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Metallic glass formers are a relatively new entry in glass physics, which has attracted large interest in both physics and materials science communities due to the unique mechanical and structural properties of these materials. Physical aging is however one of the main obstacle to their widespread use as it affects their properties at all length scales. The knowledge of the microscopic mechanisms inducing aging and relaxation is therefore extremely important for both fundamental and applied sciences. In this article we present a review of the recent advances made with the X-ray photon correlation spectroscopy technique on the study of the collective particle motion and physical aging in metallic glasses at the atomic level. We show that a careful tuning of the sample preparation or the application of specific thermal protocols have the potential to drive the glass into more aged or rejuvenated microscopic configurations with different stabilities.

Objectiu: analitzar la situació dels centres de documentació en la premsa espanyola al final de la segona dècada del segle xxi, deu anys després de l'inici de la crisi que ha tingut un gran impacte en les empreses periodístiques. -- Metodologia: s'envia un qüestionari amb opció de respostes obertes a responsables de documentació de nou diaris espanyols, amb preguntes sobre: personal, funcions documentals, programari, fonts d'informació, productes documentals, xarxes socials, noves funcions i futur de la professió. -- Resultats: entre altres, es constaten la reducció considerable de plantilles en els darrers deu anys; l'ús més important de tasques documentals en relació amb l'edició impresa que en relació amb l'edició digital (per exemple, l'anàlisi documental); l'escassa integració del programari documental de les edicions impresa i en línia; la poca evolució en l'ús de fonts d'informació; l'elaboració generalitzada de productes documentals per a ús intern de la redacció, quan, en canvi, són molt pocs els productes d'aquest tipus que arriben al lector; l'interès per participar en activitats emergents com la verificació de dades (fact-checking) o la cura de continguts, i, finalment, el fet que, en les opinions sobre el futur professional, conviuen percepcions pessimistes sobre la continuïtat dels centres de documentació amb propostes per a donar valor a la professió. Objective: To analyse the situation of documentation services in Spanish newspapers in 2020, ten years after the start of the recession, which had such a great impact on news agencies. -- Methodology: An open-ended questionnaire was sent to the documentation managers of nine Spanish newspapers, with questions about: staff, documentary functions, software use, sources of information, documentary products, social networks, new features and the future of the profession. -- Results: The following points emerged from the responses to the questionnaires: the considerable reduction in staff over the last ten years; the greater use of documentation in relation to print publishing than in digital publishing (e.g., document analysis); the low level of integration of documentary software in print and online editions; the low use of information sources; the widespread creation of documentary products for internal use, when in fact very few of these products reach the reader; the interest in participating in emerging activities such as fact-checking and vetting content; and, finally, the fact that, when asked to predict the future of the profession, respondents combined pessimistic perceptions about the continuity of the documentation centres with a number of proposals for raising the profession’s profile.

Objetivo: analizar la situación de los centros de documentación en la prensa española a finales de la segunda década del siglo xxi, diez años después del inicio de la crisis que ha tenido un gran impacto en las empresas periodísticas. -- Metodología: se envía un cuestionario con opción de respuestas abiertas a responsables de documentación de nueve diarios españoles, con cuestiones sobre: personal, funciones documentales, software, fuentes de información, productos documentales, redes sociales, nuevas funciones y futuro de la profesión. -- Resultados: entre otros, se constatan la reducción considerable de plantillas en los últimos diez años; el mayor uso de tareas documentales con relación a la edición impresa que con relación a la edición digital (por ejemplo, el análisis documental);la escasa integración del software documental de las ediciones impresa y en línea; la poca evolución enel uso de fuentes de información; la realización generalizada de productos documentales para uso interno de la redacción,cuando, en cambio, son muy pocos los productos de este tipo que llegan al lector; el interés por participar en actividades emergentes como la verificación de datos (fact-checking) o la curación de contenidos, y, finalmente, que, en las opiniones sobre el futuro profesional, conviven percepciones pesimistas sobre la continuidad de los centros de documentación con propuestas para valorizar la profesión. Objective: To analyse the situation of documentation services in Spanish newspapers in 2020, ten years after the start of the recession, which had such a great impact on news agencies. -- Methodology: An open-ended questionnaire was sent to the documentation managers of nine Spanish newspapers, with questions about: staff, documentary functions, software use, sources of information, documentary products, social networks, new features and the future of the profession. -- Results: The following points emerged from the responses to the questionnaires: the considerable reduction in staff over the last ten years; the greater use of documentation in relation to print publishing than in digital publishing (e.g., document analysis); the low level of integration of documentary software in print and online editions; the low use of information sources; the widespread creation of documentary products for internal use, when in fact very few of these products reach the reader; the interest in participating in emerging activities such as fact-checking and vetting content; and, finally, the fact that, when asked to predict the future of the profession, respondents combined pessimistic perceptions about the continuity of the documentation centres with a number of proposals for raising the profession’s profile.

Abstract Background Cystic Fibrosis (CF) is a monogenic disease caused by mutations in the gene coding the Cystic Fibrosis Transmembrane Regulator (CFTR) protein, but its overall physio-pathology cannot be solely explained by the loss of the CFTR chloride channel function. Indeed, CFTR belongs to a yet not fully deciphered network of proteins participating in various signalling pathways. Methods We propose a systems biology approach to study how the absence of the CFTR protein at the membrane leads to perturbation of these pathways, resulting in a panel of deleterious CF cellular phenotypes. Results Based on publicly available transcriptomic datasets, we built and analyzed a CF network that recapitulates signalling dysregulations. The CF network topology and its resulting phenotypes were found to be consistent with CF pathology. Conclusion Analysis of the network topology highlighted a few proteins that may initiate the propagation of dysregulations, those that trigger CF cellular phenotypes, and suggested several candidate therapeutic targets. Although our research is focused on CF, the global approach proposed in the present paper could also be followed to study other rare monogenic diseases.

Purpose: This study aims at understanding how higher education institutions (HEIs) can contribute to sustainable development, by designing their programmes for bringing about a transformative impact on communities and students, and also to examine what alternative pedagogical approaches could be used for that. In the past decades, HEIs have increasingly created social innovation (SI) programmes, as a way to achieve United Nations Sustainable Development Goals. These community-oriented and field-based programmes are difficult to ally with conventional classroom education. This study explores how these programmes could integrate the participatory approach and what would be the benefits. It also investigates the effectiveness of the experiential learning approach for teaching sustainability. Design/methodology/approach: A case study method is used to document SI projects initiated by an HEI programme in rural India. Findings: It was found that the participatory approach contributes to empowering communities and also benefits the students in terms of academic, professional and personal growth. Empirical findings show that experiential learning is an efficient method to teach sustainability. Ultimately, both pedagogical approaches are found to be mutually beneficial. Originality/value: This study fills a gap in the literature, by providing empirical evidence on how HEI can implement innovative educational strategies such as participatory approach and experiential learning in their programmes towards teaching sustainability. A conceptual model for HEI interested in developing similar programmes is also proposed. To the best of the authors' knowledge, this study is one of the first studies focusing on the context of Indian HEI.

Trypanosoma cruzi, the causative agent of Chagas disease, can be congenitally transmitted by crossing the placental barrier. This study investigates the role of T. cruzi-derived exovesicles (TcEVs) in facilitating parasite infection and the consequent tissue damage and apoptotic cell death in human placental explants (HPEs). Our findings demonstrate that TcEVs significantly enhance the parasite load and induce tissue damage in HPEs, both in the presence and absence of the parasite. Through histopathological and immunohistochemical analyses, we show that TcEVs alone can disrupt the placental barrier, affecting the basal membrane and villous stroma. The induction of apoptotic cell death is evidenced by DNA fragmentation, caspase 8 and 3, and p18 fragment immunodetection. This damage is exacerbated when TcEVs are combined with T. cruzi infection. These findings suggest that TcEVs play a critical role in the pathogenesis of congenital Chagas disease by disrupting the placental barrier and facilitating parasite transmission to the fetus. This study provides new insights into the mechanisms of transplacental transmission of T. cruzi and highlights the potential of targeting TcEVs as a therapeutic strategy against congenital Chagas disease.

Abstract Background The COVID‐19 pandemic negatively affected child and adolescent mental health and at the end of the pandemic (April 2022) child mental health had not returned to pre‐pandemic levels. We investigated whether this observed increase in mental health problems has continued, halted, or reversed after the end of the pandemic in children from the general population and in children in psychiatric care. Methods We collected parent‐reported and child‐reported data at two additional post‐pandemic time points (November/December 2022 and March/April 2023) in children (8–18 years) from two general population samples (N = 818–1056 per measurement) and one clinical sample receiving psychiatric care (N = 320–370) and compared these with data from before the pandemic. We collected parent‐reported data on internalizing and externalizing problems with the Brief Problem Monitor and self‐reported data on Anxiety, Depressive symptoms, Sleep‐related impairments, Anger, Global health, and Peer relations with the Patient‐Reported Outcomes Measurement Information System (PROMIS®). Results In the general population, parents reported no changes in externalizing problems but did report higher internalizing problems post‐pandemic than pre‐pandemic (p

We performed Monte Carlo simulations of single-wavelength lidar signals from multi-layered clouds with special attention focused on the multiple-scattering (MS) effect in regions of the cloud-free molecular atmosphere (i.e. between layers or outside a cloud system). Despite the fact that the strength of lidar signals from the molecular atmosphere is much lower compared to the in-cloud intervals, studies of MS effects in such regions are of interest from scientific and practical points of view. The MS effect on lidar signals always decreases with the increasing distance from the cloud far edge. The decrease is the direct consequence of the fact that the forward peak of particle phase functions is much larger than the receiver field of view (RFOV). Therefore, the photons scattered within the forward peak escape the sampling volume formed by the RFOV (i.e. the escape effect). We demonstrated that the escape effect is an inherent part of MS properties within the free atmosphere beyond the cloud far edge. In the cases of the ground-based lidar, the MS contribution is lower than 5 % within the regions of the cloud-free molecular atmosphere with a distance from the cloud far edge of about 1 km or higher. In the cases of the space-borne lidar, the rate of decrease of the MS contribution is so slow that the threshold of 5 % can hardly be reached. In addition, the effect of non-uniform beam filling is extremely strong. Therefore, practitioners should employ, with proper precautions, lidar data from regions below the cloud base when treating data of a space-borne lidar. In the case of two-layered cloud, the distance of 1 km is sufficiently large so that the scattered photons emerging from the first layer do not affect signals from the second layer when we are dealing with the ground-based lidar. In contrast, signals from the near edge of the second cloud layer are severely affected by the photons emerging from the first layer in the case of a space-borne lidar. We evaluated the Eloranta model (EM) in extreme conditions and showed its good performance in the cases of ground-based and space-borne lidars. At the same time, we revealed the shortcoming that can affect practical applications of the EM. Namely, values of the key parameters – i.e. the ratios of phase functions in the backscatter direction for the nth-order-scattered photon and a singly scattered photon – depend not only on the particle phase function but also on the distance from a lidar to the cloud and the receiver field of view. Those ratios vary within a quite large range, and the MS contribution to lidar signals can be largely overestimated or underestimated if erroneous values of the ratios are assigned to the EM.

AI holds the potential to transform healthcare, promising improvements in patient care. Yet, realizing this potential is hampered by over-reliance on limited datasets and a lack of transparency in validation processes. To overcome these obstacles, we advocate the creation of a detailed registry for AI algorithms. This registry would document the development, training, and validation of AI models, ensuring scientific integrity and transparency. Additionally, it would serve as a platform for peer review and ethical oversight. By bridging the gap between scientific validation and regulatory approval, such as by the FDA, we aim to enhance the integrity and trustworthiness of AI applications in healthcare.

A new experimental setup combining X-ray photon correlation spectroscopy (XPCS) in the hard X-ray regime and a high-pressure sample environment has been developed to monitor the pressure dependence of the internal motion of complex systems down to the atomic scale in the multi-gigapascal range, from room temperature to 600 K. The high flux of coherent high-energy X-rays at fourth-generation synchrotron sources solves the problems caused by the absorption of diamond anvil cells used to generate high pressure, enabling the measurement of the intermediate scattering function over six orders of magnitude in time, from 10−3 s to 103 s. The constraints posed by the high-pressure generation such as the preservation of X-ray coherence, as well as the sample, pressure and temperature stability, are discussed, and the feasibility of high-pressure XPCS is demonstrated through results obtained on metallic glasses.

Abstract Background Children with advanced pulmonary disease due to cystic fibrosis (CF) are at risk of acute respiratory failure due to pulmonary exacerbations leading to their admission to pediatric intensive care units (PICU). The objectives of this study were to determine short and medium-term outcomes of children with CF admitted to PICU for acute respiratory failure due to pulmonary exacerbation and to identify prognosis factors. Methods This retrospective monocentric study included patients less than 18 years old admitted to the PICU of a French university hospital between 2000 and 2020. Cox proportional hazard regression methods were used to determine prognosis factors of mortality or lung transplant. Results Prior to PICU admission, the 29 patients included (median age 13.5 years) had a severe lung disease (median Forced Expiratory Volume in 1 s percentage predicted at 29%). Mortality rates were respectively 17%, 31%, 34%, 41% at discharge and at 3, 12 and 36 months post-discharge. Survival rates free of lung transplant were 34%, 32%, 24% and 17% respectively. Risk factors associated with mortality or lung transplant using the univariate analysis were female sex and higher pCO2 and chloride levels at PICU admission, and following pre admission characteristics: home respiratory and nutritional support, registration on lung transplant list and Stenotrophomonas Maltophilia bronchial colonization. Conclusion Children with CF admitted to PICU for acute respiratory failure secondary to pulmonary exacerbations are at high risk of death, both in the short and medium terms. Lung transplant is their main chance of survival and should be considered early.

Abstract Background Quality traits are essential determinants of consumer preferences. Dioscorea alata (Greater Yam), is a starchy tuber crop in tropical regions. However, a comprehensive understanding of the genetic basis underlying yam tuber quality remains elusive. To address this knowledge gap, we employed population genomics and candidate gene association approaches to unravel the genetic factors influencing the quality attributes of boiled yam. Methods and Results Comparative genomics analysis of 45 plant species revealed numerous novel genes absent in the existing D. alata gene annotation. This approach, adding 48% more genes, significantly enhanced the functional annotation of three crucial metabolic pathways associated with boiled yam quality traits: pentose and glucuronate interconversions, starch and sucrose metabolism, and flavonoid biosynthesis. In addition, the whole-genome sequencing of 127 genotypes identified 27 genes under selection and 22 genes linked to texture, starch content, and color through a candidate gene association analysis. Notably, five genes involved in starch content and cell wall composition, including 1,3-beta Glucan synthase, β-amylase, and Pectin methyl esterase, were common to both approaches and their expression levels were assessed by transcriptomic data. Conclusions The analysis of the whole-genome of 127 genotypes of D. alata and the study of three specific pathways allowed the identification of important genes for tuber quality. Our findings provide insights into the genetic basis of yam quality traits and will help the enhancement of yam tuber quality through breeding programs.

Nanostructural characteristics of polycrystalline SnO2 thin films determine their psychical and chemical properties as semiconductor gas sensor. Tin oxide thin films obtained by spray pyrolysis deposition on glass substrates have been studied (35nm - 300nm). We have studied the influence of the pyrolysis temperature (300ºC - 530ºC) on the crystallographic structure of the films. These samples have been characterised by X-ray diffraction, and high-resolution transmission electron microscopy. Some atomic models of growing have been proposed, with a double pyramidal structure and rhombic base.Las características nanoestructurales de las capas finas policristalinas de SnO2 determinan sus propiedades físicas y químicas como material sensor de gas. Se han analizado un conjunto de muestras (35nm - 300nm) crecidas por pirólisis en fase aerosol sobre substratos de vidrio, estudiando la influencia de la temperatura de pirólisis (375ºC - 530ºC) en la estructura cristalina de las capas. Estas muestras han sido caracterizadas mediante difracción de rayos X y microscopia electrónica de transmisión de alta resolución. Se han propuesto modelos atómicos de crecimiento, de estructura doble piramidal truncada y base rómbica, para las diferentes temperaturas de depósito.

We aimed to evaluate the performance of supervised machine learning algorithms in predicting articles relevant for full-text review in a systematic review. Overall, 16,430 manually screened titles/abstracts, including 861 references identified relevant for full-text review were used for the analysis. Of these, 40% (n = 6573) were sub-divided for training (70%) and testing (30%) the algorithms. The remaining 60% (n = 9857) were used as a validation set. We evaluated down- and up-sampling methods and compared unigram, bigram, and singular value decomposition (SVD) approaches. For each approach, Naïve Bayes, Support Vector Machines (SVM), regularized logistic regressions, neural networks, random forest, Logit boost, and XGBoost were implemented using simple term frequency or Tf-Idf feature representations. Performance was evaluated using sensitivity, specificity, precision and area under the Curve. We combined predictions of the best-performing algorithms (Youden Index [greater than or equal to]0.3 with sensitivity/specificity [greater than or equal to]70/60%). In a down-sample unigram approach, Naïve Bayes, SVM/quanteda text models with Tf-Idf, and linear SVM e1071 package with Tf-Idf achieved >90% sensitivity at specificity >65%. Combining the predictions of the 10 best-performing algorithms improved the performance to reach 95% sensitivity and 64% specificity in the validation set. Crude screening burden was reduced by 61% (5979) (adjusted: 80.3%) with 5% (27) false negativity rate. All the other approaches yielded relatively poorer performances. The down-sampling unigram approach achieved good performance in our data. Combining the predictions of algorithms improved sensitivity while screening burden was reduced by almost two-third. Implementing machine learning approaches in title/abstract screening should be investigated further toward refining these tools and automating their implementation.

Liquid pyrolysis is presented as a new production method of SnO2 nanocrystalline powders suitable for gas sensor devices. The method is based on a pyrolytic reaction of high tensioned stressed drops of an organic solution of SnCl4•5(H2O). The main advantages of the method are its capability to produce SnO2 nanopowders with high stability, its accurate control over the grain size and other structural characteristics, its high level of repeatability and its low industrialization implementation cost. The characterization of samples of SnO2 nanoparticles obtained by liquid pyrolysis in the range between 200ºC and 900ºC processing temperature is carried out by X-ray diffraction, transmission electron microscopy, Raman and X-ray photoelectron spectroscopy. Results are analyzed and discussed so as to validate the advantages of the liquid pyrolysis method.La pirólisis líquida se presenta como un nuevo método para producir SnO2 nanocristalino en polvo ideal para sensores de gas. El método se basa en una reacción pirolítica de gotas altamente tensionadas procedentes de una solución orgánica de SnCl4•5(H2O). Las principales ventajas del método son la capacidad para producir nanopartículas de SnO2 con una gran estabilidad, el preciso control sobre el tamaño de grano y sobre otras características estructurales, el alto nivel de repetibilidad y el bajo coste en su implementación industrial.La caracterización de las muestras de las nanopartículas de SnO2 obtenidas por pirólisis líquida en un rango de temperatura de procesado que va de 200ºC a 900ºC se ha realizado mediante difracción de rayos X, microscopía electrónica de transmisión, espectroscopía Raman y espectroscopía fotoelectrónica de rayos X. Los resultados se han analizado y discutido. Éstos validan las ventajas del método de la pirólisis líquida.

IntroductionSmartphone use during caregiving has become increasingly common, especially around infants and very young children, and this use around young children has been linked with lower quality and quantity of parent-child interaction, with potential implications for child behavior, and parent-child attachment. To understand drivers and consequences of parent phone use, we were interested in the daily associations between parent phone use and depressed mood, as well as the potential for parent perceptions of their responsiveness toward their infant to alter the association between parent phone use and mood.MethodsIn the present study, we explored associations between day-to-day changes in parent smartphone use (objectively-measured via passive sensing) around their infant, depressed mood, and parent perceptions of their responsiveness to their infants among a sample of 264 parents across 8 days. We utilized multilevel modeling to examine these within-person daily associations.ResultsObjectively-measured parent smartphone use during time around their infant was significantly associated with depressed mood on a daily basis. Interestingly, this was not true on days when parents perceived themselves to be more responsive to their infant.DiscussionThese results suggest that parent judgements and perceptions of their parenting behavior may impact the potential link between parent phone use and parent mood. This is the first study utilizing intensive daily data to examine how parent perceptions may alter the felt effects of phone use on their parenting. Future work examining potential impacts of smartphone use on parenting should consider the effects of both actual use and perceptions about that use.

IntroductionThe conect4children (c4c) project aims to facilitate efficient planning and delivery of paediatric clinical trials. One objective of c4c is data standardization and reuse. Interoperability and reusability of paediatric clinical trial data is challenging due to a lack of standardization. The Clinical Data Interchange Standards Consortium (CDISC) standards that are required or recommended for regulatory submissions in several countries lack paediatric specificity with limited awareness within academic institutions. To address this, c4c and CDISC collaborated to develop the Pediatrics User Guide (PUG) consisting of cross-cutting data items that are routinely collected in paediatric clinical trials, factoring in all paediatric age ranges.Methods and ResultsThe development of the PUG consisted of six stages. During the scoping phase, subtopics (each containing several clinically relevant concepts) were suggested and debated for inclusion in the PUG. Ninety concepts were selected for the modelling phase. Concept maps describing the Research Topic and representation procedure were developed for the 19 concepts that had no (or partial) previous modelling in CDISC. Next, metadata and implementation examples were developed for concepts. This was followed by a CDISC internal review and a public review. For both these review stages, the feedback comments were either implemented or rejected based on budget, timelines, expert review, and scope. The PUG was published on the CDISC website on February 23, 2023.DiscussionThe PUG is a first step in bridging the lack of child specific CDISC standards, particularly within academia. Several academic and industrial partners were involved in the development of the PUG, and c4c has undertaken multiple steps to publicize the PUG within its academic partner organizations – in particular, the European Reference Networks (ERNs) that are developing registries and dictionaries in 24 disease areas. In the long term, continued use of the PUG in paediatric clinical trials will enable the pooling of data from multiple trials, which is particularly important for medical domains with small populations.

This article describes the methods used to build a large-scale database of more than 250,000 electronic fetal monitoring (EFM) records linked to a comprehensive set of clinical information about the infant, the mother, the pregnancy, labor, and outcome. The database can be used to investigate how birth outcome is related to clinical and EFM features. The main steps involved in building the database were: (1) Acquiring the raw EFM recording and clinical records for each birth. (2) Assigning each birth to an objectively defined outcome class that included normal, acidosis, and hypoxic-ischemic encephalopathy. (3) Removing all personal health information from the EFM recordings and clinical records. (4) Preprocessing the deidentified EFM records to eliminate duplicates, reformat the signals, combine signals from different sensors, and bridge gaps to generate signals in a format that can be readily analyzed. (5) Post-processing the repaired EFM recordings to extract key features of the fetal heart rate, uterine activity, and their relations. (6) Populating a database that links the clinical information, EFM records, and EFM features to support easy querying and retrieval. • A multi-step process is required to build a comprehensive database linking electronic temporal fetal monitoring signals to a comprehensive set of clinical information about the infant, the mother, the pregnancy, labor, and outcome. • The current database documents more than 250,000 births including almost 4,000 acidosis and 400 HIE cases. This represents more than 80% of the births that occurred in 15 Northern California Kaiser Permanente Hospitals between 2011–2019. This is a valuable resource for studying the factors predictive of outcome. • The signal processing code and schemas for the database are freely available. The database will not be permitted to leave Kaiser firewalls, but a process is in place to allow interested investigators to access it.

Abstract Despite increasing evidence that cholesterol precursors and oxysterols, oxidized cholesterol metabolites, play a role in numerous pathological processes and diseases including breast cancer, little is known about correlates of these sterols in women with breast cancer. In this study, 2282 women with breast cancer and blood draw post diagnosis were included and cross-sectional associations between circulating levels of 15 sterols/oxysterols and (a) lifestyle, anthropometric, reproductive characteristics, (b) comorbidities and medication use, and (c) breast cancer tumor and treatment characteristics were calculated using generalized linear models. Obesity was strongly associated with circulating levels of 7-dehydrocholesterol (DC) (body mass index ≥ 30 vs. 18.5–24.9 kg/m2: 51.7% difference) and 7-ketocholesterol (KC) (40.0% difference). After adjustment for BMI, comorbidities such as cardiovascular disease were associated with higher levels of 7-DC (26.1% difference) and lower levels of desmosterol (− 16.4% difference). Breast cancer tumor characteristics including hormone receptor status, tumor stage, and endocrine therapy were associated with lanosterol, 24-DHLan, 7b-HC, and THC (e.g., THC; tumor stage IIIa vs. I: 36.9% difference). Weaker associations were observed for lifestyle characteristics and for any of the other oxysterols. The findings of this study suggest that cholesterol precursors are strongly associated with metabolic factors, while oxysterols are associated with breast cancer tumor characteristics, warranting further investigation into the role of cholesterol precursors and oxysterols in women with breast cancer and other populations.

Genomic contamination remains a pervasive challenge in (meta)genomics, prompting the development of numerous detection tools. Despite the attention that this issue has attracted, a comprehensive comparison of the available tools is absent from the literature. Furthermore, the potential effect of horizontal gene transfer on the detection of genomic contamination has been little studied. In this study, we evaluated the efficiency of detection of six widely used contamination detection tools. To this end, we developed a simulation framework using orthologous group inference as a robust basis for the simulation of contamination. Additionally, we implemented a variable mutation rate to simulate horizontal transfer. Our simulations covered six distinct taxonomic ranks, ranging from phylum to species. The evaluation of contamination levels revealed the suboptimal precision of the tools, attributed to significant cases of both over-detection and under-detection, particularly at the genus and species levels. Notably, only so-called “redundant” contamination was reliably estimated. Our findings underscore the necessity of employing a combination of tools, including Kraken2, for accurate contamination level assessment. We also demonstrate that none of the assayed tools confused contamination and horizontal gene transfer. Finally, we release CRACOT, a freely accessible contamination simulation framework, which holds promise in evaluating the efficacy of future algorithms.

Abstract The efficiency of analyzing high-throughput data in systems biology has been demonstrated in numerous studies, where molecular data, such as transcriptomics and proteomics, offers great opportunities for understanding the complexity of biological processes. One important aspect of data analysis in systems biology is the shift from a reductionist approach that focuses on individual components to a more integrative perspective that considers the system as a whole, where the emphasis shifted from differential expression of individual genes to determining the activity of gene sets. Here, we present the rROMA software package for fast and accurate computation of the activity of gene sets with coordinated expression. The rROMA package incorporates significant improvements in the calculation algorithm, along with the implementation of several functions for statistical analysis and visualizing results. These additions greatly expand the package’s capabilities and offer valuable tools for data analysis and interpretation. It is an open-source package available on github at: www.github.com/sysbio-curie/rROMA . Based on publicly available transcriptomic datasets, we applied rROMA to cystic fibrosis, highlighting biological mechanisms potentially involved in the establishment and progression of the disease and the associated genes. Results indicate that rROMA can detect disease-related active signaling pathways using transcriptomic and proteomic data. The results notably identified a significant mechanism relevant to cystic fibrosis, raised awareness of a possible bias related to cell culture, and uncovered an intriguing gene that warrants further investigation.

RESUMO Este artigo argumenta que o estabelecimento de um código de salvaguardas é uma das questões básicas a serem enfrentadas pela atual rodada de negociações do GATT. A Seção II discute o papel das medidas de salvaguardas como instrumentos de proteção, mostra os problemas decorrentes da falta de um código sobre o assunto e indica as opções viáveis de regulamentação. A Seção III analisa o funcionamento dos códigos antidumping e de subsídios na década de 80, com ênfase nos impactos das ações de outros países contra as exportações brasileiras, e revela a interação desses códigos com outros instrumentos de proteção utilizados pelos países desenvolvidos. A Seção IV resume os principais pontos do artigo.