage (tB). A two-tailed Student’s t-test was used to compare morphokinetic parameters between embryo sexes. A p < 0.05 was considered statistically significant.

Participants/materials, setting, methods

The study included retrospective time-lapse data from preimplantation embryos giving rise to 51 baby boys and 51 baby girls, as seen at birth. This is a single-center study with standardized culture conditions. Embryos in both study groups issued from cycles with donated oocytes. Only elective blastocyst stage single-embryo transfers (SET) on day 5 were assessed.

Main results and the role of chance

A tendency to statistical difference (p = [0.1–0.05]) was observed for blastocyst-related morphokinetic parameters: tSB (mean time was 89.6±6.3 hours in male embryos vs. 86.9±8.1 hours in female embryos, p = 0.06) and tB (100.2±5.9 hours versus 97.9±6.5 hours, p = 0.07). Male embryos showed an increased average time of 2.7 hours to tSB and 2.3 hours to tB, while no differences were found in the mean times of all the other morphokinetic paraments measured (p > 0.50): tPNf (∼21.8±3.0 hours) t2 (∼24.4±3.2 hours); t3 (∼35.6±3.9 hours); t4 (∼36.6±4.6 hours); t5 (∼46.9±6.0 hours); t6 (∼53.5±7.0 hours); t7 (∼54.1±7.3 hours) and t8 (∼54.1±7.3 hours). This finding suggests a sex-specific difference in reaching blastocyst stages.

Limitations, reasons for caution

The main limitation of the study is its retrospective nature and the small sample size. We analyzed the data of embryos leading to a live birth (high-quality embryos), therefore, caution should be made when generalizing results to non-implanting embryos (of potentially lower quality).

Wider implications of the findings: Sex-specific differences in developmental timings of preimplantation embryos at blastocyst stage, as evidenced by time-lapse data, should be considered to avoid selection biases during embryo transfers in ART clinic.

Trial registration number

Not applicable

Productivity in older versus younger workers: A systematic literature review

BACKGROUND

Worldwide ageing and thus, workforce ageing, is a concern for both developed and developing nations.

OBJECTIVE

The aim of the current research was to determine, through a systematic literature review, the effects of age in three dimensions that are often used to define or assess productivity at work.

METHODS

PICO framework was used to generate search strategies, inclusion criteria and terms. Scopus and PubMed databases were used. Peer-reviewed journal papers written in English and published (or in press) between January 2014 and December 2018 were included.

RESULTS

After filtering through inclusion criteria, 74 papers were included in the review. Considering productivity, 41%of the findings showed no differences between younger and older workers, 31%report better productivity of younger workers and 28%reported that older workers had better productivity than younger workers. Performance was better in older workers (58%), presenteeism generally showed no significant differences between age groups (61%). Absenteeism was the only outcome where younger workers outperformed older workers (43%).

CONCLUSION

Overall, there was no difference in productivity between older and younger workers. Older workers performed better than younger workers, but had more absenteeism, while presenteeism showed no differences. As ageing has come to workplaces, holistic approaches addressing total health are suggested to overcome the worldwide workforce ageing phenomenon.

Cryo-EM and Single-Particle Analysis with Scipion

Cryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at near-atomic resolution. In single-particle analysis, the vitrified sample is imaged by an electron beam and the detectors at the end of the microscope column produce movies of that sample. These movies contain thousands of images of identical particles in random orientations. The data need to go through an image processing workflow with multiple steps to obtain the final 3D reconstructed volume. The goal of the image processing workflow is to identify the acquisition parameters to be able to reconstruct the specimen under study. Scipion provides all the tools to create this workflow using several image processing packages in an integrative framework, also allowing the traceability of the results. In this article the whole image processing workflow in Scipion is presented and discussed with data coming from a real test case, giving all the details necessary to go from the movies obtained by the microscope to a high resolution final 3D reconstruction. Also, the power of using consensus tools that allow combining methods, and confirming results along every step of the workflow, improving the accuracy of the obtained results, is discussed.

Lung cancer patients with COVID-19 in Spain: GRAVID study

INTRODUCTION

Patients with cancer may be at increased risk of more severe COVID-19 disease; however, prognostic factors are not yet clearly identified. The GRAVID study aimed to describe clinical characteristics, outcomes, and predictors of poor outcome in patients with lung cancer and COVID-19.

METHODS

Prospective observational study that included medical records of patients with lung cancer and PCR-confirmed COVID-19 diagnosis across 65 Spanish hospitals. The primary endpoint was all-cause mortality; secondary endpoints were hospitalization and admission to intensive care units (ICU).

RESULTS

A total of 447 patients with a mean age of 67.1 ± 9.8 years were analysed. The majority were men (74.3 %) and current/former smokers (85.7 %). NSCLC was the most frequent type of cancer (84.5 %), mainly as adenocarcinoma (51.0 %), and stage III metastatic or unresectable disease (79.2 %). Nearly 60 % of patients were receiving anticancer treatment, mostly first-line chemotherapy. Overall, 350 (78.3 %) patients were hospitalized for a mean of 13.4 ± 11.4 days, 9 (2.0 %) were admitted to ICU and 146 (32.7 %) died. Advanced disease and the use of corticosteroids to treat COVID-19 during hospitalization were predictors of mortality. Hospitalized, non-end-of-life stage patients with lymphocytopenia and high LDH had an increased risk of death. Severity of COVID-19 correlated to higher mortality, ICU admission, and mechanical ventilation rates.

CONCLUSIONS

Mortality rate was higher among patients treated with corticosteroids during hospitalization, while anticancer therapy was not associated with an increased risk of hospitalization or death. Tailored approaches are warranted to ensure effective cancer management while minimizing the risk of exposure to SARS-CoV-2.

Computational evaluation of rebreathing and effective dead space on a helmet-like interface during the COVID-19 pandemic

The coronavirus disease 2019 (COVID-19) is a potentially severe acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2. The potential for transmission of this disease has led to an important scarcity of health-care resources. Consequently, alternative solutions have been explored by many physicians and researchers. Non-invasive Ventilation has been revealed as one alternative for patients with associated acute respiratory distress syndrome. This technique is being used in combination with helmet-like interfaces because of their versatility and affordability. However, these interfaces could experience important problems of CO2 rebreathing, especially under low flow rate conditions. This work proposes a Computational Fluid Dynamics method to accurately characterize the fluid flow in a pre-design environment of helmet-like interfaces. Parameters as effective dead space, rebreathing, pressure, or temperature field distribution are quantified and analysed in detail in order to study the performance and feasibility of such devices to relieve the effects of respiratory infections.

The novel Mechanical Ventilator Milano for the COVID-19 pandemic

This paper presents the Mechanical Ventilator Milano (MVM), a novel intensive therapy mechanical ventilator designed for rapid, large-scale, low-cost production for the COVID-19 pandemic. Free of moving mechanical parts and requiring only a source of compressed oxygen and medical air to operate, the MVM is designed to support the long-term invasive ventilation often required for COVID-19 patients and operates in pressure-regulated ventilation modes, which minimize the risk of furthering lung trauma. The MVM was extensively tested against ISO standards in the laboratory using a breathing simulator, with good agreement between input and measured breathing parameters and performing correctly in response to fault conditions and stability tests. The MVM has obtained Emergency Use Authorization by U.S. Food and Drug Administration (FDA) for use in healthcare settings during the COVID-19 pandemic and Health Canada Medical Device Authorization for Importation or Sale, under Interim Order for Use in Relation to COVID-19. Following these certifications, mass production is ongoing and distribution is under way in several countries. The MVM was designed, tested, prepared for certification, and mass produced in the space of a few months by a unique collaboration of respiratory healthcare professionals and experimental physicists, working with industrial partners, and is an excellent ventilator candidate for this pandemic anywhere in the world.

Sistema de pesaje automatizado que facilita el manejo de cuyes (Cavia porcellus)

La base de la economía de miles de familias Nariñenses se fundamenta en el desarrollo de actividades de cría de pequeñas especies, como los cuyes (Cavia porcellus). En cifras, se estima que existen 20,000 criaderos pequeños de cuyes en Nariño que generan transacciones mensuales por trescientos mil dólares, un sector que tiene una tendencia constante de crecimiento. No obstante, la producción de cuyes se realiza de forma artesanal debido a la falta de tecnificación de este sector. Una problemática identificada en la cría de estos animales es la pérdida de peso, afectando su salud, debido a lesiones causadas en el pesaje de forma tradicional. En este proceso, el animal es inmovilizando y llevado manualmente hacia la báscula, lo que puede ocasionar lesiones, variaciones de peso, reducción de movilidad y hasta la muerte. Conscientes que dichas problemáticas podrían solucionarse a través de la tecnología, en este artículo se presenta un sistema de pesaje e identificación automatizado que permita a los productores realizar el proceso de pesaje sin intervención humana, facilitando el manejo de cuyes, con la posibilidad de mantener el estado de salud del animal, registrar información de su crecimiento y facilitar el proceso de toma de decisiones sobre la venta. Se presenta el diseño propuesto desde un punto de vista estructural y operativo, y resultados experimentales obtenidos en un escenario real.

Secular changes in the anthropometrics of Chilean workers and its implication in design

BACKGROUND

Anthropometrics is very important when ensuring a physical match between end users and product or workstations.

OBJECTIVES

The purpose of this study are twofold, to provide anthropometric data for the design of products and to examine the secular changes in the adult Chilean workers in a period of more than 20 years.

METHODS

Nineteen anthropometric measurements from two samples from 1995 and 2016 were compared using independent t-test (95% confidence interval), where additionally absolute and relative differences were calculated.

RESULTS

The secular trend observed for Stature is characterized by an increase average of 20mm and 10.5mm per decade for females and males, respectively. There is a positive secular trend for both genders, which is observed for most of the selected body measurements. The most pronounced increases were onWeight, Shoulder breadth, Body mass index, Popliteal height; Buttock-popliteal length and Hip width.

CONCLUSIONS

Segmental dimensions that experienced a positive secular trend, together with Weight and Stature, are highly correlated with seating design, addressing the need to review products targeting Chilean adult workers, such as public transport seats, office furniture or industrial workplaces.

Algorithmic robustness to preferred orientations in single particle analysis by CryoEM

The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one of the hurdles preventing many structural analyses from yielding high-resolution structures. Although the existence of preferred orientations is mostly related to the grid preparation, in this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others to these detrimental conditions. We exemplify this argument with three different data sets in which the presence of preferred orientations hindered achieving a 3D reconstruction without artifacts or, even worse, a 3D reconstruction could never be achieved.

Bounds on Lorentz Invariance Violation from MAGIC Observation of GRB 190114C

On January 14, 2019, the Major Atmospheric Gamma Imaging Cherenkov telescopes detected GRB 190114C above 0.2 TeV, recording the most energetic photons ever observed from a gamma-ray burst. We use this unique observation to probe an energy dependence of the speed of light in vacuo for photons as predicted by several quantum gravity models. Based on a set of assumptions on the possible intrinsic spectral and temporal evolution, we obtain competitive lower limits on the quadratic leading order of speed of light modification.

Clinical risk factors for early mortality in patients with community-acquired septic shock. The importance of adequate source control

OBJECTIVE

To evaluate the incidence and risk factors for early mortality (EM) in the ICU in patients with community-acquired septic shock (CASS).

DESIGN

A retrospective cohort study of patients with CASS admitted to the ICU (2003-2016).

SETTING

ICU at a University Hospital in Spain.

PATIENTS

All consecutive patients admitted to the ICU with CASS.

INTERVENTIONS

None.

MAIN VARIABLES OF INTEREST

CASS was defined according to the Sepsis-3 definitions. EM were defined as occurring within of 72h following ICU admission. A multinomial logistic regression analysis was performed to identify the risk factors associated with early deaths.

RESULTS

During the study period, 625 patients met the Sepsis-3 criteria and admitted with CASS. 14.4% of all patients died within the first 72h. Of 161 patients who died in the ICU, 90 (55.9%) died within the first 72h. The percentage of early and late mortality did not vary significantly during the study period. The need and adequacy of source control were significantly lower in patients with EM. In the multivariate analysis, ARDS, non-respiratory infections, bacteremia and severity at admission were variables independently associated with EM. The only factor that decreased EM was adequate source control in patients with infections amenable to source control.

CONCLUSIONS

The incidence of EM has remained stable over time, which means that more than half of the patients who die from CASS do so within the first 72h. Infections where adequate source control can be performed have lower EM.

Silver nanoparticles: Toxicity in model organisms as an overview of its hazard for human health and the environment

Silver nanoparticles (AgNPs) have attracted remarkable attention due to their powerful antimicrobial action as well as their particular physicochemical properties. This has led to their application in a wide variety of products with promising results. However, their interaction with the environment and toxicity in live terrestrial or aquatic organisms is still a matter of intense debate. More detailed knowledge is still required about the toxicity of AgNPs, their possible uptake mechanisms and their adverse effects in live organisms. Several studies have reported the interactions and potential negative effects of AgNPs in different organisms. In this review, we report and discuss the current state of the art and perspectives for the impact of AgNPs on different organisms present in the environment. Recent progress in interpreting uptake, translocation and accumulation mechanisms in different organisms and/or living animals are discussed, as well as the toxicity of AgNPs and possible tolerance mechanisms in live organisms to cope with their deleterious effects. Finally, we discuss the challenges of accurate physicochemical characterization of AgNPs and their ecotoxicity in environmentally realistic conditions such as soil and water media.

Nintedanib in patients with progressive fibrosing interstitial lung diseases-subgroup analyses by interstitial lung disease diagnosis in the INBUILD trial: a randomised, double-blind, placebo-controlled, parallel-group trial

BACKGROUND

The INBUILD trial investigated the efficacy and safety of nintedanib versus placebo in patients with progressive fibrosing interstitial lung diseases (ILDs) other than idiopathic pulmonary fibrosis (IPF). We aimed to establish the effects of nintedanib in subgroups based on ILD diagnosis.

METHODS

The INBUILD trial was a randomised, double-blind, placebo-controlled, parallel group trial done at 153 sites in 15 countries. Participants had an investigator-diagnosed fibrosing ILD other than IPF, with chest imaging features of fibrosis of more than 10% extent on high resolution CT (HRCT), forced vital capacity (FVC) of 45% or more predicted, and diffusing capacity of the lung for carbon monoxide (DLco) of at least 30% and less than 80% predicted. Participants fulfilled protocol-defined criteria for ILD progression in the 24 months before screening, despite management considered appropriate in clinical practice for the individual ILD. Participants were randomly assigned 1:1 by means of a pseudo-random number generator to receive nintedanib 150 mg twice daily or placebo for at least 52 weeks. Participants, investigators, and other personnel involved in the trial and analysis were masked to treatment assignment until after database lock. In this subgroup analysis, we assessed the rate of decline in FVC (mL/year) over 52 weeks in patients who received at least one dose of nintedanib or placebo in five prespecified subgroups based on the ILD diagnoses documented by the investigators: hypersensitivity pneumonitis, autoimmune ILDs, idiopathic non-specific interstitial pneumonia, unclassifiable idiopathic interstitial pneumonia, and other ILDs. The trial has been completed and is registered with ClinicalTrials.gov, number NCT02999178.

FINDINGS

Participants were recruited between Feb 23, 2017, and April 27, 2018. Of 663 participants who received at least one dose of nintedanib or placebo, 173 (26%) had chronic hypersensitivity pneumonitis, 170 (26%) an autoimmune ILD, 125 (19%) idiopathic non-specific interstitial pneumonia, 114 (17%) unclassifiable idiopathic interstitial pneumonia, and 81 (12%) other ILDs. The effect of nintedanib versus placebo on reducing the rate of FVC decline (mL/year) was consistent across the five subgroups by ILD diagnosis in the overall population (hypersensitivity pneumonitis 73·1 [95% CI -8·6 to 154·8]; autoimmune ILDs 104·0 [21·1 to 186·9]; idiopathic non-specific interstitial pneumonia 141·6 [46·0 to 237·2]; unclassifiable idiopathic interstitial pneumonia 68·3 [-31·4 to 168·1]; and other ILDs 197·1 [77·6 to 316·7]; p=0·41 for treatment by subgroup by time interaction). Adverse events reported in the subgroups were consistent with those reported in the overall population.

INTERPRETATION

The INBUILD trial was not designed or powered to provide evidence for a benefit of nintedanib in specific diagnostic subgroups. However, its results suggest that nintedanib reduces the rate of ILD progression, as measured by FVC decline, in patients who have a chronic fibrosing ILD and progressive phenotype, irrespective of the underlying ILD diagnosis.

FUNDING

Boehringer Ingelheim.

Integration of Cryo-EM Model Building Software in Scipion

Advances in cryo-electron microscopy (cryo-EM) have made it possible to obtain structures of large biological macromolecules at near-atomic resolution. This "resolution revolution" has encouraged the use and development of modeling tools able to produce high-quality atomic models from cryo-EM density maps. Unfortunately, many practical problems appear when combining different packages in the same processing workflow, which make difficult the use of these tools by non-experts and, therefore, reduce their utility. We present here a major extension of the image processing framework Scipion that provides inter-package integration in the model building area and full tracking of the complete workflow, from image processing to structure validation.

Metabolic effects and outcomes of sleeve gastrectomy and gastric bypass: a cohort study

BACKGROUND

The outcomes of bariatric surgery should not be evaluated only for weight loss purposes but from a wider point of view that is closer to the reality of morbidly obese patients. The study of the influence of bariatric surgery over obesity-related diseases in bariatric patients is worthwhile.

METHODS

We present a cohort study of 329 patients who underwent either laparoscopic sleeve gastrectomy (LSG: 165 patients) or laparoscopic gastric bypass (LRYGBP: 164). We analyzed complication rate, comorbidities and weight loss evolution.

RESULTS

Both groups were comparable in demographic characteristics at baseline. Significant statistical differences were found in length of hospital stay and operative time (both were lower in the LSG group). Bleeding and wound infection were higher in the LRYGBP group, as it happened with intestinal occlusion as a late complication (p < 0.05). After a 5-year follow-up, the percentage of excess weight loss (%EWL) was higher in gastric bypass than sleeve gastrectomy (p = 0.01) but there was no statistical difference in percentage of total weight loss (%TWL) (p = 0.2). The resolution of comorbidities was similar in both groups except for dyslipidemia, which resolution was significantly higher in the gastric bypass group (p = 0.005). Metabolic syndrome (MeTS) resolution was similar in both groups.

CONCLUSIONS

Sleeve gastrectomy and gastric bypass achieve similar outcomes in hypertension, type 2 diabetes, obstructive sleep apnea and MeTS resolution even when there is weight regain. Although gastric bypass achieves higher weight loss in morbid obese patients, complication rates are also higher compared to those of sleeve gastrectomy. Thus, the appropriate procedure should be tailored based on patient factors and comorbidities, but also on surgeon comfort level and experience.

Author Correction: Forearc carbon sink reduces long-term volatile recycling into the mantle

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data set.

Risk and protective factors of secondary traumatic stress in Intensive Care Units: An exploratory study in a hospital in Madrid (Spain)

AIM

To propose a predictive model of secondary traumatic stress.

DESIGN

A descriptive cross-sectional study was carried out.

CONTEXT

The study was conducted in the Intensive Care Units of a hospital in Madrid (Spain).

PARTICIPANTS

The sample comprised 103 health professionals.

INTERVENTIONS

A series of questionnaires were created and completed by the participants. Network analysis and multiple regression were used for data analysis.

VARIABLES OF INTEREST

Sociodemographic variables such as gender, years of experience and position, secondary traumatic stress, passion for work, work stressors, emotional effort, empathy and self-compassion were evaluated.

RESULTS

The result identified the following: a) years of experience as a risk factor for compassion fatigue (β=0.224 and P=0.029), and harmonious passion as a protector (β=-0.363 and P=0.001); b) emotional effort and empathy as risk factors for shattered assumptions (β=0.304 and P=0.004; β=0.394 and P=0.000, respectively); and c), work stressors and empathy as risk factors for symptomatology (β=0.189 and P=0.039; β=0.395 and P=0.000, respectively), and years of experience as a protector (β=-0.266 and P=0.002).

CONCLUSIONS

This predictive model of secondary traumatic stress identifies protective factors which could be reinforced, such as harmonious passion, and risk factors which should be reduced, such as empathy and emotional effort, with a view to promoting quality of care and quality of life among these professionals.

First Results on Dark Matter Annual Modulation from the ANAIS-112 Experiment

ANAIS is a direct detection dark matter experiment aiming at the testing of the DAMA/LIBRA annual modulation result, which, for about two decades, has neither been confirmed nor ruled out by any other experiment in a model independent way. ANAIS-112, consisting of 112.5 kg of sodium iodide crystals, has been taking data at the Canfranc Underground Laboratory, Spain, since August 2017. This Letter presents the annual modulation analysis of 1.5 years of data, amounting to 157.55 kg yr. We focus on the model independent analysis searching for modulation and the validation of our sensitivity prospects. ANAIS-112 data are consistent with the null hypothesis (p values of 0.67 and 0.18 for [2-6] and [1-6] keV energy regions, respectively). The best fits for the modulation hypothesis are consistent with the absence of modulation (S_{m}=-0.0044±0.0058  cpd/kg/keV and -0.0015±0.0063  cpd/kg/keV, respectively). They are in agreement with our estimated sensitivity for the accumulated exposure, which supports our projected goal of reaching a 3σ sensitivity to the DAMA/LIBRA result in five years of data taking.

Short term changes in the abundance of nitrifying microorganisms in a soil-plant system simultaneously exposed to copper nanoparticles and atrazine

Copper nanoparticles (NCu) may co-exist with other pollutants in agricultural soils, such as pesticides. However, this has been little evaluated yet. Thus, possible effects of the simultaneous applications of pesticides and NCu on biogeochemical cycles are expected, for example on the nitrogen cycle. Therefore, the aim of this work was to evaluate the effect of simultaneous application of the herbicide atrazine (ATZ) and NCu on the abundance of total bacteria and nitrifying communities: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Moreover, the ATZ dissipation was evaluated. A soil-plant system containing ATZ at field dose (3 mg a.i. kg^-1) was mixed with two doses of NCu (0.05% or 0.15% w/w). Changes in the abundance of 16S rRNA and ammonia monooxygenase (amoA) genes of AOA and AOB were evaluated by real-time quantitative PCR (qPCR) at three sampling times (1, 15 and 30 days). The residual ATZ and nitrate production were also measured. The results showed significant differences in microbial composition and abundance over the 30 days of the experiment. Particularly, an initial decrease was observed in total bacterial abundance due to the presence of ATZ and NCu respect to ATZ alone (~60%). The abundance of AOA was also remarkably reduced (~85%), but these communities gradually recovered towards the end of the experiment. Conversely, AOB abundance initially increased (>100%) and remained mainly unaltered in soil exposed to ATZ and NCu 0.15% w/w, where nitrate formation was also constant. Moreover, NCu decreased the ATZ dissipation, which was translated in a 2-fold increase on the ATZ half-life values (T_1/2). This study demonstrates that the simultaneous presence of NCu and ATZ may represent a risk for the total bacteria present in soil and sensitive microorganisms such as nitrifying communities, and changes in the dissipation of the pesticide could influence this process.