Best practices and QA protocols for code development

The OperaHPC project aims to improve the numerical capabilities of 3D fuel performance modelling as part of its strategic objectives. To achieve this goal, an open-source approach has been chosen for the tools developed in the framework of the project, namely MMM and OFFBEAT, the latter coupled to the SCIANTIX code. As the open-source approach is relatively new in the domain of nuclear safety studies, this document presents a framework for achieving quality assurance targets for the open-source scientific computing tools within the OperaHPC project. First, the document provides a brief review of the most common QA programs and standards employed in the field, with a particular focus to the aspects that are more relevant to OperaHPC. Then, it discusses modern software development practices to improve code quality, highlighting the importance of revision control systems, testing methodologies, and documentation. Finally, it describes the concept of governance model for regulating interactions between contributors, users, and decision-makers. The framework presented in this document provides a backbone for the verification and validation actions that will be carried out within the project and contributes to the qualification of the MMM, OFFBEAT and SCIANTIX tools for nuclear safety studies

A large accumulation of avian eggs from the Late Cretaceous of Patagonia (Argentina) reveals a novel nesting strategy in Mesozoic birds

We report the first evidence for a nesting colony of Mesozoic birds on Gondwana: a fossil accumulation in Late Cretaceous rocks mapped and collected from within the campus of the National University of Comahue, Neuquén City, Patagonia (Argentina). Here, Cretaceous ornithothoracine birds, almost certainly Enanthiornithes, nested in an arid, shallow basinal environment among sand dunes close to an ephemeral water-course. We mapped and collected 65 complete, near-complete, and broken eggs across an area of more than 55 m2. These eggs were laid either singly, or occasionally in pairs, onto a sandy substrate. All eggs were found apparently in, or close to, their original nest site; they all occur within the same bedding plane and may represent the product of a single nesting season or a short series of nesting attempts. Although there is no evidence for nesting structures, all but one of the Comahue eggs were half-buried upright in the sand with their pointed end downwards, a position that would have exposed the pole containing the air cell and precluded egg turning. This egg position is not seen in living birds, with the exception of the basal galliform megapodes who place their eggs within mounds of vegetation or burrows. This accumulation reveals a novel nesting behaviour in Mesozoic Aves that was perhaps shared with the non-avian and phylogenetically more basal troodontid theropods.Fil: Fernández, Mariela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; ArgentinaFil: Garcia, Rodolfo Andres. Universidad Nacional de Rio Negro. Sede Alto Valle. Instituto de Investigaciones En Paleobiologia y Geologia; ArgentinaFil: Fiorelli, Lucas Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Regional de Investigaciones Cientificas y Transferencia Tecnológica de Anillaco; ArgentinaFil: Scolaro, Jose Alejandro. Universidad Nacional de la Patagonia "san Juan Bosco"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Salvador, Rodrigo B.. Universidade de Sao Paulo. Instituto Quã­mica de Sao Carlos; BrasilFil: Cotaro, Carlos N.. Comisión Nacional de Energía Atómica. Centro Atómico Bariloche; ArgentinaFil: Kaiser, Gary W.. Royal British Columbia Museum; CanadáFil: Dyke, Gareth J.. University Of Southampton; Reino Unid

Los comités de ética de investigación en la Ciudad Autónoma de Buenos Aires: a catorce años de la implementación de la Ley 3301

This article analyzes the implementation of research ethics committees in the Autonomous City of Buenos Aires, a process that took place in the context of a historical process of implementing health research policies at both the national and jurisdictional levels. Employing a qualitative, observational, and cross-sectional approach, we gathered secondary sources of public information and conducted semi-structured, in-depth interviews with members of the committees in the Autonomous City of Buenos Aires. The results are presented in relation to three aspects: 1) the composition of the research ethics committees; 2) work processes, emphasizing the impact of the COVID-19 pandemic; and 3) obstacles and proposals, that focuses on improvements identified by committee members.El presente artículo se propone analizar el proceso de implementación de los comités de ética en investigación en la Ciudad Autónoma de Buenos Aires, cuya conformación se observa en el marco de un proceso histórico de implementación de políticas de investigación en salud a nivel nacional y jurisdiccional. Desde un enfoque de investigación cualitativo, observacional y de corte transversal, se realizó un relevamiento de fuentes secundarias de información pública, y entrevistas semiestructuradas y en profundidad a integrantes de los comités de la Ciudad Autónoma de Buenos Aires. Los resultados se presentan agrupados en tres ejes: 1) la conformación de los comités de ética en investigación; 2) procesos de trabajo, haciendo hincapié en el impacto de la pandemia de covid-19; y 3) obstáculos y propuestas, que se focaliza en las mejoras identificadas por sus integrantes

pH Dependent Molecular Self-Assembly of Octaphosphonate Porphyrin of Nanoscale Dimensions: Nanosphere and Nanorod Aggregates

Self-assembled nanostructures of zwitterionic octaphosphanatoporphyrin 1, of either nanoparticles or nanorods, depending on small changes in the pH, is demonstrated based on the J-aggregates. Porphyrin 1 self-assembled into nanosphere aggregates with a diameter of about 70–80 nm in the pH range 5–7, and nanorod aggregates were observed at pH 8.5. Hydrogen bonding, π-π stacking and hydrophilic interactions play important roles in the formation of this nanostructure morphology. Nanostructures were characterized by UV/Vis absorbance, fluorescence, atomic force microscopy (AFM) and transmission electron microscopy (TEM). This interesting pH dependent self-assembly phenomenon could provide a basis for development of novel biomaterials

Research ethics committees in the Autonomous City of Buenos Aires: 14 years after the implementation of Law 3301

This article analyzes the implementation of research ethics committees in the Autonomous City of Buenos Aires, a process that took place in the context of a historical process of implementing health research policies at both the national and jurisdictional levels. Employing a qualitative, observational, and cross-sectional approach, we gathered secondary sources of public information and conducted semi-structured, in-depth interviews with members of the committees in the Autonomous City of Buenos Aires. The results are presented in relation to three aspects: 1) the composition of the research ethics committees; 2) work processes, emphasizing the impact of the COVID-19 pandemic; and 3) obstacles and proposals, that focuses on improvements identified by committee members

Induction chemotherapy followed by concurrent standard radiotherapy and daily low-dose cisplatin in locally advanced non-small-cell lung cancer

Both induction chemotherapy and concurrent low-dose cisplatin have been shown to improve results of thoracic irradiation in the treatment of locally advanced non-small-cell lung cancer (NSCLC). This phase II study was designed to investigate activity and feasibility of a novel chemoradiation regimen consisting of induction chemotherapy followed by standard radiotherapy and concurrent daily low-dose cisplatin. Previously untreated patients with histologically/cytologically proven unresectable stage IIIA/B NSCLC were eligible. Induction chemotherapy consisted of vinblastine 5 mg m−2 intravenously (i.v.) on days 1, 8, 15, 22 and 29, and cisplatin 100 mg m−2 i.v. on days 1 and 22 followed by continuous radiotherapy (60 Gy in 30 fractions) given concurrently with daily cisplatin at a dose of 5 mg m−2 i.v. Thirty-two patients were enrolled. Major toxicity during induction chemotherapy was haematological: grade III–IV leukopenia was observed in 31% and grade II anaemia in 16% of the patients. The most common severe toxicity during concurrent chemoradiation consisted of grade III leukopenia (21% of the patients); grade III oesophagitis occurred in only two patients and pulmonary toxicity in one patient who died of this complication. Eighteen of 32 patients (56%, 95% CI 38–73%) had a major response (11 partial response, seven complete response). With a median follow-up of 38.4 months, the median survival was 12.5 months and the actuarial survival rates at 1, 2 and 3 years were 52%, 26% and 19% respectively. The median event-free survival was 8.3 months with a probability of 40%, 23% and 20% at 1, 2 and 3 years respectively. Induction chemotherapy followed by concurrent daily low-dose cisplatin and thoracic irradiation, in patients with locally advanced NSCLC, is active and feasible with minimal non-haematological toxicity. Long-term survival results are promising and appear to be similar to those of more toxic chemoradiation regimens, warranting further testing of this novel chemoradiation strategy. © 1999 Cancer Research Campaig

Conjugation of Organoruthenium(II) 3-(1H-Benzimidazol-2-yl)pyrazolo[3,4-b]pyridines and Indolo[3,2-d]benzazepines to Recombinant Human Serum Albumin: a Strategy To Enhance Cytotoxicity in Cancer Cells

Five organoruthenium complexes [RuCl(η6-arene)(L)]Cl with a modified arene ligand, namely, 4-formylphenoxyacetyl-η6-benzylamide, and L = 3-(1H-benzimidazol-2-yl)-1H-pyrazolo[3,4-b]pyridines or indolo[3,2-d]benzazepines were synthesized and conjugated to recombinant human serum albumin in order to improve their drug targeting and delivery to cancer cells, and a marked increase in cytotoxicity was observed

Characterization of the binding sites of the anticancer ruthenium(III) complexes KP1019 and KP1339 on human serum albumin via competition studies

Indazolium trans-[tetrachloridobis(1H-indazole)ruthenate(III)] (KP1019) and its Na+ analogue (KP1339) are two of the most prominent non-platinum antitumor metal complexes currently undergoing clinical trials. After intravenous administration, they are known to bind to human serum albumin (HSA) in a noncovalent manner. To elucidate their HSA binding sites, displacement reactions with the established site markers warfarin and dansylglycine as well as bilirubin were monitored by spectrofluorimetry, ultrafiltration-UV-vis spectrophotometry, and/or capillary zone electrophoresis. Conditional stability constants for the binding of KP1019 and KP1339 to sites I and II of HSA were determined, indicating that both Ru(III) compounds bind to both sites with moderately strong affinity (log K (1)' = 5.3-5.8). No preference for either binding site was found, and similar results were obtained for both metal complexes, demonstrating low influence of the counter ion on the binding event

Conjugation of a Ru(II) Arene Complex to Neomycin or to Guanidinoneomycin Leads to Compounds with Differential Cytotoxicities and Accumulation between Cancer and Normal Cells

A straightforward methodology for the synthesis of conjugates between a cytotoxic organometallic ruthenium(II) complex and amino- and guanidinoglycosides, as potential RNA-targeted anticancer compounds, is described. Under microwave irradiation, the imidazole ligand incorporated on the aminoglycoside moiety (neamine or neomycin) was found to replace one triphenylphosphine ligand from the ruthenium precursor [(η6-p-cym)RuCl(PPh3)2]+, allowing the assembly of the target conjugates. The guanidinylated analogue was easily prepared from the neomycin-ruthenium conjugate by reaction with N,N′-di-Boc-N″-triflylguanidine, a powerful guanidinylating reagent that was compatible with the integrity of the metal complex. All conjugates were purified by semipreparative high-performance liquid chromatography (HPLC) and characterized by electrospray ionization (ESI) and matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and NMR spectroscopy. The cytotoxicity of the compounds was tested in MCF-7 (breast) and DU-145 (prostate) human cancer cells, as well as in the normal HEK293 (Human Embryonic Kidney) cell line, revealing a dependence on the nature of the glycoside moiety and the type of cell (cancer or healthy). Indeed, the neomycin-ruthenium conjugate (2) displayed moderate antiproliferative activity in both cancer cell lines (IC50 ≈ 80 μM), whereas the neamine conjugate (4) was inactive (IC50 ≈ 200 μM). However, the guanidinylated analogue of the neomycin-ruthenium conjugate (3) required much lower concentrations than the parent conjugate for equal effect (IC50 = 7.17 μM in DU-145 and IC50 = 11.33 μM in MCF-7). Although the same ranking in antiproliferative activity was found in the nontumorigenic cell line (3 2 > 4), IC50 values indicate that aminoglycoside-containing conjugates are about 2-fold more cytotoxic in normal cells (e.g., IC50 = 49.4 μM for 2) than in cancer cells, whereas an opposite tendency was found with the guanidinylated conjugate, since its cytotoxicity in the normal cell line (IC50 = 12.75 μM for 3) was similar or even lower than that found in MCF-7 and DU-145 cancer cell lines, respectively. Cell uptake studies performed by ICP-MS with conjugates 2 and 3 revealed that guanidinylation of the neomycin moiety had a positive effect on accumulation (about 3-fold higher in DU-145 and 4-fold higher in HEK293), which correlates well with the higher antiproliferative activity of 3. Interestingly, despite the slightly higher accumulation in the normal cell than in the cancer cell line (about 1.4-fold), guanidinoneomycin-ruthenium conjugate (3) was more cytotoxic to cancer cells (about 1.8-fold), whereas the opposite tendency applied for neomycin-ruthenium conjugate (2). Such differences in cytotoxic activity and cellular accumulation between cancer and normal cells open the way to the creation of more selective, less toxic anticancer metallodrugs by conjugating cytotoxic metal-based complexes such as ruthenium(II) arene derivatives to guanidinoglycosides