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Este artigo trata acerca do processo de expansão urbana em Fortaleza/CE e a ocupação de seu litoral na primeira metade do século XIX, tendo como ferramenta norteadora a seleção de alguns registros cartográficos dos urbanistas Silva Paulet e Simões de Farias. Pautado numa reflexão entorno da relação da construção dos referidos documentos com o momento de expansão urbana perpassada por Fortaleza, realizou-se levantamento dos principais registros cartográficos do período retratado. São eles: a) “Planta do Porto e Villa da Fortaleza” (1813) e b) “Planta da Vila de Fortaleza” (1818), ambas se Silva Paulet; c) “Planta da Cidade de Fortaleza” (1850) e d) “Ampliação da Planta de 1850”, ambas de Simões de Farias. Pautado numa reflexão entorno da Cartografia na construção ideológica do espaço, tratou-se os registros cartográficos como documentos geohistóricos de expressividade no debate travado nas décadas iniciais do século XIX entorno do direcionamento a ser tomado no processo de expansão urbana do município, dando ênfase no modo de projeção dado a zona costeira fortalezense. Assim, os desenhos de Paulet e Farias apresentam a partir de seus registros a complexidade do processo de organização do litoral, suscitando – com a necessidade de expansão da atividade portuária – o debate entorno da emergência do planejamento litorâneo.

Pleurotus cornucopiae is a commercial edible and medicinal fungus. Herein, we determined and analyzed its complete mitochondrial genome. The mitogenome length was 72,134 bp with a GC content of 26.7%, contained 14 conserved protein coding genes, two rRNA genes (rnl and rns), ribosomal protein gene rps3 and 24 tRNA genes. Pleurotus cornucopiae has a similar gene content and gene order of the mitogenome as P. ostreatus and P. eryngii. A phylogenetic analysis based on complete mitogenome in related fungi showed that P. cornucopiae is a member of the order Agaricales, forming a clade with P. ostreatus and P. eryngii, with P. ostreatus as a sister taxa. The mitochondrial genome sequence of P. cornucopiae appeared a promising tool for further studies of the taxonomy and evolution of Pleurotaceae and Agaricales.

Abstract Proteins are the primary targets of almost all small molecule drugs. However, even the most selectively designed drugs can potentially target several unknown proteins. Identification of potential drug targets can facilitate design of new drugs and repurposing of existing ones. Current state-of-the-art proteomics methodologies enable screening of thousands of proteins against a limited number of drug molecules. Here we report the development of a label-free quantitative proteomics approach that enables proteome-wide screening of small organic molecules in a scalable, reproducible, and rapid manner by streamlining the proteome integral solubility alteration (PISA) assay. We used rat organs ex-vivo to determine organ specific targets of medical drugs and enzyme inhibitors to identify drug targets for common drugs such as Ibuprofen. Finally, global drug profiling revealed overarching trends of how small molecules affect the proteome through either direct or indirect protein interactions.

The article offers information on artist Nicholas Hilliard and the portraits created by him of Queen Elizabeth I of England, and her ambassador in France, Amias Paulet. Topics discussed include the depiction of jewels worn by the Queen in his paintings by Hilliard; the artistic technique used by Hilliard in producing the paintings; and the depiction of color in the paintings.

Results of long-term research into the occurrence of Amanita strobiliformis in Szczecin are presented. Five new localities of the species are described and its distribution in Poland is discussed.

Abstract Imputation techniques provide means to replace missing measurements with a value and are used in almost all downstream analysis of mass spectrometry (MS) based proteomics data using label-free quantification (LFQ). Here we demonstrate how collaborative filtering, denoising autoencoders, and variational autoencoders can impute missing values in the context of LFQ at different levels. We applied our method, proteomics imputation modeling mass spectrometry (PIMMS), to an alcohol-related liver disease (ALD) cohort with blood plasma proteomics data available for 358 individuals. Removing 20 percent of the intensities we were able to recover 15 out of 17 significant abundant protein groups using PIMMS-VAE imputations. When analyzing the full dataset we identified 30 additional proteins (+13.2%) that were significantly differentially abundant across disease stages compared to no imputation and found that some of these were predictive of ALD progression in machine learning models. We, therefore, suggest the use of deep learning approaches for imputing missing values in MS-based proteomics on larger datasets and provide workflows for these.

Abstract Background Unlike Transposable Elements (TEs) and gene/genome duplication, the role of the so-called nuclear plastid DNA sequences (NUPTs) in shaping the evolution of genome architecture and function remains poorly studied. We investigate here the functional and evolutionary fate of NUPTs in the orphan crop Moringa oleifera (moringa), featured by the highest fraction of plastid DNA found so far in any plant genome, focusing on (i) any potential biases in their distribution in relation to specific nuclear genomic features, (ii) their contribution to the emergence of new genes and gene regions, and (iii) their impact on the expression of target nuclear genes. Results In agreement with their potential mutagenic effect, NUPTs are underrepresented among structural genes, although their overall transcription levels and broadness were only lower when involved exonic regions; the occurrence of plastid DNA generally did not result in a broader expression, except among those affected in introns by older NUPTs. In contrast, we found a strong enrichment of NUPTs among specific superfamilies of retrotransposons and several classes of RNA genes, including those participating in the protein biosynthetic machinery (i.e., rRNA and tRNA genes) and a specific class of regulatory RNAs. A significant fraction of NUPT RNA genes was found to be functionally expressed, thus potentially contributing to the nuclear pool. Conclusions Our results complete our view of the molecular factors driving the evolution of nuclear genome architecture and function, and support plastid DNA in moringa as a major source of (i) genome complexity and (ii) the nuclear pool of RNA genes.

BackgroundTrachoma is a leading cause of infection-related blindness worldwide. This disease is caused by recurrent Chlamydia trachomatis (Ct) infections of the conjunctiva and develops in two phases: i) active (acute trachoma, characterized by follicular conjunctivitis), then long-term: ii) scarring (chronic trachoma, characterized by conjunctival fibrosis, corneal opacification and eyelid malposition). Scarring trachoma is driven by the number and severity of reinfections. The immune system plays a pivotal role in trachoma including exacerbation of the disease. Hence the immune system may also be key to developing a trachoma vaccine. Therefore, we characterized clinical and local immune response kinetics in a non-human primate model of acute conjunctival Ct infection and disease.Methodology/principal findingsThe conjunctiva of non-human primate (NHP, Cynomolgus monkeys-Macaca fascicularis-) were inoculated with Ct (B/Tunis-864 strain, B serovar). Clinical ocular monitoring was performed using a standardized photographic grading system, and local immune responses were assessed using multi-parameter flow cytometry of conjunctival cells, tear fluid cytokines, immunoglobulins, and Ct quantification. Clinical findings were similar to those observed during acute trachoma in humans, with the development of typical follicular conjunctivitis from the 4th week post-exposure to the 11th week. Immunologic analysis indicated an early phase influx of T cells in the conjunctiva and elevated interleukins 4, 8, and 5, followed by a late phase monocytic influx accompanied with a decrease in other immune cells, and tear fluid cytokines returning to initial levels.Conclusion/significanceOur NHP model accurately reproduces the clinical signs of acute trachoma, allowing for an accurate assessment of the local immune responses in infected eyes. A progressive immune response occurred for weeks after exposure to Ct, which subsided into a persistent innate immune response. An understanding of these local responses is the first step towards using the model to assess new vaccine and therapeutic strategies for disease prevention.

Abstract Development and progression of malignancies are accompanied and influenced by alterations in the surrounding immune microenvironment. Understanding the cellular and molecular interactions between immune cells and cancer cells has not only provided important fundamental insights into the disease, but has also led to the development of new immunotherapies. The C-type lectin Dendritic Cell ImmunoReceptor (DCIR) is primarily expressed by myeloid cells and is an important regulator of immune homeostasis, as demonstrated in various autoimmune, infectious and inflammatory contexts. Yet, the impact of DCIR on cancer development remains largely unknown. Analysis of available transcriptomic data of colorectal cancer (CRC) patients revealed that high DCIR gene expression is associated with improved patients’ survival, immunologically "hot" tumors and high immunologic constant of rejection, thus arguing for a protective and immunoregulatory role of DCIR in CRC. In line with these correlative data, we found that deficiency of DCIR1, the murine homologue of human DCIR, leads to the development of significantly larger tumors in an orthotopic murine model of CRC. This phenotype is accompanied by an altered phenotype of tumor-associated macrophages (TAMs) and a reduction in the percentage of activated effector CD4+ and CD8+ T cells in CRC tumors of DCIR1-deficient mice. Overall, our results show that DCIR promotes antitumor immunity in CRC, making it an attractive target for the future development of immunotherapies to fight the second deadliest cancer in the world.

Abstract Background Beyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the plastid genome. As a result, plant nuclear genomes feature small, but variable, fraction of their genomes of plastid origin, the so-called nuclear plastid DNA sequences (NUPTs). However, the mechanisms underlying the origin and fixation of NUPTs are not yet fully elucidated and research on the topic has been mostly focused on a limited number of species and of plastid DNA. Results Here, we leveraged a chromosome-scale version of the genome of the orphan crop Moringa oleifera, which features the largest fraction of plastid DNA in any plant nuclear genome known so far, to gain insights into the mechanisms of origin of NUPTs. For this purpose, we examined the chromosomal distribution and arrangement of NUPTs, we explicitly modeled and tested the correlation between their age and size distribution, we characterized their sites of origin at the chloroplast genome and their sites of insertion at the nuclear one, as well as we investigated their arrangement in clusters. We found a bimodal distribution of NUPT relative ages, which implies NUPTs in moringa were formed through two separate events. Furthermore, NUPTs from every event showed markedly distinctive features, suggesting they originated through distinct mechanisms. Conclusions Our results reveal an unanticipated complexity of the mechanisms at the origin of NUPTs and of the evolutionary forces behind their fixation and highlight moringa species as an exceptional model to assess the impact of plastid DNA in the evolution of the architecture and function of plant nuclear genomes.

The article looks at the case of Paulet v. the United Kingdom presented to the European Court of Human Rights (Fourth Section). It mentions that that case come to the court as applicant lodged a complaint against the United Kingdom the under Article 34 of the Convention of Human Rights and Fundamental Freedoms.

ABSTRACT: Vaccination is one of the most important control tools to reduce Salmonella in poultry production. In order for a live vaccine to be licensed for field use it should be provided with the detection methods to differentiate it from field strains. This paper aims to describe the validation of an alternative method for the differentiation of the Salmonella 441/014 vaccine strain from field strains, using a chromogenic Media, ASAP from bioMérieux. The ASAP-based differentiation method was compared with already authorized methods, namely the Anicon SE Kylt PCR DIVA 1 assay and Ceva S-Check Salmonella differentiation kit, following the ISO 16140-6:2019 validation method guidelines. A Generalised Linear Model was fitted to the data to determine the inclusivity and exclusivity of differentiation methods (PCR Kylt vs. S-Check vs. ASAPTM). Statistical differences were based on a P-value level of < 0.05 (SPSS Inc., Chicago, IL). In this study, we show that the ASAP media was able to differentiate Salmonella Enteritidis vaccine strains from field strains, obtaining 100% agreement between the three differentiation assays. This differentiation approach is quicker, easier to deploy and cheaper as compared to alternative methods.

The article discusses proposals regarding addition of the unpaginated index of Traité des champignons and two editions of Tabula plantarum fugosarum by botanist J.-J. Paulet to the list of "Suppressed Works." Topics discussed include the 21 generic names published in Traite des champignons, the nomenclatural implications of accepting binomial designations as species names, and the nonacceptance of unpaginated index by Paulet.

Introduction: Global coronal alignment is mainly assessed by C7 plumbline and central sacral vertical line (CSVL), pelvic obliquity and shoulder alignment. A detailed analysis is mandatory when treating spinal deformity. It remains unclear to what extent mild scoliosis influences global coronal alignment. Research question: The objective was to define a comprehensive set of coronal alignment parameters and to investigate differences between individuals without spinal deformity and with mild scoliosis. The relationship between coronal and sagittal alignment and the influence of age were studied. Methods: Radiographs of 236 normal individuals (Group N) and 140 patients with scoliosis

IntroductionAmid the rising interest in sustainable urban development, Positive Energy Districts (PEDs) have become a focus of research. This study examines the dynamic processes that influence the development and scalability of PEDs from a co-evolutionary business ecosystem perspective.MethodsTo delve into the dynamics of Positive Energy Districts, we applied the business ecosystem framework to a real-world case study, namely the Hunziker Areal. Our research methodology involved the development and validation of a high-level conceptual model. This was achieved through workshops and guided interviews with experts engaged in pilot and research projects related to PEDs.ResultsThe study highlights the significance of employing a systemic approach to evaluate the potential of PEDs in enhancing housing sustainability while creating value for diverse stakeholders. Through the utilization of causal loop diagrams, key feedback loops explaining the diffusion of PEDs are identified. Moreover, the study reveals varying perceptions of PED utility among stakeholders, who assess the impact using different Key Performance Indicators (KPIs) such as CO2 target achievement and well-being. Key factors influencing technology adoption, such as low prosumer electricity unit cost, are also identified.DiscussionOur findings further shed light on crucial aspects affecting value capture and the attractiveness of the ecosystem to investors. Additionally, the study underscores the critical role of supportive policies and regulations in facilitating the diffusion and scalability of Positive Energy Districts.

Confronting the current educational reality involves developing intercultural competence during and after training to produce an impact on educational practices that promote positive classroom interactions with culturally and linguistically diverse students. In this context, this article presents the results of the construction and validation of the Intercultural Competence for Pedagogy Students (ICPE) instrument in a Chilean university. Taking into account the focus of interest, intercultural education in initial teacher training, the validation sample of the survey included 521 students in initial teacher training. This research aimed to establish the goodness of fit of the scale by analyzing the reliability and validity of the construct through confirmatory factor analysis. The scale presented adequate psychometric properties, contributing to the measurement of intercultural competence in initial teacher training to support attention to students in their cultural diversity.

Abstract Background Bud dormancy is a phenological adaptation of temperate perennials that ensures survival under winter temperature conditions by ceasing growth and increasing cold hardiness. SHORT VEGETATIVE PHASE (SVP)-like factors, and particularly a subset of them named DORMANCY-ASSOCIATED MADS-BOX (DAM), are master regulators of bud dormancy in perennials, prominently Rosaceae crops widely adapted to varying environmental conditions. Results SVP-like proteins from recently sequenced Rosaceae genomes were identified and characterized using sequence, phylogenetic and synteny analysis tools. SVP-like proteins clustered in three clades (SVP1–3), with known DAM proteins located within SVP2 clade, which also included Arabidopsis AGAMOUS-LIKE 24 (AthAGL24). A more detailed study on these protein sequences led to the identification of a 15-amino acid long motif specific to DAM proteins, which affected protein heteromerization properties by yeast two-hybrid system in peach PpeDAM6, and the unexpected finding of predicted DAM-like genes in loquat, an evergreen species lacking winter dormancy. DAM gene expression in loquat trees was studied by quantitative PCR, associating with inflorescence development and growth in varieties with contrasting flowering behaviour. Conclusions Phylogenetic, synteny analyses and heterologous overexpression in the model plant Arabidopsis thaliana supported three major conclusions: 1) DAM proteins might have emerged from the SVP2 clade in the Amygdaloideae subfamily of Rosaceae; 2) a short DAM-specific motif affects protein heteromerization, with a likely effect on DAM transcriptional targets and other functional features, providing a sequence signature for the DAM group of dormancy factors; 3) in agreement with other recent studies, DAM associates with inflorescence development and growth, independently of the dormancy habit.

Encystment is a process that allows free-living and parasitic amoebae to survive in unfavorable environments. Here, Bernard et al. provide detailed insights into the early stages of encystment of Acanthamoeba castellanii by integrating RNA-Seq, proteomics and phosphoproteomics data sets.

Nursing education, like education in higher education, has made a gradual digital turn, combining face-to-face and distance learning phases, “supported” by an increasingly efficient technical and pedagogical environment. Our study aims to shed light on how trainers of six nursing schools in the same university area implemented this blended approach. Professional development is approached through the prism of trainers' experience and through the characterization of blended courses. This study reveals the profound meaning that trainers attribute to their profession. It underlines through the expression of their experience several obstacles and potentialities in this process.

Amoebae found in aquatic and terrestrial environments encompass various pathogenic species, including the parasite Entamoeba histolytica and the free-living Acanthamoeba castellanii. Both microorganisms pose significant threats to public health, capable of inducing life-threatening effects on humans. These amoebae exist in two cellular forms: trophozoites and cysts. The trophozoite stage is the form used for growth and reproduction while the cyst stage is the resistant and disseminating form. Cysts occur after cellular metabolism slowdown due to nutritional deprivation or the appearance of environmental conditions unfavourable to the amoebae’s growth and division. The initiation of encystation is accompanied by the activation of stress responses, and scarce data indicate that encystation shares factors and mechanisms identified in stress responses occurring in trophozoites exposed to toxic compounds derived from human immune defence. Although some “omics” analyses have explored how amoebae respond to diverse stresses, these studies remain limited and rarely report post-translational modifications that would provide knowledge on the molecular mechanisms underlying amoebae-specific stress responses. In this review, we discuss ubiquitin-like proteins associated with encystation and cell survival during oxidative damage. We aim to shed light on the signalling pathways involved in amoebic defence mechanisms, with a focus on their potential clinical implications against pathogenic amoebae, addressing the pressing need for effective therapies.

The prevailing concept is that gestational alloimmune liver disease (GALD) is caused by maternal antibodies targeting a currently unknown antigen on the liver of the fetus. This leads to deposition of complement on the fetal hepatocytes and death of the fetal hepatocytes and extensive liver injury. In many cases, the newborn dies. In subsequent pregnancies early treatment of the woman with intravenous immunoglobulin can be instituted, and the prognosis for the fetus will be excellent. Without treatment the prognosis can be severe. Crucial improvements of diagnosis require identification of the target antigen. For this identification, this work was based on two hypotheses: 1. The GALD antigen is exclusively expressed in the fetal liver during normal fetal life in all pregnancies; 2. The GALD antigen is an alloantigen expressed in the fetal liver with the woman being homozygous for the minor allele and the father being, most frequently, homozygous for the major allele. We used three different experimental approaches to identify the liver target antigen of maternal antibodies from women who had given birth to a baby with the clinical GALD diagnosis: 1. Immunoprecipitation of antigens from either a human liver cell line or human fetal livers by immunoprecipitation with maternal antibodies followed by mass spectrometry analysis of captured antigens; 2. Construction of a cDNA expression library from human fetal liver mRNA and screening about 1.3 million recombinants in Escherichia coli using antibodies from mothers of babies diagnosed with GALD; 3. Exome/genome sequencing of DNA from 26 presumably unrelated women who had previously given birth to a child with GALD with husband controls and supplementary HLA typing. In conclusion, using the three experimental approaches we did not identify the GALD target antigen and the exome/genome sequencing results did not support the hypothesis that the GALD antigen is an alloantigen, but the results do not yield basis for excluding that the antigen is exclusively expressed during fetal life., which is the hypothesis we favor.

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

There are international protocols for the management of hypothyroidism induced by autoimmune thyroid disease during pregnancy. In this descriptive study, we analyzed the implementation of international protocols regarding these pathologies, in local clinical practice. Analyzing the cases admitted to the Obstetrics and Gynecology department of Bucharest University Emergency Hospital on a period of 55 months, we identified the pregnancies with autoimmune hypothyroidism treated with Levothyroxine (LT4). We determined the prevalence of specific immunological markers for autoimmune hypothyroidism in pregnant women, we analyzed whether they are associated with distinct clinical phenotypes and ultrasound characteristics, and also, we evaluated the treatment of choice. Measurement of thyroglobulin antibodies, thyroid peroxidase antibodies, Thyroid-Stimulating Hormone, free fractions of Triiodothyronine and Thyroxine with substitute treatment instituted early (in the first 2 weeks postnatal) determine the normalization of cognitive development, especially in areas known for iodine deficiency, including Romania.

The number of publicly available proteomics datasets is growing rapidly, but a standardized approach for describing the associated metadata is lacking. Here, the authors propose a format and a software pipeline to present and validate metadata, and integrate them into ProteomeXchange repositories.