Mancha3D code: Multi-purpose Advanced Non-ideal MHD Code for High resolution simulations in Astrophysics

The Mancha3D code is a versatile tool for numerical simulations of magnetohydrodynamic processes in solar/stellar atmospheres. The code includes non-ideal physics derived from plasma partial ionization, a realistic equation of state and radiative transfer, which allows performing high quality realistic simulations of magneto-convection, as well as idealized simulations of particular processes, such as wave propagation, instabilities or energetic events. The paper summarizes the equations and methods used in the Mancha3D code. It also describes its numerical stability and parallel performance and efficiency. The code is based on a finite difference discretization and memory-saving Runge-Kutta (RK) scheme. It handles non-ideal effects through super-time stepping and Hall diffusion schemes, and takes into account thermal conduction by solving an additional hyperbolic equation for the heat flux. The code is easily configurable to perform different kinds of simulations. Several examples of the code usage are given. It is demonstrated that splitting variables into equilibrium and perturbation parts is essential for simulations of wave propagation in a static background. A perfectly matched layer (PML) boundary condition built into the code greatly facilitates a non-reflective open boundary implementation. Spatial filtering is an important numerical remedy to eliminate grid-size perturbations enhancing the code stability. Parallel performance analysis reveals that the code is strongly memory bound, which is a natural consequence of the numerical techniques used, such as split variables and PML boundary conditions. Both strong and weak scalings show adequate performance up till several thousands of CPUs

Near-infrared-actuated devices for remotely controlled drug delivery

A reservoir that could be remotely triggered to release a drug would enable the patient or physician to achieve on-demand, reproducible, repeated, and tunable dosing. Such a device would allow precise adjustment of dosage to desired effect, with a consequent minimization of toxicity, and could obviate repeated drug administrations or device implantations, enhancing patient compliance. It should exhibit low off-state leakage to minimize basal effects, and tunable on-state release profiles that could be adjusted from pulsatile to sustained in real time. Despite the clear clinical need for a device that meets these criteria, none has been reported to date to our knowledge. To address this deficiency, we developed an implantable reservoir capped by a nanocomposite membrane whose permeability was modulated by irradiation with a near-infrared laser. Irradiated devices could exhibit sustained on-state drug release for at least 3 h, and could reproducibly deliver short pulses over at least 10 cycles, with an on/off ratio of 30. Devices containing aspart, a fast-acting insulin analog, could achieve glycemic control after s.c. implantation in diabetic rats, with reproducible dosing controlled by the intensity and timing of irradiation over a 2-wk period. These devices can be loaded with a wide range of drug types, and therefore represent a platform technology that might be used to address a wide variety of clinical indications

Neutrino Masses and Mixings from Supersymmetry with Bilinear R--Parity Violation: A Theory for Solar and Atmospheric Neutrino Oscillations

The simplest unified extension of the MSSM with bi-linear R--Parity violation naturally predicts a hierarchical neutrino mass spectrum, in which one neutrino acquires mass by mixing with neutralinos, while the other two get mass radiatively. We have performed a full one-loop calculation of the neutralino-neutrino mass matrix in the bi-linear \rp MSSM, taking special care to achieve a manifestly gauge invariant calculation. Moreover we have performed the renormalization of the heaviest neutrino, needed in order to get meaningful results. The atmospheric mass scale and maximal mixing angle arise from tree-level physics, while solar neutrino scale and oscillations follow from calculable one-loop corrections. If universal supergravity assumptions are made on the soft-supersymmetry breaking terms then the atmospheric scale is calculable as a function of a single \rp violating parameter by the renormalization group evolution due to the non-zero bottom quark Yukawa coupling. The solar neutrino problem must be accounted for by the small mixing angle (SMA) MSW solution. If these assumptions are relaxed then one can implement large mixing angle solutions, either MSW or just-so. The theory predicts the lightest supersymmetic particle (LSP) decay to be observable at high-energy colliders, despite the smallness of neutrino masses indicated by experiment. This provides an independent way to test this solution of the atmospheric and solar neutrino anomalies.Comment: 46 pages, references added + several misprints correcte

Desigualdades en el impacto de la pandemia de Covid-19 en los registros de cáncer de REDECAN

XLI Reunión anual de la Sociedad Española de Epidemiología (SEE) y XVIII Congresso da Associação Portuguesa de Epidemiología (APE). Porto (Portugal), del 5 al 8 de septiembre de 2023.Antecedentes/Objetivos: La pandemia COVID-19 ha producido un fuerte impacto en la sociedad y sistema sanitario. Con el objetivo de conocer cómo ha afectado a la vigilancia del cáncer en España, la Sociedad Española de Epidemiología (SEE) y la Red Española de Registros de Cáncer (REDECAN) desarrollaron una encuesta para valorar la repercusión en los Registros, durante la primera (marzo-junio de 2020) y sexta ola (noviembre de 2021-enero de 2022). Métodos: Encuesta web ad hoc a los Registros de REDECAN en noviembre de 2022. Se recogió información acerca de las fuentes de información, número y tipo de profesionales de los equipos, horas semanales dedicadas a registro de cáncer, a gestión de actividades relacionadas con pandemia COVID-19, bajas laborales por COVID-19, referido a distintos momentos de la pandemia: el momento actual, primera y la sexta ola. Resultados: Respuesta de 11 registros de 21 (52,3%). En la primera ola, ocho (72,7%) registros vieron afectados sus equipos debido a la pandemia. Médicos/as, enfermeras e informáticos dedicaron la mitad de su horario a dar soporte a COVID-19, mientras que los/las documentalistas redujeron su actividad, pero sin soporte a COVID-19. Los auxiliares administrativos/as mantuvieron sus horas de registro con un número similar de horas extras para gestión COVID-19 (37 y 34 horas). Tres registros (27,3%) declararon afectación en la actividad por bajas laborales por COVID-19. En la sexta ola, cinco registros (45,5%) reportaron afectación de actividad por la pandemia. Médicos/as, enfermeras e informáticos aumentaron las horas de actividad de registro y disminuyeron las de COVID-19. Los auxiliares administrativos/as siguieron realizando actividad de registro junto con actividad extra-COVID-19 (27 y 21 horas). En siete registros (63,6%) hubo bajas laborales por COVID-19. Los tres registros que no vieron afectados sus equipos por gestión COVID-19 fueron los que no dependían de las autoridades de salud pública. Conclusiones/Recomendaciones: En la primera ola la mayoría de registros REDECAN declararon una reducción de actividad para dar soporte a COVID-19. En la sexta ola, con la variante ómicron, menos registros se vieron afectados a nivel funcional, pero aumentaron las bajas laborales por COVID-19, afectando a su actividad. Los registros no ubicados en Direcciones Generales de Salud Pública tuvieron que destinar menos recursos a gestión COVID-19. Esta desigualdad también se mostró a nivel profesional, donde los auxiliares administrativos/as tuvieron que soportar su actividad habitual y actividad extra para gestión COVID-19.N

The degradation of p53 and its major E3 ligase Mdm2 is differentially dependent on the proteasomal ubiquitin receptor S5a.

p53 and its major E3 ligase Mdm2 are both ubiquitinated and targeted to the proteasome for degradation. Despite the importance of this in regulating the p53 pathway, little is known about the mechanisms of proteasomal recognition of ubiquitinated p53 and Mdm2. In this study, we show that knockdown of the proteasomal ubiquitin receptor S5a/PSMD4/Rpn10 inhibits p53 protein degradation and results in the accumulation of ubiquitinated p53. Overexpression of a dominant-negative deletion of S5a lacking its ubiquitin-interacting motifs (UIM)s, but which can be incorporated into the proteasome, also causes the stabilization of p53. Furthermore, small-interferring RNA (siRNA) rescue experiments confirm that the UIMs of S5a are required for the maintenance of low p53 levels. These observations indicate that S5a participates in the recognition of ubiquitinated p53 by the proteasome. In contrast, targeting S5a has no effect on the rate of degradation of Mdm2, indicating that proteasomal recognition of Mdm2 can be mediated by an S5a-independent pathway. S5a knockdown results in an increase in the transcriptional activity of p53. The selective stabilization of p53 and not Mdm2 provides a mechanism for p53 activation. Depletion of S5a causes a p53-dependent decrease in cell proliferation, demonstrating that p53 can have a dominant role in the response to targeting S5a. This study provides evidence for alternative pathways of proteasomal recognition of p53 and Mdm2. Differences in recognition by the proteasome could provide a means to modulate the relative stability of p53 and Mdm2 in response to cellular signals. In addition, they could be exploited for p53-activating therapies. This work shows that the degradation of proteins by the proteasome can be selectively dependent on S5a in human cells, and that this selectivity can extend to an E3 ubiquitin ligase and its substrate

ENE-COVID nationwide serosurvey served to characterize asymptomatic infections and to develop a symptom-based risk score to predict COVID-19

Objectives: To characterize asymptomatic SARS-CoV-2 infections and develop a symptom-based risk score useful in primary healthcare. Study design and setting: Sixty-one thousand ninty-two community-dwelling participants in a nationwide population-based serosurvey completed a questionnaire on COVID-19 symptoms and received an immunoassay for SARS-CoV-2 IgG antibodies between April 27 and June 22, 2020. Standardized prevalence ratios for asymptomatic infection were estimated across participant characteristics. We constructed a symptom-based risk score and evaluated its ability to predict SARS-CoV-2 infection. Results: Of all, 28.7% of infections were asymptomatic (95% CI 26.1-31.4%). Standardized asymptomatic prevalence ratios were 1.19 (1.02-1.40) for men vs. women, 1.82 (1.33-2.50) and 1.45 (0.96-2.18) for individuals <20 and ≥80 years vs. those aged 40-59, 1.27 (1.03-1.55) for smokers vs. nonsmokers, and 1.91 (1.59-2.29) for individuals without vs. with case contact. In symptomatic population, a symptom-based score (weights: severe tiredness = 1; absence of sore throat = 1; fever = 2; anosmia/ageusia = 5) reached standardized seroprevalence ratio of 8.71 (7.37-10.3), discrimination index of 0.79 (0.77-0.81), and sensitivity and specificity of 71.4% (68.1-74.4%) and 74.2% (73.1-75.2%) for a score ≥3. Conclusion: The presence of anosmia/ageusia, fever with severe tiredness, or fever without sore throat should serve to suspect COVID-19 in areas with active viral circulation. The proportion of asymptomatics in children and adolescents challenges infection control.The ENE-COVID study was supported by the Spanish Ministry of Health, the Institute of Health Carlos III, and the Spanish National Health System. The funders were in- volved in the study logistics, but they had no role in study design or in the collection, analysis, interpretation of data, or the decision to submit the article for publicationS

Evaluating the Applicability of Data-Driven Dietary Patterns to Independent Samples with a Focus on Measurement Tools for Pattern Similarity

BACKGROUND: Diet is a key modifiable risk for many chronic diseases, but it remains unclear whether dietary patterns from one study sample are generalizable to other independent populations. OBJECTIVE: The primary objective of this study was to assess whether data-driven dietary patterns from one study sample are applicable to other populations. The secondary objective was to assess the validity of two criteria of pattern similarity. METHODS: Six dietary patterns-Western (n=3), Mediterranean, Prudent, and Healthy- from three published studies on breast cancer were reconstructed in a case-control study of 973 breast cancer patients and 973 controls. Three more internal patterns (Western, Prudent, and Mediterranean) were derived from this case-control study's own data. STATISTICAL ANALYSIS: Applicability was assessed by comparing the six reconstructed patterns with the three internal dietary patterns, using the congruence coefficient (CC) between pattern loadings. In cases where any pair met either of two commonly used criteria for declaring patterns similar (CC ≥0.85 or a statistically significant [P0.9) to their corresponding dietary pattern derived from the case-control study's data. Similar associations with risk for breast cancer were found in all pairs of dietary patterns that had high CC but not in all pairs of dietary patterns with statistically significant correlations. CONCLUSIONS: Similar dietary patterns can be found in independent samples. The P value of a correlation coefficient is less reliable than the CC as a criterion for declaring two dietary patterns similar. This study shows that diet scores based on a particular study are generalizable to other populations.This study was funded by Fundación Científica Asociación Española Contra el Cáncer (Scientific Foundation of the Spanish Association Against Cancer), the Spanish Ministry of Economy and Competitiveness (IJCI-2014-20900); Fundación Cerveza y Salud 2005 (Beer and Health Foundation 2005), Sociedad Española de Oncología Médica (Spanish Society of Medical Oncology), Federación de Mujeres con Cáncer de Mama (Association of Women with Breast Cancer) (EPY 1169-10 grant) and Association of Women with Breast Cancer from Elche (EPY 1394/15 grant)

A New Hierarchy of Research Evidence for Tumor Pathology: A Delphi Study to Define Levels of Evidence in Tumor Pathology

The hierarchy of evidence is a fundamental concept in evidence-based medicine, but existing models can be challenging to apply in laboratory-based health care disciplines, such as pathology, where the types of evidence and contexts are significantly different from interventional medicine. This project aimed to define a comprehensive and complementary framework of new levels of evidence for evaluating research in tumor pathology-introducing a novel Hierarchy of Research Evidence for Tumor Pathology collaboratively designed by pathologists with help from epidemiologists, public health professionals, oncologists, and scientists, specifically tailored for use by pathologists-and to aid in the production of the World Health Organization Classification of Tumors (WCT) evidence gap maps. To achieve this, we adopted a modified Delphi approach, encompassing iterative online surveys, expert oversight, and external peer review, to establish the criteria for evidence in tumor pathology, determine the optimal structure for the new hierarchy, and ascertain the levels of confidence for each type of evidence. Over a span of 4 months and 3 survey rounds, we collected 1104 survey responses, culminating in a 3-day hybrid meeting in 2023, where a new hierarchy was unanimously agreed upon. The hierarchy is organized into 5 research theme groupings closely aligned with the subheadings of the WCT, and it consists of 5 levels of evidence-level P1 representing evidence types that merit the greatest level of confidence and level P5 reflecting the greatest risk of bias. For the first time, an international collaboration of pathology experts, supported by the International Agency for Research on Cancer, has successfully united to establish a standardized approach for evaluating evidence in tumor pathology. We intend to implement this novel Hierarchy of Research Evidence for Tumor Pathology to map the available evidence, thereby enriching and informing the WCT effectively.The overall project, International Agency for Research on Cancer, and beneficiaries (German Heart Centre Munich, Maria Sklodowska-Curie National Research Institute of Oncology, and Instituto de Salud Carlos III) are funded by the European Commission (HORIZON grant no. 101057127). R.C. and F.C. are funded by UK Research and Innovation. S.H. has received research funding or honoraria from Roche, BMS, Merck, Sysmex, Thermo, Volition, Trillium, Medica, and Instand and is a founder of SFZ BioCoDE and CEBIO. P.H.T. has received honoraria from AstraZeneca.S

RANK signaling increases after anti-HER2 therapy contributing to the emergence of resistance in HER2-positive breast cancer

Background: Around 15-20% of primary breast cancers are characterized by HER2 protein overexpression and/or HER2 gene amplification. Despite the successful development of anti-HER2 drugs, intrinsic and acquired resistance represents a major hurdle. This study was performed to analyze the RANK pathway contribution in HER2-positive breast cancer and anti-HER2 therapy resistance. Methods: RANK and RANKL protein expression was assessed in samples from HER2-positive breast cancer patients resistant to anti-HER2 therapy and treatment-naive patients. RANK and RANKL gene expression was analyzed in paired samples from patients treated with neoadjuvant dual HER2-blockade (lapatinib and trastuzumab) from the SOLTI-1114 PAMELA trial. Additionally, HER2-positive breast cancer cell lines were used to modulate RANK expression and analyze in vitro the contribution of RANK signaling to anti-HER2 resistance and downstream signaling. Results: RANK and RANKL proteins are more frequently detected in HER2-positive tumors that have acquired resistance to anti-HER2 therapies than in treatment-naive ones. RANK (but not RANKL) gene expression increased after dual anti-HER2 neoadjuvant therapy in the cohort from the SOLTI-1114 PAMELA trial. Results in HER2-positive breast cancer cell lines recapitulate the clinical observations, with increased RANK expression observed after short-term treatment with the HER2 inhibitor lapatinib or dual anti-HER2 therapy and in lapatinib-resistant cells. After RANKL stimulation, lapatinib-resistant cells show increased NF-κB activation compared to their sensitive counterparts, confirming the enhanced functionality of the RANK pathway in anti-HER2-resistant breast cancer. Overactivation of the RANK signaling pathway enhances ERK and NF-κB signaling and increases lapatinib resistance in different HER2-positive breast cancer cell lines, whereas RANK loss sensitizes lapatinib-resistant cells to the drug. Our results indicate that ErbB signaling is required for RANK/RANKL-driven activation of ERK in several HER2-positive cell lines. In contrast, lapatinib is not able to counteract the NF-κB activation elicited after RANKL treatment in RANK-overexpressing cells. Finally, we show that RANK binds to HER2 in breast cancer cells and that enhanced RANK pathway activation alters HER2 phosphorylation status. Conclusions: Our data support a physical and functional link between RANK and HER2 signaling in breast cancer and demonstrate that increased RANK signaling may contribute to the development of lapatinib resistance through NF-κB activation. Whether HER2-positive breast cancer patients with tumoral RANK expression might benefit from dual HER2 and RANK inhibition therapy remains to be elucidated

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020 - the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland's border closures de-coupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86-98% reduction in introductions during Switzerland's strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred, using a phylodynamic model. We found that transmission slowed 35-63% upon outbreak detection in summer 2020, but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics