Scientific Questions Research Articles

Assessment on the Impact of Mining and Industrial Activities in Groundwater Quality in Chandrapur, Maharashtra Through Remote Sensing and GIS Applications

This study evaluated the quality of groundwater in Chandrapur Taluka, Maharashtra, using geospatial techniques and data from 2014 and 2018. The study assessed various water quality parameters such as chloride, fluoride, pH, residual sodium carbonate (RSC), and sodium adsorption ratio (SAR). The findings showed that chloride concentrations were mostly within acceptable limits, but there was a slight increase in areas near mining and industrial sites, which was statistically significant (p < 0.05). Fluoride levels were generally within permissible bounds, but there was a noticeable increase near industrial areas in 2018 compared to 2014, which was statistically significant (p < 0.05) and raised environmental concerns. Variations in pH values were also observed, which could impact aquatic ecosystems, with a decrease noted from 2014 to 2018. RSC levels were higher near mining and industrial zones in 2018, exceeding recommended limits, indicating a potential threat to water quality. SAR levels in 2018 were higher, potentially impacting agriculture, but still within acceptable limits. Sulphate levels showed a reduction from 2014 to 2018. These comprehensive findings highlight the specific impacts of mining and industrial activities on groundwater quality and raise broader scientific questions. They can be used to develop evidence-based policies for effective mitigation measures and engage a wider readership.

Inoculating Enceladus

The discovery of environments in the Solar System that possess conditions capable of supporting known types of life raises the question of whether they could be deliberately inoculated in order to study the process of the emergence of biospheres. We discuss the case of Enceladus, the first planetary body to convincingly be shown to possess all the requirements for habitability in the present-day, and consider ways in which inoculation would be achieved. We present examples of the scientific questions that might be investigated. The compelling science that could be done shows how habitable worlds will create new ethical questions. As we might not have certainty on their status as being uninhabited, we would have to decide on a principled objection to any inoculation experiments or whether some level of confidence in their status as being uninhabited, determined by a suitable sampling regimen, would allow for inoculation. As the inoculation of extraterrestrial oceans, causing planetary scale changes, might be accomplished in a far shorter time scale than, for example, the more speculative terraforming of a planet such as Mars, the scientific possibilities and their attendant ethical challenges potentially represent a near-term challenge.

Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2

AbstractAccurate taxonomic classification is essential to understanding microbial diversity and function through metagenomic sequencing. However, this task is complicated by the vast variety of microbial genomes and the computational limitations of bioinformatics tools. The aim of this study was to evaluate the impact of reference database selection and confidence score (CS) settings on the performance of Kraken2, a widely used k-mer-based metagenomic classifier. In this study, we generated simulated metagenomic datasets to systematically evaluate how the choice of reference databases, from the compact Minikraken v1 to the expansive nt- and GTDB r202, and different CS (from 0 to 1.0) affect the key performance metrics of Kraken2. These metrics include classification rate, precision, recall, F1 score, and accuracy of true versus calculated bacterial abundance estimation. Our results show that higher CS, which increases the rigor of taxonomic classification by requiring greater k-mer agreement, generally decreases the classification rate. This effect is particularly pronounced for smaller databases such as Minikraken and Standard-16, where no reads could be classified when the CS was above 0.4. In contrast, for larger databases such as Standard, nt and GTDB r202, precision and F1 scores improved significantly with increasing CS, highlighting their robustness to stringent conditions. Recovery rates were mostly stable, indicating consistent detection of species under different CS settings. Crucially, the results show that a comprehensive reference database combined with a moderate CS (0.2 or 0.4) significantly improves classification accuracy and sensitivity. This finding underscores the need for careful selection of database and CS parameters tailored to specific scientific questions and available computational resources to optimize the results of metagenomic analyses.

Comparing methylation levels assayed in GC-rich regions with current and emerging methods

DNA methylation is an epigenetic mechanism that regulates gene expression, and for mammals typically occurs on cytosines within CpG dinucleotides. A significant challenge for methylation detection methods is accurately measuring methylation levels within GC-rich regions such as gene promoters, as inaccuracies compromise downstream biological interpretation of the data. To address this challenge, we compared methylation levels assayed using four different Methods Enzymatic Methyl-seq (EM-seq), whole genome bisulphite sequencing (WGBS), Infinium arrays (Illumina MethylationEPIC, “EPIC”), and Oxford Nanopore Technologies nanopore sequencing (ONT) applied to human DNA. Overall, all methods produced comparable and consistent methylation readouts across the human genome. The flexibility offered by current gold standard WGBS in interrogating genome-wide cytosines is surpassed technically by both EM-seq and ONT, as their coverages and methylation readouts are less prone to GC bias. These advantages are tempered by increased laboratory time (EM-seq) and higher complexity (ONT). We further assess the strengths and weaknesses of each method, and provide recommendations in choosing the most appropriate methylation method for specific scientific questions or translational needs.

An integrated model of semantics and control.

Understanding the mechanisms enabling the learning and flexible use of knowledge in context-appropriate ways has been a major focus of research in the study of both semantic cognition and cognitive control. We present a unified model of semantics and control that addresses these questions from both perspectives. The model provides a coherent view of how semantic knowledge, and the ability to flexibly access and deploy that knowledge to meet current task demands, arises from end-to-end learning of the statistics of the environment. We show that the model addresses unresolved issues from both literatures, including how control operates over features that covary with one another and how control representations themselves are structured and emerge through learning, through a series of behavioral experiments and simulations. We conclude by discussing the implications of our approach to other fundamental questions in cognitive science, machine learning, and artificial intelligence. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Unravelling Influence Factors in Pattern Recognition Myoelectric Control Systems: The Impact of Limb Positions and Electrode Shifts.

Pattern recognition (PR)-based myoelectric control systems can naturally provide multifunctional and intuitive control of upper limb prostheses and restore lost limb function, but understanding their robustness remains an open scientific question. This study investigates how limb positions and electrode shifts-two factors that have been suggested to cause classification deterioration-affect classifiers' performance by quantifying changes in the class distribution using each factor as a class and computing the repeatability and modified separability indices. Ten intact-limb participants took part in the study. Linear discriminant analysis (LDA) was used as the classifier. The results confirmed previous studies that limb positions and electrode shifts deteriorate classification performance (14-21% decrease) with no difference between factors (p > 0.05). When considering limb positions and electrode shifts as classes, we could classify them with an accuracy of 96.13 ± 1.44% and 65.40 ± 8.23% for single and all motions, respectively. Testing on five amputees corroborated the above findings. We have demonstrated that each factor introduces changes in the feature space that are statistically new class instances. Thus, the feature space contains two statistically classifiable clusters when the same motion is collected in two different limb positions or electrode shifts. Our results are a step forward in understanding PR schemes' challenges for myoelectric control of prostheses and further validation needs be conducted on more amputee-related datasets.

Large language models in science

Large language models (LLMs) are gaining popularity due to their ability to communicate in ahuman-like manner. Their potential for science, including urology, is increasingly recognized. However, unresolved concerns regarding transparency, accountability, and the accuracy of LLM results still exist. This review examines the ethical, technical, and practical challenges as well as the potential applications of LLMs in urology and science. Aselective literature review was conducted to analyze current findings and developments in the field of LLMs. The review considered studies on technical aspects, ethical considerations, and practical applications in research and practice. LLMs, such as GPT from OpenAI and Gemini from Google, show great potential for processing and analyzing text data. Applications in urology include creating patient information and supporting administrative tasks. However, for purely clinical and scientific questions, the methods do not yet seem mature. Currently, concerns about ethical issues and the accuracy of results persist. LLMs have the potential to support research and practice through efficient data processing and information provision. Despite their advantages, ethical concerns and technical challenges must be addressed to ensure responsible and trustworthy use. Increased implementation could reduce the workload of urologists and improve communication with patients.

The astrobiological potential of the Makgadikgadi Basin, Botswana: Field analogue for planetary exploration

Terrestrial analogue sites have been crucial for studying Martian geology and mineralogy, integrating the direct evidence available from Mars through remote sensing and in situ measurements carried out by the instruments on board robotic missions. Studying readily available and accessible terrestrial analogues of Martian fossil or extant environments is considered the most efficient way to answer crucial scientific questions. These analogues offer opportunities to collect a range of geological and microbiological data. The Makgadikgadi Basin (MKB) in Botswana is one of such environments hosting a system of salt pans presenting striking similarities with Mars playa deposits. The MKB presents layered mounds, relict fan deltas with inverted channels, polygonal structures and evaporitic crusts harboring communities of extremophiles. The present-day MKB is predominantly fed by groundwater and local precipitations in an overall arid to semi-arid climate, characterized by high UV radiation and salinity, deposition of evaporitic minerals and authigenic clays. The shallow subsurface of the MKB pans is covered by diagenetic features (duricrusts) including silcretes and calcretes. These pans can serve as test beds for the physical and chemical characteristics of playa deposits on Mars and help improve our understanding of the conditions that might support life outside our planet.

High-fidelity imaging of fatty liver in vivo with a fluorescent and photoacoustic dual-mode probe by taking advantage of the liver “first pass effect”

Intravenous injection is the most commonly used method for probe delivery in bio-imaging. While, the oral administration method might be more efficient than intravenous injection for fatty liver imaging due to the existence of liver “first pass effect”. However, this fundamental question has not yet been clarified. Meanwhile, in consideration of the deep tissue imaging and signal fidelity, fluorescent-photoacoustic (PA) dual-mode probes are much more desirable. Herein, an orally administrable dual-mode probe WSP-3 is revealed as a tool for imaging of the fatty liver disease and providing an insight into the above scientific question. A D-π-A system is linked with a rotatable CC single bond in WSP-3, which facilitates the formation of a TICT state in low viscosity environments and an ICT state in high viscosity environments. Base on the positive correlation between fatty liver disease and cell viscosity, dual-mode imaging of non-alcoholic fatty liver disease (NAFLD) and drug-induced fatty liver disease (DIFLD) in vivo was accomplished. Moreover, control experiments indicated that the oral administration method demonstrated higher efficiency in fatty liver disease imaging, providing a fundamental reference for further probe-based fatty liver imaging.

From nutrients to fish: Impacts of mesoscale processes in a global CESM-FEISTY eddying ocean model framework

The ocean sustains ecosystems that are essential for human livelihood and habitability of the planet. The ocean holds an enormous amount of carbon, and serves as a critical source of nutrition for human societies worldwide. Climate variability and change impact marine biogeochemistry and ecosystems. Thus, having state-of-the-art simulations of the ocean, which include marine biogeochemistry and ecosystems, is critical for understanding the role of climate variability and change on the ocean biosphere. Here we present a novel global eddy-resolving (0.1° horizontal resolution) simulation of the ocean and sea ice, including ocean biogeochemistry, performed with the Community Earth System Model (CESM). The simulation is forced by the atmospheric dataset based on the Japanese Reanalysis (JRA-55) product over the 1958–2021 period. We present a novel configuration of the CESM marine ecosystem model in this simulation which includes two zooplankton classes: microzooplankton and mesozooplankton. This novel planktonic food web structure facilitates “offline” coupling with the Fisheries Size and Functional Type (FEISTY) model. FEISTY is a size- and trait-based model of fish functional types contributing to fisheries. We present an evaluation of the ocean biogeochemistry, marine ecosystem (including fish types), and sea ice in this high resolution simulation compared to available observations and a corresponding low resolution (nominal 1°) simulation. Our analysis offers insights into environmental controls on trophodynamics within the ocean. We find that this high resolution simulation provides a realistic reconstruction of nutrients, oxygen, sea ice, plankton and fish distributions over the global ocean. On global and large regional scales the high resolution simulation is comparable to the standard 1° simulation, but on smaller scales, explicitly resolving the mesoscale dynamics is shown to be important for accurately capturing trophodynamic structuring, especially in coastal ecosystems. We show that fine-scale ocean features leave imprints on ocean ecosystems, from plankton to fish, from the tropics to polar regions. This simulation also offers insights on ocean acidification over the past 64 years, as well as how large-scale climate variations may impact upper trophic levels. The data generated by the simulations are publicly available and will be a fruitful community resource for a large variety of oceanographic science questions.

Microplastics with different functional groups modulate cellular and molecular mechanisms of reduced graphene oxide toxicity on the green microalga, Scenedesmus obliquus

Even though microplastics (MPs) and graphene nanomaterials (GNMs) have demonstrated individual toxicity towards aquatic organisms, the knowledge gap lies in the lack of understanding regarding their combined toxicity. The difference between the combined toxicity of MPs and GNMs, in contrast to their individual toxicities, and furthermore, the elucidation of the mechanism of this combined toxicity are scientific questions that remain to be addressed. In this study, we examined the individual and combined toxicity of three polystyrene microplastics (MPs) with different functional groups—unmodified, carboxyl-modified (COOH-), and amino-modified (NH2-) MPs—in combination with reduced graphene oxide (RGO) on the freshwater microalga Scenedesmus obliquus. More importantly, we explored the cellular and molecular mechanisms responsible for the observed toxicity. The results indicated that the growth inhibition toxicity of RGO, either alone or in combination with the three MPs, against S. obliquus increased gradually with higher particle concentrations. The mitigating effect of MPs-NH2 on RGO-induced toxicity was most significant at a higher concentration, surpassing the effect of unmodified MPs. However, the MPs-COOH did not exhibit a substantial impact on the toxicity of RGO. Unmodified MPs and MPs-COOH aggravated the inhibition effects of RGO on the cell membrane integrity and oxidative stress-related biomarkers. Additionally, MPs-COOH exhibited a stronger inhibition effect on RGO-induced biomarkers compared to unmodified MPs. In contrast, the MPs-NH2 alleviated the inhibition effect of RGO on the biomarkers. Furthermore, the presence of differently functionalized MPs did not significantly affect RGO-induced oxidative stress and photosynthesis-related gene expression in S. obliquus, indicating a limited ability to modulate RGO genotoxicity at the molecular level. These findings can offer a more accurate understanding of the combined risks posed by these micro- and nano-materials and assist in designing more effective mitigation strategies.

Investigation of Eighth-Grade Students’ processes of solving skill- based science questions by eye tracking technique

AbstractThe aim of this study was to determine the visual measurement results related to the behavior/processes of solving skill-based science questions of eighth grade students by eye tracking technique. Non-experimental quantitative research method was used in the research and visual measurement results were supported by heat maps and eye splash movements. Nine questions, with difficulty and discrimination indexes calculated, were applied to 56 eighth grade students. Data were collected with a skill-based test, eye tracking device, think-aloud protocols and a perception scale towards next generation science questions. The data obtained from the eye tracking device was examined using Gaze Viewer software and the results were shown as images. The results revealed that visual measurement results differed according to gender and 2023 high schools entrance exam scores. Additionally, negative relationships were found between visual measurement results and students’ practice test scores and their perceptions towards solving next generation science questions. It was determined that average duration of fixation had a significant predictive effect on students’ self-efficacy levels for solving next generation science questions.

Higher‐order dissimilarity in biodiversity: Identifying dissimilarities of spatial or temporal dissimilarity structures

Abstract Elucidating biodiversity patterns and their background processes is critical in biodiversity science. Dissimilarity, which is calculated based on multivariate biological quantities, is a major component of biodiversity. As spatial and temporal biodiversity information availability increases, the scope of dissimilarity studies has been expanded to cover various levels and types of spatiotemporal biodiversity facets (e.g. gene, community and ecosystem function), and diverse pairwise dissimilarity indices have been developed. However, further development of the dissimilarity concept is required in comparative studies on spatiotemporal structures of biodiversity compositional patterns, such as those exploring commonalities of biogeographical boundaries among taxa, compared to the conventional ones to consider higher dimensions of dissimilarity: dissimilarity of dissimilarity structures. This study proposes a novel and general concept, higher‐order dissimilarity (HOD), for quantitatively evaluating the dissimilarities of spatial or temporal dissimilarity structures among different datasets, proposes specific implementations of HOD as operational indices, and illustrates the potential resolution of scientific and practical questions through HOD. We further demonstrate the advantages of the HOD concept by applying it to actual patterns, such as long‐term and/or large‐spatial hypothetical monitoring datasets. Our conceptual framework on HOD extends the existing framework of biodiversity science and is versatile, with many potential applications in acquiring more valuable information from ever‐increasing biodiversity data.

The Epigraphic Testimonies from Timacum Maius (Eastern Moesia Superior): The Important Clues for the Character and Organization of Naissus Region

For more than ten years in a row, archaeologists of the Institute for Balkan Studies of SASA of the Serbian Academy of Sciences and Arts, in cooperation with the Ausonius Institute from Bordeaux, have been conducting archaeological research on the Roman and Byzantine settlement located in the area of the village of Niševac near Svrljig, in the Svrljiški Timok River valley. It was the first station on the Roman itinerary road between Naissus (Niš) and Trajan's colony of Ratiaria on the Danube (Archar in northwestern Bulgaria). In addition to significant architectural remains and various archaeological findings, some inscriptions in Latin and Greek are also known from this area. This bilingualism of the texts indicates the very location of Timacum Maius, which was located on a vital communication line and a linguistic and administrative interprovincial barrier. Although chronologically different, the epigraphic findings I report raise broader scientific questions about the significance of this ancient settlement and its population, especially in the early military history of the Naissus region.

“Shadowy Objects in Test Tubes”: Gene Fetishism and Racialized Biocapital in Kazuo Ishiguro’s Never Let Me Go

ABSTRACT This paper engages with the entwined questions of science and ideology through a symptomatic reading of Kazuo Ishiguro’s Never Let Me Go (2005), studying how power, racism, and capital intervene into the genetic enterprise of tampering with the limitations of the human and produce a supplicant race of clones for organ harvest and extraction. I commence by drawing on Donna Haraway’s concept of gene fetishism and Evelyn Fox Keller’s notion of gene talk to trace how an elision of the ideological frameworks of race and capital subtending genomics in Ishiguro’s dystopian world instrumentalizes the creation of the clones as racialized products. I bring into dialogue the clones’ obsessive quest for familial origins with Deborah Bolnick’s exploration of the reification of race as biology through ancestry tests to analyze how technology can be used to create and legitimize racism. Deploying Kaushik Sundar Rajan’s theorization of biocapital and James Doucet-Battle’s analysis of the intersections of race, capitalism, and time, I study how the clones are discursively defined as fungible commodities in service to a futurity from which they are precluded. I conclude by positing the call for “slow science” as a potential strategy against the accelerationism and market-ready speculations that dictate biotechnical enterprises today.

Get Ready to Sharpen Your Tools: A Short Guide to Heterotrimeric G Protein Activity Biosensors.

G protein-coupled receptors (GPCRs) are the largest class of transmembrane receptors encoded in the human genome, and they initiate cellular responses triggered by a plethora of extracellular stimuli ranging from neurotransmitters and hormones to photons. Upon stimulation, GPCRs activate heterotrimeric G proteins (Gαβγ) in the cytoplasm, which then convey signals to their effectors to elicit cellular responses. Given the broad biological and biomedical relevance of GPCRs and G proteins in physiology and disease, there is great interest in developing and optimizing approaches to measure their signaling activity with high accuracy and across experimental systems pertinent to their functions in cellular communication. This review provides a historical perspective on approaches to measure GPCR-G protein signaling, from quantification of second messengers and other indirect readouts of activity to biosensors that directly detect the activity of G proteins. The latter is the focus of a more detailed overview of the evolution of design principles for various optical biosensors of G protein activity with different experimental capabilities. We will highlight advantages and limitations of biosensors that detect different G protein activation hallmarks, like dissociation of Gα and Gβγ or nucleotide exchange on Gα, as well as their suitability to detect signaling mediated by endogenous versus exogenous signaling components or in physiologically relevant systems like primary cells. Overall, this review intends to provide an assessment of the state-of-the-art for biosensors that directly measure G protein activity to allow readers to make informed decisions on the selection and implementation of currently available tools. SIGNIFICANCE STATEMENT: G protein activity biosensors have become essential and widespread tools to assess GPCR signaling and pharmacology. Yet, investigators face the challenge of choosing from a growing list of G protein activity biosensors. This review provides an overview of the features and capabilities of different optical biosensor designs for the direct detection of G protein activity in cells, with the aim of facilitating the rational selection of systems that align with the specific scientific questions and needs of investigators.

Mechanism of Histone Arginine Methylation Dynamic Change in Cellular Stress.

Histone arginine residue methylation is crucial for individual development and gene regulation. However, the dynamics of histone arginine methylation in response to cellular stress remains largely unexplored. In addition, the interplay and regulatory mechanisms between this and other histone modifications are important scientific questions that require further investigation. This study aimed to investigate the changes in histone arginine methylation in response to DNA damage. We report a global decrease in histone H3R26 symmetric dimethylation (H3R26me2s) and hypoacetylation at the H3K27 site in response to DNA damage. Notably, H3R26me2s exhibits a distribution pattern similar to that of H3K27ac across the genome, both of which are antagonistic to H3K27me3. Additionally, histone deacetylase 1 (HDAC1) may be recruited to the H3R26me2s demethylation region to mediate H3K27 deacetylation. These findings suggest crosstalk between H3R26me2s and H3K27ac in regulating gene expression.

DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data.

The ability to sequence ancient genomes has revolutionized the way we study evolutionary history by providing access to the most important aspect of evolution-time. Until recently, studying human demography, ecology, biology, and history using population genomic inference relied on contemporary genomic datasets. Over the past decade, the availability of human ancient DNA (aDNA) has increased rapidly, almost doubling every year, opening the way for spatiotemporal studies of ancient human populations. However, the multidimensionality of aDNA, with genotypes having temporal, spatial and genomic coordinates, and integrating multiple sources of data, poses a challenge for developing meta-analyses pipelines. To address this challenge, we developed a publicly-available interactive tool, DORA, which integrates multiple data types, genomic and non-genomic, in a unified interface. This web-based tool enables browsing sample metadata alongside additional layers of information, such as population structure, climatic data, and unpublished samples. Users can perform analyses on genotypes of these samples, or export sample subsets for external analyses. DORA integrates analyses and visualizations in a single intuitive interface, resolving the technical issues of combining datasets from different sources and formats, and allowing researchers to focus on the scientific questions that can be addressed through analysis of aDNA datasets.

Perceptions and preferences for redistribution

Abstract The relationship between the degree of inequality and the demand for redistribution has been a central question in political science and political economy. The famous median-voter model predicts that higher inequality, reflected in a growing gap between the income of the average and the median voter, should lead to increased demand for redistribution, as policymakers cater to the median voter’s preferences. Yet data from Organisation for Economic Co-operation and Development (OECD) countries show that, despite increases in inequality in those countries, there was no corresponding increase in demand for redistribution. Part of the explanation of this puzzle lies in the realization that it is not only (or even mainly) reality but also perceptions that shape support for policy. This article will explore recent evidence, using large-scale social economics surveys and experiments, that sheds light on beliefs about inequality, social mobility, diversity and immigration, social position, and understanding of how policies work.

Labour market inequality: a comparative political economy perspective

Abstract Large and rising earnings and employment inequalities in countries such as the USA and the UK pose fundamental questions for social scientists and challenges for policymakers. Mainstream economists have explained these outcomes mainly in terms of competitive market forces, particularly the mismatch between technology-driven demands for skills and those supplied by workers. In contrast, political economy perspectives focus on employer–employee bargaining power, driven by the monopsony power of firms and declining institutional and policy protections for workers. We critically assess the evidence on the education wage premium and employment polarization used to support the competitive market explanation for US wage inequality. We then show that the incidence of decent pay for young less-educated workers varies sharply across similarly rich countries and that new indices of institutional bargaining power closely correspond to differences in pay distributions but are uncorrelated with conventional measures of employment performance. We conclude that well-designed institutional and policy changes can substantially promote shared growth and the well-being of working families.