Unsupervised modeling of mutational landscapes of adeno-associated viruses viability.

Adeno-associated viruses 2 (AAV2) are minute viruses renowned for their capacity to infect human cells and akin organisms. They have recently emerged as prominent candidates in the field of gene therapy, primarily attributed to their inherent non-pathogenic nature in humans and the safety associated with their manipulation. The efficacy of AAV2 as gene therapy vectors hinges on their ability to infiltrate host cells, a phenomenon reliant on their competence to construct a capsid capable of breaching the nucleus of the target cell. To enhance their infection potential, researchers have extensively scrutinized various combinatorial libraries by introducing mutations into the capsid, aiming to boost their effectiveness. The emergence of high-throughput experimental techniques, like deep mutational scanning (DMS), has made it feasible to experimentally assess the fitness of these libraries for their intended purpose. Notably, machine learning is starting to demonstrate its potential in addressing predictions within the mutational landscape from sequence data. In this context, we introduce a biophysically-inspired model designed to predict the viability of genetic variants in DMS experiments. This model is tailored to a specific segment of the CAP region within AAV2's capsid protein. To evaluate its effectiveness, we conduct model training with diverse datasets, each tailored to explore different aspects of the mutational landscape influenced by the selection process. Our assessment of the biophysical model centers on two primary objectives: (i) providing quantitative forecasts for the log-selectivity of variants and (ii) deploying it as a binary classifier to categorize sequences into viable and non-viable classes.

Statistical Considerations for the Design and Analysis of Pragmatic Trials in Aging Research.

Pragmatic trials aim to assess intervention efficacy in usual patient care settings, contrasting with explanatory trials conducted under controlled conditions. In aging research, pragmatic trials are important designs for obtaining real-world evidence in elderly populations, which are often underrepresented in trials. In this review, we discuss statistical considerations from a frequentist approach for the design and analysis of pragmatic trials. When choosing the dependent variable, it is essential to use an outcome that is highly relevant to usual medical care while also providing sufficient statistical power. Besides traditionally used binary outcomes, ordinal outcomes can provide pragmatic answers with gains in statistical power. Cluster randomization requires careful consideration of sample size calculation and analysis methods, especially regarding missing data and outcome variables. Mixed effects models and generalized estimating equations (GEEs) are recommended for analysis to account for center effects, with tools available for sample size estimation. Multi-arm studies pose challenges in sample size calculation, requiring adjustment for design effects and consideration of multiple comparison correction methods. Secondary analyses are common but require caution due to the risk of reduced statistical power and false-discovery rates. Safety data collection methods should balance pragmatism and data quality. Overall, understanding statistical considerations is crucial for designing rigorous pragmatic trials that evaluate interventions in elderly populations under real-world conditions. In conclusion, this review focuses on various statistical topics of interest to those designing a pragmatic clinical trial, with consideration of aspects of relevance in the aging research field.

Filling the gaps on root hair development under salt stress and phosphate starvation using current evidence coupled with a meta-analysis approach.

Population expansion is a global issue, especially for food production. Meanwhile, global climate change is damaging our soils, making it difficult for crops to thrive and lowering both production and quality. Poor nutrition and salinity stress affect plant growth and development. Although the impact of individual plant stresses has been studied for decades, the real stress scenario is more complex due to the exposure to multiple stresses at the same time. Here we investigate using existing evidence and a meta-analysis approach to determine molecular linkages between two contemporaneous abiotic stimuli, phosphate (Pi) deficiency and salinity, on a single plant cell model, the root hairs (RHs), which is the first plant cell exposed to them. Understanding how these two stresses work molecularly in RHs may help us build super-adaptable crops and sustainable agriculture in the face of global climate change.

Decision analysis with IDOCRIW-QUALIFLEX approach in the 2TLq-ROF environment: An application of accident prediction models in Pakistan.

In Pakistan, the assessment of road safety measures within road safety management systems is commonly seen as the most deficient part. Accident prediction models are essential for road authorities, road designers, and road safety specialists. These models facilitate the examination of safety concerns, the identification of safety improvements, and the projection of the potential impact of these modifications in terms of collision reduction. In the context described above, the goal of this paper is to utilize the 2-tuple linguistic q-rung orthopair fuzzy set (2TLq-ROFS), a new and useful decision tool with a strong ability to address uncertain or imprecise information in practical decision-making processes. In addition, for dealing with the multi-attribute group decision-making problems in road safety management, this paper proposes a new 2TLq-ROF integrated determination of objective criteria weights (IDOCRIW)-the qualitative flexible multiple criteria (QUALIFLEX) decision analysis method with a weighted power average (WPA) operator based on the 2TLq-ROF numbers. The IDOCRIW method is used to calculate the weight of attributes and the QUALIFLEX method is used to rank the options. To show the viability and superiority of the proposed approach, we also perform a case study on the evaluation of accident prediction models in road safety management. Finally, the results of the experiments and comparisons with existing methods are used to explain the benefits and superiority of the suggested approach. The findings of this study show that the proposed approach is more practical and compatible with other existing approaches.

On a deterministic mathematical model which efficiently predicts the protective effect of a plant extract mixture in cirrhotic rats.

In this work, we propose a mathematical model that describes liver evolution and concentrations of alanine aminotransferase and aspartate aminotransferase in a group of rats damaged with carbon tetrachloride. Carbon tetrachloride was employed to induce cirrhosis. A second groups damaged with carbon tetrachloride was exposed simultaneously a plant extract as hepatoprotective agent. The model reproduces the data obtained in the experiment reported in [Rev. Cub. Plant. Med. 22(1), 2017], and predicts that using the plants extract helps to get a better natural recovery after the treatment. Computer simulations show that the extract reduces the damage velocity but does not avoid it entirely. The present paper is the first report in the literature in which a mathematical model reliably predicts the protective effect of a plant extract mixture in rats with cirrhosis disease. The results reported in this manuscript could be used in the future to help in fighting cirrhotic conditions in humans, though more experimental and mathematical work is required in that case.

Expression and purification of active shikimate dehydrogenase from Plasmodium falciparum.

Plasmodium falciparum is known to cause severe malaria, current treatment consists in artemisinin-based combination therapy, but resistance can lead to treatment failure. Knowledge concerning P. falciparum essential proteins can be used for searching new antimalarials, among these a potential candidate is shikimate dehydrogenase (SDH), an enzyme part of the shikimate pathway which is responsible for producing endogenous aromatic amino acids. SDH from P. falciparum (PfSDH) is unexplored by the scientific community, therefore, this study aims to establish the first protocol for active PfSDH expression. Putative PfSDH nucleotide sequence was used to construct an optimized expression vector pET28a+PfSDH inserted in E. coli BL21(DE3). As a result, optimal expression conditions were acquired by varying IPTG and temperature through time. Western Blot analysis was applied to verify appropriate PfSDH expression, solubilization and purification started with lysis followed by two-steps IMAC purification. Enzyme activity was measured spectrophotometrically by NADPH oxidation, optimal PfSDH expression occur at 0.1 mM IPTG for 48 hours growing at 37 °C and shaking at 200 rpm, recombinant PfSDH obtained after purification was soluble, pure and its physiological catalysis was confirmed. Thus, this study describes the first protocol for heterologous expression of PfSDH in soluble and active form.

Past, present and future in the geographical distribution of Mexican Tepezmaite cycads: Genus Ceratozamia.

Ceratozamia morettii, C. brevifrons, and C. tenuis are cycads considered endangered in montane forests in the center of Veracruz state. However, the amount of theoretical and empirical information available on the historical distribution of these species and how they could be affected in the future by the effects of climate change still needs to be increased. Our objective was to generate information on the spatial distribution of the species since the last glacial maximum, present, and future. To map the spatial distribution of species, we created a potential distribution model for each species. The spatial data used for the models included 19 bioclimatic data variables in the present, at the last glacial maximum using two models (CCSM4 and MIROC), and in the future (2080) using two models of the RCP 8.5 scenario of climate change (HadGEM2-CC and MIROC5). We found that each species occupies a unique ecoregion and climatic niche. Ceratozamia morettii and C. tenuis have a similar pattern with an expansion of their distribution area since the last glacial maximum with a larger distribution area in the present and a projected reduction in their distribution under future climatic conditions. For C. brevifrons, we also showed an increase in their distributional area since the last glacial maximum. We also showed that this expansion will continue under future climatic conditions when the species reaches its maximum distributional area. Projections about the future of these endemic cycad species show changes in their habitat, highlighting that temperate zone species (C. morettii and C. tenuis) will face imminent extinction if no effort is made to protect them. On the other hand, the tropical climate species (C. brevifrons) will be favored.

Inference of annealed protein fitness landscapes with AnnealDCA.

The design of proteins with specific tasks is a major challenge in molecular biology with important diagnostic and therapeutic applications. High-throughput screening methods have been developed to systematically evaluate protein activity, but only a small fraction of possible protein variants can be tested using these techniques. Computational models that explore the sequence space in-silico to identify the fittest molecules for a given function are needed to overcome this limitation. In this article, we propose AnnealDCA, a machine-learning framework to learn the protein fitness landscape from sequencing data derived from a broad range of experiments that use selection and sequencing to quantify protein activity. We demonstrate the effectiveness of our method by applying it to antibody Rep-Seq data of immunized mice and screening experiments, assessing the quality of the fitness landscape reconstructions. Our method can be applied to several experimental cases where a population of protein variants undergoes various rounds of selection and sequencing, without relying on the computation of variants enrichment ratios, and thus can be used even in cases of disjoint sequence samples.

Alterations of mRNAs and Non-coding RNAs Associated with Neuroinflammation in Alzheimer's Disease.

Alzheimer's disease is a neurodegenerative pathology whose pathognomonic hallmarks are increased generation of ß-amyloid (Aß) peptide, production of hyperphosphorylated (pTau), and neuroinflammation. The last is an alteration closely related to the progression of AD and although it is present in multiple neurodegenerative diseases, the pathophysiological events that characterize neuroinflammatory processes vary depending on the disease. In this article, we focus on mRNA and non-coding RNA alterations as part of the pathophysiological events characteristic of neuroinflammation in AD and the influence of these alterations on the course of the disease through interaction with multiple RNAs related to the generation of Aß, pTau, and neuroinflammation itself.

Is the time below 90% of SpO2 during sleep (T90%) a metric of good health? A longitudinal analysis of two cohorts.

BACKGROUND: Novel wireless-based technologies can easily record pulse oximetry at home. One of the main parameters that are recorded in sleep studies is the time under 90% of SpO2 (T90%) and the oxygen desaturation index 3% (ODI-3%). We assessed the association of T90% and/or ODI-3% in two different scenarios (a community-based study and a clinical setting) with all-cause mortality (primary outcome). METHODS: We included all individuals from the Sleep Heart Health Study (SHHS, community-based cohort) and Santiago Obstructive Sleep Apnea (SantOSA, clinical cohort) with complete data at baseline and follow-up. Two measures of hypoxemia (T90% and ODI-3%) were our primary exposures. The adjusted hazard ratios (HRs) per standard deviation (pSD) between T90% and incident all-cause mortality (primary outcome) were determined by adjusted Cox regression models. In the secondary analysis, to assess whether T90% varies across clinical factors, anthropometrics, abdominal obesity, metabolic rate, and SpO2, we conducted linear regression models. Incremental changes in R2 were conducted to test the hypothesis. RESULTS: A total of 4323 (56% male, median 64 years old, follow-up: 12 years, 23% events) and 1345 (77% male, median 55 years old, follow-up: 6 years, 11.6% events) patients were included in SHHS and SantOSA, respectively. Every 1 SD increase in T90% was associated with an adjusted HR of 1.18 [95% CI: 1.10-1.26] (p value < 0.001) in SHHS and HR 1.34 [95% CI: 1.04-1.71] (p value = 0.021) for all-cause mortality in SantOSA. Conversely, ODI-3% was not associated with worse outcomes. R2 explains 62% of the variability in T90%. The main contributors were baseline-mean change in SpO2, baseline SpO2, respiratory events, and age. CONCLUSION: The findings suggest that T90% may be an important marker of wellness in clinical and community-based scenarios. Although this nonspecific metric varies across the populations, ventilatory changes during sleep rather than other physiological or comorbidity variables explain their variability.

Migraña poscierre percutáneo de defectos septales auriculares

La migraña es una enfermedad que se ha visto asociada a defectos septales auriculares y a su cierre percutáneo, estipulándose en la literatura que sería una rara complicación, pero la evidencia al respecto es escasa. Se realizó una revisión narrativa sobre definiciones, epidemiología, fisiopatología y tratamiento de la migraña y de la entidad migraña poscierre percutáneo de defectos del septum auricular, incluyendo trabajos observacionales (retrospectivos, prospectivos), estudios randomizados, reportes de casos, artículos de revisión y metaanálisis existentes en PubMed y Cochrane, para aportar al conocimiento de esta entidad.

Migraine is a disease that has been associated with atrial septal defects and its percutaneous closure, stipulating in the literature that it would be a rare complication, but evidence is scarce. A narrative review was conducted on definitions, epidemiology, pathophysiology and treatment of migraine and the migraine entity after percutaneous closure of atrial septum defects, including observational studies (retrospective, prospective), randomized studies, case reports, review articles and meta-analyses existing in PubMed and Cochrane, to contribute to the knowledge of this entity.

A enxaqueca é uma doença que tem sido associada a defeitos do septo atrial e seu fechamento percutâneo, estipulando na literatura que seria uma complicação rara, mas as evidências são escassas. Foi realizada uma revisão narrativa sobre definições, epidemiologia, fisiopatologia e tratamento da enxaqueca e da entidade migranosa após fechamento percutâneo de defeitos do septo atrial, incluindo estudos observacionais (retrospectivos, prospectivos), estudos randomizados, relatos de caso, artigos de revisão e metanálises existentes no PubMed e Cochrane, para contribuir com o conhecimento dessa entidade.

Sexually Transmitted Infections in Male Patients with Urethritis.

(1) Background: Sexually Transmitted Infections (STIs) in men are a significant public health problem due to the consequences they can have, such as chronic diseases, infertility, cancer, and even death. This study aimed to determine the frequency of microorganisms associated with STIs in men with urethritis attending urology consultations, and to explore their clinical correlations. (2) Methods: A population that attended the urology consultation of the University Hospital "Dr. José E. González" was studied. Written consent was obtained, and interviews and clinical history were conducted about specific risk factors identifying signs and symptoms associated with any genitourinary condition; after that, urine samples were collected. Identification of C. trachomatis, N. gonorrhoeae, U. urealyticum, and M. genitalium was based on amplifying species-specific DNA fragments. (3) Results: A total of 200 patients were included. The mean age was 55 years (20-95). According to the interviews, only 32.5% (n = 65) had received prior sex education. Additionally, 75% (n = 150) do not usually use any protection during sexual intercourse. Regarding clinical factors, 69.4% (n = 138) presented burning or pain when urinating. Molecular analysis revealed the presence of C. trachomatis to be 9.5% (n = 19), with U. urealyticum at 13% (n = 26), and M. genitalium at 2% (n = 4). (4) Conclusions: This is the most extensive molecular epidemiological study of the frequency of STIs in men in Mexico in third-level care and its association with different risk factors. As reported globally, a similar frequency of C. trachomatis, U. urealyticum, and M. genitalium was detected.

Green synthesis trends and potential applications of bimetallic nanoparticles towards the sustainable development goals 2030.

The world faces threats that the United Nations has classified into 17 categories with different objectives as solutions for each challenge that are enclosed in the Sustainable Development Goals (SDGs). These actions involved the widespread use of science and technology as pathways to ensure their implementation. In this regard, sustainability science seeks the research community's contribution to addressing sustainable development challenges. Specifically, nanotechnology has been recognized as a key tool to provide disruptive and effective strategies to reach the SDGs. This review proposes the application of bimetallic nanoparticle substances capable of providing possible solutions to achieve target SDG 3: good health and well-being, SDG 6: clean water and sanitation, and SDG 12: responsible consumption and production. Furthermore, the term green nanotechnology is introduced in each section to exemplify how green synthesized bimetallic nanoparticles have been used to resolve each target SDG. This review also outlines the current scenario regarding the utilization of metallic nanomaterials in the market, together with the upscaling challenges and the lack of understanding of the long-term effects and hazards to the environment regarding bimetallic nanoparticles.

Caveolin-1-dependent tenascin C inclusion in extracellular vesicles is required to promote breast cancer cell malignancy.

Background: Elevated expression of CAV1 in breast cancer increases tumor progression. Extracellular vesicles (EVs) from CAV1-expressing MDA-MB-231 breast cancer cells contain Tenascin C (TNC), but the relevance of TNC remained to be defined. Methods: EVs were characterized by nanotracking analysis, microscopy and western blotting. The uptake of EVs by cells was studied using flow cytometry. The effects of EVs on breast cancer cells were tested in migration, invasion, colony formation and in vivo assays. Results: EVs were taken up by cells; however, only those containing TNC promoted invasiveness. In vivo, EVs lacking TNC ceased to promote tumor growth. Conclusion: CAV1 and TNC contained in breast cancer cell-derived EVs were identified as proteins that favor progression of breast cancer.

Caveolin-1 (CAV1) is a protein that in breast cancer increases with disease progression. Extracellular vesicles (EVs) from breast cancer cells with CAV1 also contain Tenascin C (TNC) protein, but the importance of TNC remained to be defined. EVs were identified by size, microscopy and protein analysis. The effects of EVs on breast cancer cells were studied using cells and experiments in animals. CAV1 expression promotes TNC inclusion into EVs, which increased the aggressiveness of recipient breast cancer cells. In animals, only EVs with TNC increased features associated with cancer spread, while EVs lacking TNC reduced tumor growth.

Case Report: Molecular Characterization of Bloodstream Infections due to Carbapenem-Resistant Acinetobacter baumannii: A Pediatric Case Series.

Acinetobacter baumannii poses a significant threat to public health due to the high rate of multidrug-resistant strains. However, information on the molecular characterization of carbapenem-resistant Acinetobacter baumannii (CRAB) bloodstream infections in children is scarce. This study aimed to describe the molecular characterization of carbapenem-resistant A. baumannii infections in children from a hospital in Mexico. A retrospective study was conducted during the period 2017-2022. Clinical and demographic data were collected from the clinical records. Mass spectrometry was used for the identification of the strains. To confirm A. baumannii strains, a polymerase chain reaction (PCR) method was applied using a gyrB sequence. The carbapenemase-encoding resistance genes were detected by PCR. Six cases of CRAB were documented, including five in neonates. The median intensive care unit stay was 20 days, and all cases had an invasive medical device. Half of the patients had at least one medical condition. A high prevalence of coresistance was observed in most of the antibiotic groups. Three of the six strains coharbored carbapenemase genes: blaOXA-51, blaOXA-24, and blaIMP. Mortality was reported in two neonate patients. The present study shows a high rate of coharboring blaOXA-51, blaOXA-24, and blaIMP-1, which has a direct impact on therapeutic decisions. Implementation of antimicrobial stewardship programs is urgent to stop the spread of this microorganism.

N-Sulfonyl-1,2,3,4-tetrahydroisoquinoline Derivatives: Synthesis, Antimicrobial Evaluations, and Theoretical Insights.

Microbial contamination remains a significant economic challenge in the food industry, emphasizing the need for innovative antimicrobial solutions. In this study, we synthesized N-sulfonyl-1,2,3,4-tetrahydroisoquinolines (NSTHIQ) derivatives using an environmentally friendly Preyssler heteropolyacid catalyst, obtaining moderate to high yields (35-91 %) under mild conditions. Two derivatives (5 and 6) exhibited significant antifungal properties against various fungal species, including Aspergillus spp, Penicillium spp, and Botrytis cinerea. ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analysis revealed the absence of hepatic toxicity in all compounds, making derivatives 2, 3, 4, and 5 potential candidates for further development. However, derivatives 6 and 7 exhibited immunotoxicity. In support of our experimental findings, reactivity indices were computed using Density Functional Theory principles, deriving valuable insights into the chemical properties of these derivatives. This study underscores the potential of NSTHIQ compounds as potent antifungal agents, coupled with the importance of employing environmentally friendly catalysts in drug discovery.

Novel and Accessible Physical Recycling for Expanded Polystyrene Waste with the Use of Acetone as a Solvent and Additive Manufacturing (Direct Ink-Write 3D Printing).

The current high production of plastics has prompted the exploration of alternative pathways to facilitate recycling, aiming for a progressively sustainable society. This paper presents an alternative and affordable technology for treating waste expanded polystyrene (EPS) mixed with acetone in a 100:1 volume ratio to be used as 3D printing ink for Direct Ink Write technology. In order to optimize the printing parameters, a comprehensive study was conducted, evaluating different needle diameters, printing speeds, and bed temperature values to achieve homogenous pieces and a highly repeatable 3D printing process. Results showed that the main optimum printing parameters were using needles with diameters of 14 to 16 G and printing speeds ranging from 2 to 12 mm/s, which were found to yield the most uniform ribbons. Increasing the bed temperature, despite favoring acetone evaporation, led to the generation of more heterogeneous structures due to void growth inside the printed ribbons. Thus, employing room temperature for the bed proved to be the optimal value. Lastly, a comparative study between the starting material and the EPS after the printing process was conducted using FTIR-ATR and GPC analyses, ensuring the preservation of the original polymer's integrity during physical recycling.

Quorum sensing modulates bacterial virulence and colonization dynamics of the gastrointestinal pathogen Citrobacter rodentium.

Quorum Sensing (QS) is a form of cell-to-cell communication that enables bacteria to modify behavior according to their population density. While QS has been proposed as a potential intervention against pathogen infection, QS-mediated communication within the mammalian digestive tract remains understudied. Using an LC-MS/MS approach, we discovered that Citrobacter rodentium, a natural murine pathogen used to model human infection by pathogenic Escherichia coli, utilizes the CroIR system to produce three QS-molecules. We then profiled their accumulation both in vitro and across different gastrointestinal sites over the course of infection. Importantly, we found that in the absence of QS capabilities the virulence of C. rodentium is enhanced. This highlights the role of QS as an effective mechanism to regulate virulence according to the pathogen's spatio-temporal context to optimize colonization and transmission success. These results also demonstrate that inhibiting QS may not always be an effective strategy for the control of virulence.

HEK293 producing the extracellular domain HER1: Full datasets of continuous fermentation process and metabolites analysis.

The data for provide evidences of the multi steady state of the human cell line HEK 293 was obtained from 2 L bioreactor continuous culture. A HEK 293 cell line transfected to produce soluble HER1 receptor was used. The bioreactor was operated at three different dilution rates in sequential manner. Daily samples of culture broth were collected, a total of 85 samples were processed. Viable cell concentration and culture viability was addressing by trypan blue exclusion method using a hemocytometer. Heterologous HER1 supernatant concentration was quantified by a specific ELISA and the metabolites by mass spectrometry coupled to a liquid chromatography. The primary data were collected in excel files, where it was calculated the kinetic and other variables by using mass balance and mathematical principles. It was compared the steady states behavior each other's to find out the existence of steady states' multiplicity, taking into account the stationary phase with respect to the cell density (which means its coefficient of variation is less than 20 %). From the metabolic measurements by using Liquid Chromatography coupled to mass spectrometry (LC-MS), it was also built the data matrix with the specific rates of the 76 metabolites obtained. The data were processed and analyzed, using multivariate data asssnalysis (MVDA) to reduce the complexity and to find the main patterns present in the data. We describe also the full data of the metabolites not only for steady states but also in the time evolution, which could help others in terms of modeling and deep understanding of HEK293 metabolism, especially under different culture conditions.