Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluid-rock interactions during continental red bed diagenesis: implications for theoretical models of mineralization in sedimentary basins

Abstract Continental red beds are first-cycle, immature sediments which are deposited in oxidizing conditions and owe their red colouration to the early diagenetic development of hematite. Previously published work on the fluid/rock interactions which occur during the diagenesis of such sediments highlights that pH and redox are critical fluid parameters which control diagenesis and ore formation. However, except in modern surface water and shallow groundwater systems, these parameters cannot be measured directly, and must be estimated from theoretical considerations. These suggest that mixing between fluids of different redox states is likely to be a critical control on heavy metal mobility. Many diagenetic features can be explained largely by the chemical heterogeneity of red beds, and by the diagenetic ranges of redox conditions and pH which are among the greatest for any type of sediment. Such features include: the formation of red bed-hosted ore deposits; the extensive development of hematite; and the development of early diagenetic non-ferroan carbonate and late diagenetic ferroan carbonate cements. In order to develop theoretical models of fluid/rock interactions during such diagenesis, it is important to consider the interrelationships between fluid flow, mineral dissolution and precipitation, and sorption. At the present time such models are at an early stage of development.
CELLULAR RNA INTERACTS WITH MAVS TO PROMOTE ANTIVIRAL SIGNALING

Immune signaling needs to be well-regulated to promote clearance of pathogens, while preventing aberrant inflammation. Interferons (IFNs) and antiviral genes are activated by the detection of viral RNA by RIG-I-like receptors (RLRs). Signal transduction downstream of RLRs proceeds through a multi-protein complex organized around the central adaptor protein MAVS. Recent work has shown that protein complex function can be modulated by RNA molecules providing allosteric regulation or acting as molecular guides or scaffolds. Thus, we hypothesized that RNA plays a role in organizing MAVS signaling platforms. Here, we show that MAVS, through its central intrinsically disordered domain, directly interacts with the 3′ untranslated regions of cellular mRNAs. Importantly, elimination of RNA by RNase treatment disrupts the MAVS signalosome, including newly identified regulators of RLR signaling, and inhibits phosphorylation of the transcription factor IRF3. This supports the hypothesis that RNA molecules scaffold proteins in the MAVS signalosome to induce IFNs. Together, this work uncovers a function for cellular RNA in promoting signaling through MAVS and highlights a generalizable principle of RNA regulatory control of cytoplasmic immune signaling complexes.
Assessing the status of European laboratories in evaluating biomarkers for chronic kidney diseases (CKD) and recommendations for improvement: insights from the 2022 EFLM Task Group on CKD survey

Abstract Objectives Chronic kidney disease (CKD) is a global health issue, ranking as the third leading cause of death worldwide. CKD diagnosis and management depend on clinical laboratory tests, necessitating consistency for precise patient care. Global harmonization of CKD testing through clinical practice guidelines (CPGs) is recommended. Prior to CPG development, assessing the current CKD testing landscape is crucial. In 2022, the European Federation of Laboratory Medicine (EFLM) conducted an online survey among European laboratories associated with EFLM, evaluating CKD testing practices, including new glomerular filtration rate (GFR) estimation methods. This report summarizes the 2022 survey findings and offers recommendations for improving CKD test standardization. Methods An online survey was conducted in November 2022 using a questionnaire hosted on LimeSurvey sent to European laboratories affiliated with the EFLM. The survey results were recorded in Excel files and analysed. Results The results highlight significant discrepancies among countries in unit expression, methods, cystatin C use, and GFR calculation equations. Additionally, limited attention to pediatric renal biology specifics, varied proteinuria and albuminuria result expressions, and limited awareness of GFR measurement methods through iohexol clearance are noted. Conclusions In an effort to enhance the standardization of crucial biomarkers utilized in nephrology for evaluating renal function and diagnosing kidney injuries, the EFLM Task Group on CKD suggests nine practical recommendations tailored for European laboratories. The group is confident that implementing these measures will minimize result expression discrepancies, ultimately leading to enhanced patient care.
Navigation by Computer Processing of Marine Radar Images

The advantages of being able to process marine radar imagery in an on-line computer system have been illustrated by study of some navigational problems. The experiments suggest that accuracies of the order of 100 metres may be obtained in navigation in coastal regions using map overlays with marine radar data. A similar technique using different radar imagery of the same location suggests that the pattern-recognition technique may well yield a position-keeping ability of better than 10 metres.
Glacier extinction homogenizes functional diversity

Questions The disappearance of glaciers threatens biodiversity and the functioning of ecosystems. To date, questions remain about the response of functional diversity to glacier extinction and its potential for adaptation to climate change. How does glacier retreat and extinction affect plant functional diversity? How do mean and variation of plant traits change with glacier retreat and extinction? Location Four glacier ecosystems in Italian Alps. Plant communities spanning 0 to ca 5,000 years on average after glacier retreat. Methods We quantify how glacier retreat affects functional diversity of plant communities analysing twelve functional traits of 117 plant species across 170 plots. First, we addressed the impact of glacier retreat on functional divergence and functional homogeneity, analysing both trait average and trait variation. Next, we explored how biodiversity (i.e., plant species richness) influenced functional diversity and how glacier retreat affected such relationship. Finally, we explored the effects of glacier retreat on mean and variation of single traits associated to carbon and nitrogen cycling and resource allocation. Results Glacier retreat homogenizes functional diversity by reducing trait variation and making communities more functionally similar. While biodiversity positively contributes to trait heterogeneity, glacier retreat erodes the support of species richness to functional diversity. We also show how glacier extinction has medium to large negative effects on the average and variation of key functional traits associated to carbon economy, but small positive effects on leaf nitrogen content. Conclusions Our results demonstrate the pervasive impact of glacier extinction on the functioning of plant communities. We stress that functional diversity and trait variation should be the focus of adaptation and mitigation actions.
Comparison of wide and narrow gastric conduit in esophageal cancer surgery

Background: Gastric conduit is most widely used method for esophageal reconstruction. Despite its popularity, certain complications, such as anastomotic leakage and strictures, remain to be resolved. In the present study, we reviewed the outcomes of narrow gastric conduit compared to wide gastric conduit reconstruction. Methods: We retrospectively reviewed 493 patients with esophageal cancer who received esophagectomy with reconstruction in Taichung Veteran General Hospital, Taiwan between January 2010 and December 2019. We performed gastric conduit reconstruction with two different methods, narrow gastric conduit made of multistaples (more than four staples) and wide gastric conduit made of two or three staples. Among the 493 patients, 170 patients underwent wide gastric conduit formation and 323 patients underwent narrow gastric conduit. After propensity score matching, 140 patients from each group were matched by 1:1. Results: The average anastomotic leakage rate is 80 of 493 (16.23%). The leakage rate, length of hospital stay, intensive care unit (ICU) admission, and ICU stay were significantly lower in the narrow gastric conduit group than in the wide gastric conduit group. The need for postoperation dilatation was significantly higher in wide gastric conduit group (19.41% vs 11.76%, p = 0.0217), and the time to first dilatation was similar in both groups (p = 0.9808). Similar results were observed even after propensity score matching. In univariate analysis, the narrow gastric conduit, circular stapler, video-assisted thoracic surgery, and laparoscopic surgery were associated with a reduced risk of anastomotic leakage. However, these factors are not statistically significant in a multivariate logistic regression analysis. Conclusion: The narrow gastric conduit is not inferior to the wide gastric conduit and can be considered an alternative option for gastric conduit preparation.
Assessing HLA imputation accuracy in a West African population

The Human Leukocyte Antigen (HLA) region plays an important role in autoimmune and infectious diseases. HLA is a highly polymorphic region and thus difficult to impute. We, therefore, sought to evaluate HLA imputation accuracy, specifically in a West African population, since they are understudied and are known to harbor high genetic diversity. The study sets were selected from 315 Gambian individuals within the Gambian Genome Variation Project (GGVP) Whole Genome Sequence datasets. Two different arrays, Illumina Omni 2.5 and Human Hereditary and Health in Africa (H3Africa), were assessed for the appropriateness of their markers, and these were used to test several imputation panels and tools. The reference panels were chosen from the 1000 Genomes (1kg-All), 1000 Genomes African (1kg-Afr), 1000 Genomes Gambian (1kg-Gwd), H3Africa, and the HLA Multi-ethnic datasets. HLA-A, HLA-B, and HLA-C alleles were imputed using HIBAG, SNP2HLA, CookHLA, and Minimac4, and concordance rate was used as an assessment metric. The best performing tool was found to be HIBAG, with a concordance rate of 0.84, while the best performing reference panel was the H3Africa panel, with a concordance rate of 0.62. Minimac4 (0.75) was shown to increase HLA-B allele imputation accuracy compared to HIBAG (0.71), SNP2HLA (0.51) and CookHLA (0.17). The H3Africa and Illumina Omni 2.5 array performances were comparable, showing that genotyping arrays have less influence on HLA imputation in West African populations. The findings show that using a larger population-specific reference panel and the HIBAG tool improves the accuracy of HLA imputation in a West African population.
LIMITED ACCUMULATION AND PERSISTENCE OF AN INFLUENZA A VIRUS IN TADPOLE SNAILS (PHYSA SPP.)

Abstract: Waterfowl infected with avian influenza A viruses (IAVs) shed infectious virus into aquatic environments, providing a mechanism for transmission among waterfowl, while also exposing the entire aquatic ecosystem to the virus. Aquatic invertebrates such as freshwater snails are likely exposed to IAVs in the water column and sediment. Freshwater snails comprise a significant portion of some waterfowl species' diets, so this trophic interaction may serve as a novel route of IAV transmission. In these experiments, tadpole snails (Physa spp.) were exposed to a low-pathogenicity IAV (H3N8) to determine whether snails can accumulate the virus and, if so, how long virus persists in snail tissues. Snail tissues were destructively sampled and tested by reverse-transcription quantitative real-time PCR. Our experiments demonstrated that tadpole snails do accumulate IAV RNA in their tissues, although at low titers, for at least 96 h. These results indicate that it may be possible for IAV transmission to occur between waterfowl via ingestion of a natural invertebrate prey item; however, the time frame for transmission may be limited.
A comparison of dissolved chlorofluorocarbons in seawater measured by MRI and JMA CFCs Systems.

In 2002, a new system for measuring dissolved chlorofluorocarbons (CFC-11, CFC-12, and CFC-113: CFCs) in seawater was developed by the Climate and Marine Department, Japan Meteorological Agency (JMA). During the Ryofu Maru RF03-04 cruise in the western North Pacific in April and May 2003, CFCs concentrations measured by this system were compared with those measured by the Meteorological Research Institute's (MRI's) system that had been used for CFCs measurements in this region since 2000, using a common calibration scale and the same sampling protocol. The precisions of analysis by the MRI system, as determined from analysis of replicate samples, were 0.037 pmol/kg seawater (1.4%) for CFC-12, 0.049 pmol/kg (1.0%) for CFC-11 and 0.012 pmol/kg (2.3%) for CFC-113. The precisions of analysis by the JMA system were 0.008 pmol/kg seawater (0.4%) for CFC-12, 0.011 pmol/kg (0.2%) for CFC-11 and 0.012 pmol/kg (3.0%) for CFC-113. The no discrepancy in the concentrations of CFCs measured by the MRI and JMA systems was found at the 95% of significance level for these CFCs. These results suggest that if only the calibration scale were inter-compared, we could obtain comparable CFCs data in seawater.
Nanoconnectivity: a quantitative approach to examine the structural complexity of the brain

Unraveling the highly complex connectivity at the synaptic level is critical for the understanding of brain function. However, investigating the structure of the brain is time consuming and technically demanding. We have developed and applied a tracing method that allows us to obtain a simplified or skeletonized version of all nerve fibers present within a given brain sample, without the need for full 3D reconstructions. Every tracing or “skeleton” is linked to its corresponding synaptic contacts, so the result is an intricate meshwork of axons and dendrites interconnected by a cloud of synaptic junctions. The tissue sample is obtained by volume electron microscopy (FIB-SEM) and tracing is performed by dedicated software. In addition, the software provides the length of each skeleton as well as the number and positions of its corresponding synapses. With this approach, we have identified clear as well as subtle quantitative differences between three brain regions (the stratum radiatum of the hippocampus and layers 1 and 3 of the somatosensory cortex). For example, we have found that axons and dendrites are densely packed in the neuropil of these three regions, reaching close to 8 kilometers of nerve fibers per cubic mm in layer 1. In all cases, the predominant fibers were excitatory axons, followed by spiny dendrites, inhibitory axons and smooth dendrites. Other examples include the fact that the excitatory axons in the stratum radiatum establish many more synapses per micron than the axons of the other regions, or the lack of correlation between the number of synapses established on the spines of a given dendrite and the number of synapses established on the dendritic shaft. Using this methodology, we obtain a set of quantitative parameters including the number and proportions of excitatory and inhibitory synapses; the numbers of dendrites and axons; the proportion of excitatory and inhibitory axons; the linear densities of synapses established on dendritic spines and dendritic shafts; the linear densities of synapses established by excitatory and inhibitory axons; and the lengths of the different types of dendrites and axons. Taken together, these data characterize each region, allowing us to compare them on a quantitative basis and to identify subtle traits and differences that would have escaped a qualitative analysis. With this strategy, we can achieve a better understanding of the structure and dynamics of the brain, and we are better equipped to explore how they change during both normal and pathological conditions.
Application of spheroid models to account for aerosol particle nonsphericity in remote sensing of desert dust

[ 1] The possibility of using shape mixtures of randomly oriented spheroids for modeling desert dust aerosol light scattering is discussed. For reducing calculation time, look-up tables were simulated for quadrature coefficients employed in the numerical integration of spheroid optical properties over size and shape. The calculations were done for 25 bins of the spheroid axis ratio ranging from similar to 0.3 ( flattened spheroids) to similar to 3.0 ( elongated spheroids) and for 41 narrow size bins covering the size parameter range from similar to 0.012 to similar to 625. The look-up tables were arranged into a software package, which allows fast, accurate, and flexible modeling of scattering by randomly oriented spheroids with different size and shape distributions. In order to evaluate spheroid model and explore the possibility of aerosol shape identification, the software tool has been integrated into inversion algorithms for retrieving detailed aerosol properties from laboratory or remote sensing polarimetric measurements of light scattering. The application of this retrieval technique to laboratory measurements by Volten et al. ( 2001) has shown that spheroids can closely reproduce mineral dust light scattering matrices. The spheroid model was utilized for retrievals of aerosol properties from atmospheric radiation measured by AERONET ground-based Sun/sky-radiometers. It is shown that mixtures of spheroids allow rather accurate fitting of measured spectral and angular dependencies of observed intensity and polarization. Moreover, it is shown that for aerosol mixtures with a significant fraction of coarse-mode particles ( radii >= similar to 1 mu m), the nonsphericity of aerosol particles can be detected as part of AERONET retrievals. The retrieval results indicate that nonspherical particles with aspect ratios similar to 1.5 and higher dominate in desert dust plumes, while in the case of background maritime aerosol spherical particles are dominant. Finally, the potential of using AERONET derived spheroid mixtures for modeling the effects of aerosol particle nonsphericity in other remote sensing techniques is discussed. For example, the variability of lidar measurements ( extinction to backscattering ratio and signal depolarization ratio) is illustrated and analyzed. Also, some potentially important differences in the sensitivity of angular light scattering to parameters of nonspherical versus spherical aerosols are revealed and discussed.
Enhanced Creutzfeldt‐Jakob disease surveillance in the older population: Assessment of a protocol for screening brain tissue donations for prion disease

Abstract Human prion diseases, including Creutzfeldt‐Jakob disease (CJD), occur in sporadic, genetic, and acquired forms. Variant Creutzfeldt‐Jakob disease (vCJD) first reported in 1996 in the United Kingdom (UK), resulted from contamination of food with bovine spongiform encephalopathy. There is a concern that UK national surveillance mechanisms might miss some CJD cases (including vCJD), particularly in the older population where other neurodegenerative disorders are more prevalent. We developed a highly sensitive protocol for analysing autopsy brain tissue for the misfolded prion protein (PrPSc) associated with prion disease, which could be used to screen for prion disease in the elderly. Brain tissue samples from 331 donors to the Edinburgh Brain and Tissue Bank (EBTB), from 2005 to 2022, were analysed, using immunohistochemical analysis on fixed tissue, and five biochemical tests on frozen specimens from six brain regions, based on different principles for detecting PrPSc. An algorithm was established for classifying the biochemical results. To test the effectiveness of the protocol, several neuropathologically confirmed prion disease controls, including vCJD, were included and blinded in the study cohort. On unblinding, all the positive control cases had been correctly identified. No other cases tested positive; our analysis uncovered no overlooked prion disease cases. Our algorithm for classifying cases was effective for handling anomalous biochemical results. An overall analysis suggested that a reduced biochemical protocol employing only three of the five tests on only two brain tissue regions gave sufficient sensitivity and specificity. We conclude that this protocol may be useful as a UK‐wide screening programme for human prion disease in selected brains from autopsies in the elderly. Further improvements to the protocol were suggested by enhancements of the in vitro conversion assays made during the course of this study.
Numerical simulations of a compact convergent system of ice floes

The granular nature of the Arctic pack ice, and the plastic nature of the deformation of the pack due to ridging, has long been recognised. However, because of a lack of experimental data, assumptions must be made to define the shape of the yield curve and the associated flow rule which characterize the aggregate rheology of the ice pack. In this work, the results of numerical experiments with a simulated granular viscous-plastic material are presented. The experiments model the granular texture of the ice pack as a dense assembly of non-uniform diameter disks in a rectangular control area. Deformation of the control area is driven by constant strain rates. In the experiments, the ratio of the principal strain rates is varied from isotropic convergence through uniaxial divergence. The stresses computed in the experiments, at the various strain-rate ratios, define a yield curve in principal-stress space. The effects of different coefficients of friction and viscous damping on the shape of the yield curve are explored.
Identification of invasive trees in a Brazilian subtropical forest using remotely piloted aircraft systems and machine learning

Abstract. We aimed to combine the use of images obtained from remotely piloted aircraft systems (RPAS) and machine learning (ML) to identify the invasive alien species Psidium guajava in a protected area in southern Brazil. Field data were obtained in a sampling area, where the species’ geographic coordinates were collected with a global positioning system device. Remote data were collected with the Parrot Sequoia® multispectral camera onboard the Phantom 4® Pro platform. Image processing was used to generate reflectance maps and vegetation indices, after which four classes of interest were defined for model training. The supervised classification involved two approaches (pixel-based—BP and object-based image analysis—OBIA) and two ML algorithms compared (random forest—RF and support vector machine—SVM). For performance analysis, confusion matrices with user and producer accuracies, Kappa values and overall accuracy (OA) were calculated. The results demonstrate that the multispectral composition was excellent in identifying the invasive P. guajava, in an OBIA approach with the RF algorithm (0.90 Kappa and 93% OA). Thus, considering the priority of biodiversity conservation and the importance of the Brazilian Atlantic Forest for the maintenance of endemic and endangered species, we present a robust methodology to identify the invasive species P. guajava in subtropical forest, which can be applied in management strategies for the species control and eradication.
Solving Multiple-instance and Multiple-part Learning Problems with Decision Trees and Decision Rules

A hydrostatic transmission includes two axially aligned radial piston machines operating as a pump and motor, and having cylinder blocks secured to a housing and to an output shaft, respectively, and actuator rings whose eccentricities are simultaneously adjusted by adjusting means surrounding the actuator means and connected therewith by cam slots and cam followers so that power can be hydraulically and mechanically transmitted between the input and output shafts.