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The issue of reproducibility of computational models and the related FAIR principles (findable, accessible, interoperable, and reusable) are examined in a specific test case. I analyze a computational model of the segment polarity network in Drosophila embryos published in 2000. Despite the high number of citations to this publication, 23 years later the model is barely accessible, and consequently not interoperable. Following the text of the original publication allowed successfully encoding the model for the open source software COPASI. Subsequently saving the model in the SBML format allowed it to be reused in other open source software packages. Submission of this SBML encoding of the model to the BioModels database enables its findability and accessibility . This demonstrates how the FAIR principles can be successfully enabled by using open source software, widely adopted standards, and public repositories, facilitating reproducibility and reuse of computational cell biology models that will outlive the specific software used.

Computational models can be created more efficiently by composing them from smaller, well-defined sub-models that represent specific cellular structures that appear often in different contexts. Cellular iron metabolism is a prime example of this as multiple cell types tend to rely on a similar set of components (proteins and regulatory mechanisms) to ensure iron balance. One recurrent component, ferritin, is the primary iron storage protein in mammalian cells and is necessary for cellular iron homeostasis. Its ability to sequester iron protects cells from rising concentrations of ferrous iron limiting oxidative cell damage. The focus of the present work is establishing a model that tractably represents the ferritin iron sequestration kinetics such that it can be incorporated into larger cell models, in addition to contributing to the understanding of general ferritin iron sequestration dynamics within cells. The model’s parameter values were determined from published kinetic and binding experiments and the model was validated against independent data not used in its construction. Simulation results indicate that FT concentration is the most impactful on overall sequestration dynamics, while the FT iron saturation (number of iron atoms sequestered per FT cage) fine tunes the initial rates. Finally, because this model has a small number of reactions and species, was built to represent important details of FT kinetics, and has flexibility to include subtle changes in subunit composition, we propose it to be used as a building block in a variety of specific cell type models of iron metabolism.

Intestinal mucosal block is the transient reduction in iron absorption ability of intestinal epithelial cells (enterocytes) in response to previous iron exposures that occur at the cell scale. The block characteristics have been shown to depend both on iron exposure magnitude and temporality, and understanding block control will enable deeper understanding of how intestinal iron absorption contributes to pathological iron states. Three biochemical mechanisms implicated in driving the block behavior are divalent metal transporter 1 endocytosis, ferritin iron sequestration, and iron regulatory protein regulation of iron related protein expression. In this work, a model of enterocyte iron metabolism is built based on published experimental data that is capable of reproducing the mucosal block phenomena. The model is then used to estimate the quantitative contribution of each of the three mechanisms on the properties of the mucosal block. Analysis reveals that ferritin and iron regulatory proteins are the main intracellular mechanisms contributing to the mucosal block, findings congruent with experimental predictions. Lastly, DMT1 endocytosis is shown to play a role in limiting total iron uptake by enterocytes but does not contribute to the decrease in total iron transfer across their basal membrane seen in the mucosal block.

In this paper, we propose a novel multiclass classifier for the open-set recognition scenario. This scenario is the one in which there are no a priori training samples for some classes that might appear during testing. Usually, many applications are inherently open set. Consequently, successful closed-set solutions in the literature are not always suitable for real-world recognition problems. The proposed open-set classifier extends upon the Nearest-Neighbor (NN) classifier. Nearest neighbors are simple, parameter independent, multiclass, and widely used for closed-set problems. The proposed Open-Set NN (OSNN) method incorporates the ability of recognizing samples belonging to classes that are unknown at training time, being suitable for open-set recognition. In addition, we explore evaluation measures for open-set problems, properly measuring the resilience of methods to unknown classes during testing. For validation, we consider large freely-available benchmarks with different open-set recognition regimes and demonstrate that the proposed OSNN significantly outperforms their counterparts in the literature.

The early epidemiology of the 2022 monkeypox epidemic in non-endemic countries differs substantially from the epidemiology previously reported from endemic countries. We aimed to describe the epidemiological and clinical characteristics among individuals with confirmed cases of monkeypox infection. We descriptively analysed data for patients with confirmed monkeypox who were included in the GeoSentinel global clinical-care-based surveillance system between May 1 and July 1 2022, across 71 clinical sites in 29 countries. Data collected included demographics, travel history including mass gathering attendance, smallpox vaccination history, social history, sexual history, monkeypox exposure history, medical history, clinical presentation, physical examination, testing results, treatment, and outcomes. We did descriptive analyses of epidemiology and subanalyses of patients with and without HIV, patients with CD4 counts of less than 500 cells per mm3 or 500 cells per mm3 and higher, patients with one sexual partner or ten or more sexual partners, and patients with or without a previous smallpox vaccination. 226 cases were reported at 18 sites in 15 countries. Of 211 men for whom data were available, 208 (99%) were gay, bisexual, or men who have sex with men (MSM) with a median age of 37 years (range 18–68; IQR 32–43). Of 209 patients for whom HIV status was known, 92 (44%) men had HIV infection with a median CD4 count of 713 cells per mm3 (range 36–1659; IQR 500–885). Of 219 patients for whom data were available, 216 (99%) reported sexual or close intimate contact in the 21 days before symptom onset; MSM reported a median of three partners (IQR 1–8). Of 195 patients for whom data were available, 78 (40%) reported close contact with someone who had confirmed monkeypox. Overall, 30 (13%) of 226 patients were admitted to hospital; 16 (53%) of whom had severe illness, defined as hospital admission for clinical care rather than infection control. No deaths were reported. Compared with patients without HIV, patients with HIV were more likely to have diarrhoea (p=0·002), perianal rash or lesions (p=0·03), and a higher rash burden (median rash burden score 9 [IQR 6–21] for patients with HIV vs median rash burden score 6 [IQR 3–14] for patients without HIV; p<0·0001), but no differences were identified in the proportion of men who had severe illness by HIV status. Clinical manifestations of monkeypox infection differed by HIV status. Recommendations should be expanded to include pre-exposure monkeypox vaccination of groups at high risk of infection who plan to engage in sexual or close intimate contact. US Centers for Disease Control and Prevention, International Society of Travel Medicine.

This article explores the patterns of class inequality and capital accumulation in Brazil, showing the drivers and limits of the decline in inequality that occurred during the Workers’ Party governments. It proposes that minimum wage hikes and greater social security changed the demand pattern and kick-started a cumulative causation process. Growth and redistribution thus reinforced each other for a period, and then spelled their own limits. As growth accelerated in the 2000s, a Gini decomposition indicates that class inequality decreased, but confined to changes between workers—capitalist income and social stratification were preserved. This also endogenously led to a regressive structural change, as low-productivity, labour-intensive services grew and international trade patterns worsened. This created a medium-term dependence on commodity prices for balance-of-trade solvency, and heightened cost-push inflation, which could not be overcome under the limited policy framework in place. The constrained basis for reducing inequality and the regressive structural change underscore that developmental strategies requires broad, multi-dimensional inequality-reducing measures and an encompassing catching-up project.

Stressing agents can cause morphophysiological and behavioural changes in several animals, including birds, which are good study models for environmental biomonitoring. The heterophil/lymphocyte ratio (H/L) is an efficient indicator of chronic stresses in birds. In this study, we aimed to compare the H/L ratio of birds between the areas with different levels of urbanisation, anthropogenic noise and carbon monoxide (CO) emission rates. A total of 1288 birds were captured in six Cerrado forest fragments between 2013 and 2019, from which we took blood samples to produce blood smears. In each of these fragments, the noise level was measured with a sound pressure level metre. The CO rates were obtained from the National Institute for Space Research database (INPE-Brazil). There was a higher H/L ratio in individuals captured in urban areas or close to urbanisation with high anthropogenic noise levels and high CO rates, and a lower H/L ratio in individuals from preserved areas, far from urban environments with low noise levels and low CO rates. Six species ( Antilophia galeata , Leoptopogon amaurocephalus , Cnemotriccus fuscatus , Lathrotriccus euleri , Turdus leucomelas  and Eucometis penicillata ) showed a significant difference between the areas and followed the pattern shown by the individuals. The present study showed that birds living in the urban and peri-urban sites have higher values of H/L ratio than birds from rural sites. These results suggest that the H/L ratio can be used as an environmental biomonitoring tool and an efficient parameter to assess chronic stress in birds in degraded environments.

Glutaminase (GLS) is directly related to cell growth and tumor progression, making it a target for cancer treatment. The RNA-binding protein HuR (encoded by the ELAVL1 gene) influences mRNA stability and alternative splicing. Overexpression of ELAVL1 is common in several cancers, including breast cancer. Here we show that HuR regulates GLS mRNA alternative splicing and isoform translation/stability in breast cancer. Elevated ELAVL1 expression correlates with high levels of the glutaminase isoforms C (GAC) and kidney-type (KGA), which are associated with poor patient prognosis. Knocking down ELAVL1 reduces KGA and increases GAC levels, enhances glutamine anaplerosis into the TCA cycle, and drives cells towards glutamine dependence. Furthermore, we show that combining chemical inhibition of GLS with ELAVL1 silencing synergistically decreases breast cancer cell growth and invasion. These findings suggest that dual inhibition of GLS and HuR offers a therapeutic strategy for breast cancer treatment. Changes in the expression of the RNA-binding protein HuR are common in several cancers. Here, the authors show that HuR regulates glutaminase mRNA metabolism in the context of breast cancer. This work reveals that dual inhibition of HuR and glutaminase may have therapeutic potential.

Purpose To describe trends in outcomes of cancer patients with unplanned admissions to intensive-care units (ICU) according to cancer type, organ support use, and performance status (PS) over an 8-year period. Methods We retrospectively analyzed prospectively collected data from all cancer patients admitted to 92 medical–surgical ICUs from July/2011 to June/2019. We assessed trends in mortality through a Bayesian hierarchical model adjusted for relevant clinical confounders and whether there was a reduction in ICU length-of-stay (LOS) over time using a competing risk model. Results 32,096 patients (8.7% of all ICU admissions; solid tumors, 90%; hematological malignancies, 10%) were studied. Bed/days use by cancer patients increased up to more than 30% during the period. Overall adjusted mortality decreased by 9.2% [95% credible interval (CI), 13.1–5.6%]. The largest reductions in mortality occurred in patients without need for organ support (9.6%) and in those with need for mechanical ventilation (MV) only (11%). Smallest reductions occurred in patients requiring MV, vasopressors, and dialysis (3.9%) simultaneously. Survival gains over time decreased as PS worsened. Lung cancer patients had the lowest decrease in mortality. Each year was associated with a lower sub-hazard for ICU death [SHR 0.93 (0.91–0.94)] and a higher chance of being discharged alive from the ICU earlier [SHR 1.01 (1–1.01)]. Conclusion Outcomes in critically ill cancer patients improved in the past 8 years, with reductions in both mortality and ICU LOS, suggesting improvements in overall care. However, outcomes remained poor in patients with lung cancer, requiring multiple organ support and compromised PS.

(1) Objectives: To evaluate the frequency and factors associated with the Post-COVID-19 Syndrome (PCS) in COVID-19 survivors after 3 and 6 months of hospital discharge; (2) Methods: We conducted a cohort study with patients who were hospitalized with COVID-19 in a referral public hospital in Brasília, Federal District, Brazil. After 3 and 6 months of discharge, patients answered a questionnaire about PCS symptoms. Poisson regression with robust variance was used to estimate the crude and adjusted prevalence ratios (PR and aPR) of PCS. (3) Results: The prevalence of PCS was 81% and 61% after 3 and 6 months of hospital discharge, respectively. The main symptoms after 3 months of discharge were hair loss (44%), fatigue (42%), and memory loss (39%); while after 6 months, they were memory loss (29%) and fatigue (27%). In the multivariate analysis, the main factor associated with PCS was female gender (aPR): 1.28 (1.16–1.41) and 1.60 (1.34–1.90), 3 and 6 months after hospital discharge, respectively. Hypercholesterolemia was also associated with PCS after 3 months aPR of 1.15 (1.04–1.27). After 6 months of discharge, obesity [aPR: 1.22 (1.03–1.45)] and pronation [aPR: 1.15 (1.06–1.25)] were relevant associated factors. (4) Conclusions: The prevalence of PCS was high in COVID-19 survivors who had the moderate and severe forms of the disease. Memory loss was the most persistent symptom. Our data pointed to female gender, hypercholesterolemia, obesity, and pronation during hospitalization as relevant PCS-associated risk factors.