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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.

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.

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.

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.

Introduction: Traditionally, to determine a length on a limb radiograph after total hip arthroplasty (THA), calibration is performed manually with the diameter of a ball or the femoral head. More recently, the development of EOS with automatic calibration has called into question the usefulness of manual calibration to highlight lower limb length inequality (LLLI). However, the validation of EOS with automatic calibration without landmarks to measure length inequalities on large images has not been verified against manual measurements on calibrated radiographs (conventional method), which motivated the present work., Hypothesis: EOS is more accurate and reproducible from one reader to another in highlighting LLLI after THA than the classic method., Patients and Methods: One hundred and ten patients included underwent primary THA surgery in 2 centers, with postoperative EOS performed. This EOS was extracted in 2 formats: a DICOM file with automatic calibration and an uncalibrated JPEG file (220 radiographic files in total). Two readers, without knowledge of the clinical data, each analyzed all of these images using 2 methods: by measuring the distance between the center of the femoral head and the center of the mortise on the operated side and the non-operated side on the DICOM file, therefore via the software integrated into the EOS image (method 1), or by measuring these same distances on the JPEG file by calibrating the measurement to the diameter of the prosthetic head (method 2). The reproducibility of the measurements from one reader to another (inter-observer reproducibility) and the agreement of the measurements between the 2 methods (inter-method agreement) were evaluated using the intraclass correlation coefficient (ICC) and the Bland- Altman graphic method., Results: Inter-method agreement was satisfactory regardless of the reader but with a significantly higher agreement for reader 1 (inter-method agreement for reader 1: CL1 = 0.95 and for reader 2: CL2 = 0.90 (p = 0.008)) and this result was also confirmed by the Bland-Altman plot with no bias tendency for each reader and less than 5% of measurements that were outside the agreement band. Inter-observer reproducibility for method 1 was better than that for method 2 to highlight an LLLI after THA according to the CCI. Inter-observer reproducibility for method 1 (RM1) was 0.96 and 0.92 for method 2 (RM2) (p = 0.009). This result was confirmed by the Bland-Altman plot with a mean difference of less than 1 mm for each of the methods (-0.2 (standard deviation = 2.23) and 0.81 (3.03) for method 1 and method 2 respectively)., Discussion: Our hypothesis has therefore been partially verified. The use of the calibrated software integrated into the EOS system and manual calibration are two valid methods for searching for an LLLI. The measurements remain more reproducible from one reader to another with the calibrated software integrated into the EOS system., Level of Evidence: III; non-randomized prospective comparative study., Competing Interests: Declaration of competing interest Henri Migaud is editor-in-chief of OTSR and consultant for Zimmer-Biomet Corin and MSD; Roger Erivan is consultant for Synthes-Depuy, Zimmer and Smith&Nephew; Pierre Klein, Pablo Lamotte-Paulet and Mehdi Hormi-Menard declare no conflicts of interest; Alain Duhamel has received emoluments from SOFCOT for the cost of statistical analyses; François Bonnomet is consultant for Amplitude and SERF., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Seeds of ten Andean lupin (Lupinus mutabilis Sweet) ecotypes were collected from different regions of Peru and treated with an aqueous debittering method. Both untreated and treated seeds were analyzed by using LC-MS to investigate flavonoid profiles of different ecotypes and impact of debittering process on these compounds. Thirteen isoflavones (mainly as glycosides of genistein and methoxy-genistein) and eight flavones (glycosylated apigenins and methyl-luteolins) were characterized as the main flavonoids in the seed samples. The untreated lupin seeds contained 187-252 mg/100 g (dry weight) of flavonoids. The main difference among lupin ecotypes was observed in the levels of genistein-malonylhexoside, methoxy-genistein-malonylhexoside, and methyl-luteolin-malonylhexoside. After the debittering treatment, the total flavonoid content in the seeds was decreased to 125-203 mg/100 g dry weight, the aglycones of genistein, methoxy-genistein, and methyl-luteolin being the key distinguishing compounds of ecotypes. The aqueous treatment was effective in degrading flavonoid glycosides and releasing the corresponding aglycones., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Ritva Repo-Carrasco-Valencia reports financial support was provided by European Commission. Jukka-Pekka Suomela reports financial support was provided by Business Finland. Ye Tian reports financial support was provided by China Scholarship Council. Paola Cortes-Avendano reports financial support was provided by Cienciactiva of CONCYTEC., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

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. ASAP TM ). 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., Competing Interests: Disclosures The study was conceived, developed, and analyzed by J.G.L, C.G, P.C-G, and S.S-N from CECAV which declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)