A dataset for soil organic carbon in agricultural systems for the Southeast Asia region.

The determination of changes in soil organic carbon (SOC) content under different cropping systems is necessary for policy development oriented towards soil conservation, C sequestration, and future C credit markets. The aim of this study was to generate an open SOC dataset resulting from a systematic literature search related to the agricultural systems for Southeast Asia. The dataset has 209 articles and 4341 observations on soils of cropping systems in this region from articles published between 1987 and 2023. This dataset included different management practices, land uses, soil sampling depth, and length of SOC content assessment. In addition, inherent features of crop production reported in the experiments were included in the dataset. This dataset can be applied to quantify and compare the impact of different land uses or management practices on SOC content, providing foundational knowledge towards identifying sustainable practices. Lastly, it is a useful guide for future regional SOC sequestration policies and the development of C credit markets.

Real-world experience of vedolizumab use in Colombian patients with inflammatory bowel disease-EXVEDOCOL.

BACKGROUND: Real-world studies about the effectiveness and safety of vedolizumab (VDZ) in the treatment of inflammatory bowel disease (IBD) in Latin America are scarce. Our study describes the effectiveness and safety of VDZ in Colombian patients with IBD. METHODS: EXVEDOCOL (EXperience of VEDOlizumab in COLombia) was a retrospective, multicenter, observational study. Adults with IBD receiving a first dose of VDZ between July 2016 and October 2018 were included. The co-primary outcomes clinical response, and remission, were determined at week 14 and last visit during the maintenance phase (LVMP). The secondary outcomes, deep remission and loss of response were recorded at LVMP. RESULTS: Thirty-one patients (25 ulcerative colitis (UC), 6 Crohn's disease (CD)) were included. At week 14, clinical response was achieved by 87.1% (27/31) of the patients treated with VDZ, while loss of response was reported in 6.7% (2/30). The remission rate at week 14 was 65.5% (19/29) and 75.9% (22/29) at LVMP. Prior anti-TNF exposure was reported in 61.3% (19 patients) of whom 84.2% (16/19) achieved clinical response at week 14 and 89.5% (17/19) at LVMP. For anti-TNF naïve patients, clinical response was recorded in 91.7% (11/12) at week 14 and 100% (12/12) at LVMP. CONCLUSIONS: High clinical remission rates and safety profile highlight VDZ as a valuable treatment option for IBD patients. Anti-TNF naïve patients may derive greater benefit from therapy. Studies with larger cohorts could confirm these findings.

Predicting the formation of NADES using a transformer-based model.

The application of natural deep eutectic solvents (NADES) in the pharmaceutical, agricultural, and food industries represents one of the fastest growing fields of green chemistry, as these mixtures can potentially replace traditional organic solvents. These advances are, however, limited by the development of new NADES which is today, almost exclusively empirically driven and often derivative from known mixtures. To overcome this limitation, we propose the use of a transformer-based machine learning approach. Here, the transformer-based neural network model was first pre-trained to recognize chemical patterns from SMILES representations (unlabeled general chemical data) and then fine-tuned to recognize the patterns in strings that lead to the formation of either stable NADES or simple mixtures of compounds not leading to the formation of stable NADES (binary classification). Because this strategy was adapted from language learning, it allows the use of relatively small datasets and relatively low computational resources. The resulting algorithm is capable of predicting the formation of multiple new stable eutectic mixtures (n = 337) from a general database of natural compounds. More importantly, the system is also able to predict the components and molar ratios needed to render NADES with new molecules (not present in the training database), an aspect that was validated using previously reported NADES as well as by developing multiple novel solvents containing ibuprofen. We believe this strategy has the potential to transform the screening process for NADES as well as the pharmaceutical industry, streamlining the use of bioactive compounds as functional components of liquid formulations, rather than simple solutes.

Heat-induced hormesis in longevity is linked to heat-stress sensitivity across laboratory populations from diverse altitude of origin in Drosophila buzzatii.

Heat-induced hormesis in longevity is the increase in life span resulting from the previous exposure to a mild heat stress early in life. Here we examined heat-induced hormesis of Drosophila buzzatii in five mass-mating populations, which were derived from five wild populations along an elevation gradient from 202 to 1855 m above sea level in North-Western Argentina. Five day old flies were exposed to 37.5 °C for 90 min to induce hormesis and its possible variation across altitudinal populations. This heat treatment strongly extended longevity in lowland-derived flies from the most heat-resistant population only. Both heat-induced effects on longevity and heat-knockdown time (heat-stress sensitivity) were negatively correlated to altitude of population of origin. Hormesis was positively correlated to heat-knockdown time across populations. These results indicate that variation in heat-induced hormesis can not be considered as independent of heat-stress sensitivity (or heat-knockdown time) in populations of insects.

Comprehensive ECG reference intervals in C57BL/6N substrains provide a generalizable guide for cardiac electrophysiology studies in mice.

Reference ranges provide a powerful tool for diagnostic decision-making in clinical medicine and are enormously valuable for understanding normality in pre-clinical scientific research that uses in vivo models. As yet, there are no published reference ranges for electrocardiography (ECG) in the laboratory mouse. The first mouse-specific reference ranges for the assessment of electrical conduction are reported herein generated from an ECG dataset of unprecedented scale. International Mouse Phenotyping Consortium data from over 26,000 conscious or anesthetized C57BL/6N wildtype control mice were stratified by sex and age to develop robust ECG reference ranges. Interesting findings include that heart rate and key elements from the ECG waveform (RR-, PR-, ST-, QT-interval, QT corrected, and QRS complex) demonstrate minimal sexual dimorphism. As expected, anesthesia induces a decrease in heart rate and was shown for both inhalation (isoflurane) and injectable (tribromoethanol) anesthesia. In the absence of pharmacological, environmental, or genetic challenges, we did not observe major age-related ECG changes in C57BL/6N-inbred mice as the differences in the reference ranges of 12-week-old compared to 62-week-old mice were negligible. The generalizability of the C57BL/6N substrain reference ranges was demonstrated by comparison with ECG data from a wide range of non-IMPC studies. The close overlap in data from a wide range of mouse strains suggests that the C57BL/6N-based reference ranges can be used as a robust and comprehensive indicator of normality. We report a unique ECG reference resource of fundamental importance for any experimental study of cardiac function in mice.

Graph-based clinical recommender: Predicting specialists procedure orders using graph representation learning.

OBJECTIVE: To determine whether graph neural network based models of electronic health records can predict specialty consultation care needs for endocrinology and hematology more accurately than the standard of care checklists and other conventional medical recommendation algorithms in the literature. METHODS: Demand for medical expertise far outstrips supply, with tens of millions in the US alone with deficient access to specialty care. Rather than potentially months long delays to initiate diagnostic workup and medical treatment with a specialist, referring primary care supported by an automated recommender algorithm could anticipate and directly initiate patient evaluation that would otherwise be needed at subsequent a specialist appointment. We propose a novel graph representation learning approach with a heterogeneous graph neural network to model structured electronic health records and formulate recommendation/prediction of subsequent specialist orders as a link prediction problem. RESULTS: Models are trained and assessed in two specialty care sites: endocrinology and hematology. Our experimental results show that our model achieves an 8% improvement in ROC-AUC for endocrinology (ROC-AUC = 0.88) and 5% improvement for hematology (ROC-AUC = 0.84) personalized procedure recommendations over prior medical recommender systems. These recommender algorithm approaches provide medical procedure recommendations for endocrinology referrals more effectively than manual clinical checklists (recommender: precision = 0.60, recall = 0.27, F1-score = 0.37) vs. (checklist: precision = 0.16, recall = 0.28, F1-score = 0.20), and similarly for hematology referrals (recommender: precision = 0.44, recall = 0.38, F1-score = 0.41) vs. (checklist: precision = 0.27, recall = 0.71, F1-score = 0.39). CONCLUSION: Embedding graph neural network models into clinical care can improve digital specialty consultation systems and expand the access to medical experience of prior similar cases.

Melatonin production by rhizobacteria native strains: Towards sustainable plant growth promotion strategies.

In the current context of climate change and water deficit, the selection of native beneficial microorganisms, such as plant growth-promoting rhizobacteria (PGPR), has become a trend for sustainable agriculture due to their ability to improve plant-bacteria interaction with a minimal adverse effect on the soil microbiota compared to commercial PGPR. Until now, the production of phytohormones like melatonin (MT) by native PGPR and their effect on endogenous MT levels in plants have been poorly studied. MT is a ubiquitous phytohormone that protects plants against biotic and abiotic stress by improving the tolerance of stressed plants. In this work, the production of MT by two native PGPR, Enterobacter 64S1 and Pseudomonas 42P4, was evaluated and both PGPR were applied in Arabidopsis thaliana plants grown under drought conditions to assess the inoculation effects. Parameters such as plant growth, leaf cellular membrane damage, leaf protective compounds, and endogenous MT levels under drought and irrigation conditions were evaluated. The results demonstrated that the native strains Pseudomonas 42P4 and Enterobacter 64S1 produce MT and increase the content of endogenous MT in A. thaliana plants under drought. These native strains improved the tolerance of arabidopsis plants to drought by preventing oxidative and membrane damages and improving plant growth. To the best of our knowledge, this is the first report on MT production by native PGPR and their effects on endogenous MT levels in arabidopsis plants, setting the bases to elucidate the role of native PGPR on water deficit conditions.

NADES blend for bioactive coating design as a sustainable strategy for postharvest control.

Bioactive functional coatings constitute a trendy topic due to they reduce postharvest fruit losses worldwide. Also, they could be carriers of biocompounds providing health benefits to the consumer. In this work, an innovative natural bioactive coating based on Natural Deep Eutectic Solvents (NADES) and Larrea divaricata extract was optimized by mixture-mixture design for the management of postharvest diseases caused by Monilinia fructicola. A NADES composed of lactic acid-glucose-water (LGH) for phenolic extraction from L. divaricata was optimized by a Simplex Lattice design and response surface methodology (RSM).Then, a d-optimal mixture-mixture design was carried out in order to optimize the bioactive coating composition, being the optimal proportion of 0.7 L. divaricata-LGH extract and 0.3 NADES plasticizer (composed by glycerol, citric acid and water). The optimal biocoating achieved an in vitro antimicrobial activity of 72 % against M. fructicola. Interestingly, NADES plasticizer improves the biocoating functionality, creating a smooth and uniform surface.

Exploratory Analysis of South American Wines Using Artificial Intelligence.

In this work, microwave-induced plasma optical emission spectrometry was applied for multielement determination in South American wine samples. The analytes were determined after acid digestion of 47 samples of Brazilian and Argentinian wines. Then, logistic regression, support vector machine, and decision tree for exploratory analysis and comparison of these algorithms in differentiating red wine samples by region of origin were carried out. All wine samples were classified according to their geographical origin. The quantification limits (mg L-1) were P: 0.06, B: 0.08, K: 0.17, Mn: 0.002, Cr: 0.002, and Al: 0.02. The accuracy of the method was evaluated by analyzing the wine samples by ICP OES for results' comparison. The concentrations in mg L-1 found for each element in wine samples were as follows: Al (< 0.02-1.82), Cr (0.15-0.50), Mn (< 0.002-0.8), P (97-277), B (1.7-11.6), Pb (< 0.06-0.3), Na (8.84-41.57), and K (604-1701), in mg L-1.

PDCM Finder: an open global research platform for patient-derived cancer models.

PDCM Finder (www.cancermodels.org) is a cancer research platform that aggregates clinical, genomic and functional data from patient-derived xenografts, organoids and cell lines. It was launched in April 2022 as a successor of the PDX Finder portal, which focused solely on patient-derived xenograft models. Currently the portal has over 6200 models across 13 cancer types, including rare paediatric models (17%) and models from minority ethnic backgrounds (33%), making it the largest free to consumer and open access resource of this kind. The PDCM Finder standardises, harmonises and integrates the complex and diverse data associated with PDCMs for the cancer community and displays over 90 million data points across a variety of data types (clinical metadata, molecular and treatment-based). PDCM data is FAIR and underpins the generation and testing of new hypotheses in cancer mechanisms and personalised medicine development.

The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease.

The International Mouse Phenotyping Consortium (IMPC; https://www.mousephenotype.org/) web portal makes available curated, integrated and analysed knockout mouse phenotyping data generated by the IMPC project consisting of 85M data points and over 95,000 statistically significant phenotype hits mapped to human diseases. The IMPC portal delivers a substantial reference dataset that supports the enrichment of various domain-specific projects and databases, as well as the wider research and clinical community, where the IMPC genotype-phenotype knowledge contributes to the molecular diagnosis of patients affected by rare disorders. Data from 9,000 mouse lines and 750 000 images provides vital resources enabling the interpretation of the ignorome, and advancing our knowledge on mammalian gene function and the mechanisms underlying phenotypes associated with human diseases. The resource is widely integrated and the lines have been used in over 4,600 publications indicating the value of the data and the materials.

Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology.

Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.

Desarrollo de habilidades investigativas sobre ambiente saludable y sostenible en estudiantes de postgrado / Development of investigative skills on healthy and sustainable environment in postgraduate students

El desarrollo sostenible y sustentable de nuestro mundo, es un punto clave en la mejora de la salud. Aplicando estrategias inteligentes y "verdes" constituyen la mejor y única opción en estos momentos para mejorar la pobreza en el mundo entero. En ese sentido, las habilidades adquiridas de investigación en ambientes sostenibles constituyen la base imprescindibles en los estudios de postgrado: maestría y doctorado, ya que estos nuevos profesionales serán los responsables de llevar a cabo esta nueva manera de vivir. En este trabajo se determina, cómo los estudiantes de posgrado se enfrentan a las habilidades de investigación: pensamiento crítico, comunicación oral y escrita, y habilidades de investigación sostenible y sustentable(AU)

The sustainable development of our world is a key point in improving health. Applying intelligent and "green" strategies, constituting the best and only option at this time to improve poverty in the entire world. In this sense, the skills acquired in research on sustainable environments constitute the essential base in postgraduate studies: master's and doctorate, since these new professionals will be responsible for carrying out this new way of living. In this work, it is determined how postgraduate students face research skills: critical thinking, oral and written communication, and sustainable research skills(AU)

Genetic variation in the heat-stress survival of embryos is largely decoupled from adult thermotolerance in an intercontinental set of recombinant lines of Drosophila melanogaster.

In insects, thermal adaptation works on the genetic variation for thermotolerance of not only larvae and adults but also of the immobile stages of the life cycle including eggs. In contrast to adults and larvae, the genetic basis for thermal adaptation in embryos (eggs) remains to be tested in the model insect Drosophila melanogaster. Quantitative-trait loci (QTL) for heat-stress resistance in embryos could largely differ from previously identified QTL for larvae and adults. Here we used an intercontinental set of recombinant inbred lines (RIL), which were previously used to identify thermotolerance-QTLs in adults and larvae because of their high variation segregating for adult thermotolerance. Eggs appeared to be more heat resistant than larvae and adults from previous studies on these RIL, though different heat-shock assays were used in previous studies. We found that variation in thermotolerance in embryos can be, at least partially, genetically decoupled from thermotolerance in the adult insect. Some RIL that are heat resistant in the adult and larvae can be heat susceptible in embryos. Only one small-effect QTL out of five autosomal QTL co-localized between embryo and other ontogenetic stages. These results suggest that selection for thermal adaptation in adult flies and larvae is predicted to have only a small impact on embryo thermotolerance. In addition, heat-stress tolerance of insects can be measured across ontogenetic stages including embryos in order to better predict thermal adaptive limits of populations and species.

Micro to macro scale simulation coupling for stray light analysis.

Stray light in an optical system is unwanted parasitic light that may degrade performance. It can originate from different sources and may lead to different problems in the optical system such as fogging, ghost images for imagers, or inaccurate measurements for time of flight applications. One of the root causes is the reflectivity of the sensor itself. In this paper we present a new optical simulation methodology to analyze the stray light contribution due to the sensor reflectivity by coupling electromagnetic simulation (to calculate the pixels' bidirectional reflectance distribution function, also named BRDF) and ray-tracing simulation (for stray light analysis of the camera module). With this simulation flow we have been able to reproduce qualitatively red ghost images observed on different sensors in our laboratory.

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.

Structural analysis of receptors and actin polarity in platelet protrusions.

During activation the platelet cytoskeleton is reorganized, inducing adhesion to the extracellular matrix and cell spreading. These processes are critical for wound healing and clot formation. Initially, this task relies on the formation of strong cellular-extracellular matrix interactions, exposed in subendothelial lesions. Despite the medical relevance of these processes, there is a lack of high-resolution structural information on the platelet cytoskeleton controlling cell spreading and adhesion. Here, we present in situ structural analysis of membrane receptors and the underlying cytoskeleton in platelet protrusions by applying cryoelectron tomography to intact platelets. We utilized three-dimensional averaging procedures to study receptors at the plasma membrane. Analysis of substrate interaction-free receptors yielded one main structural class resolved to 26 Å, resembling the αIIbß3 integrin folded conformation. Furthermore, structural analysis of the actin network in pseudopodia indicates a nonuniform polarity of filaments. This organization would allow generation of the contractile forces required for integrin-mediated cell adhesion.

Brand new Dual Absorption and Emission Smartphone-Based Spectrophotometer (DAESS) for the study of the role of water in the preparation of Natural Deep Eutectic Solvents.

Natural Deep Eutectic Solvents (NADES) are highly important for Green Chemistry principles and can be used instead of harmful organic solvents. Indeed, nowadays smartphone-based analytical devices can replace some traditional laboratory equipment. In the present work, a smartphone based dual spectrophotometer and spectrofluorometer device was designed, 3D manufactured, and validated. A resolution of 0.241 ± 0.010 pixel.nm-1 and a stability comparable with commercial instruments were obtained. Using the proposed device it was possible, for the first time, to study the role of water in NADES (fructose:urea:water) preparation, by testing the influence of structural and dilution water. In this sense, it was observed that when water was added before NADES preparation (integrated into the superstructure of the solvent), fluorescence and absorbance intensities sharply decayed (up to 90% and 95%, respectively). In contrast, dilution water had minor effects on spectroscopic features of the eutectic system, which was expressed as 29% and 23% of diminution of signal intensities for both techniques. The obtained results suggest that the moment the water is added plays a significant role in NADES properties.

Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods.

Cryo-electron microscopy has established as a mature structural biology technique to elucidate the three-dimensional structure of biological macromolecules. The Coulomb potential of the sample is imaged by an electron beam, and fast semi-conductor detectors produce movies of the sample under study. These movies have to be further processed by a whole pipeline of image-processing algorithms that produce the final structure of the macromolecule. In this chapter, we illustrate this whole processing pipeline putting in value the strength of "meta algorithms," which are the combination of several algorithms, each one with different mathematical rationale, in order to distinguish correctly from incorrectly estimated parameters. We show how this strategy leads to superior performance of the whole pipeline as well as more confident assessments about the reconstructed structures. The "meta algorithms" strategy is common to many fields and, in particular, it has provided excellent results in bioinformatics. We illustrate this combination using the workflow engine, Scipion.