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Automating the practice of science: Opportunities, challenges, and implications

Automation transformed various aspects of our human civilization, revolutionizing industries and streamlining processes. In the domain of scientific inquiry, automated approaches emerged as powerful tools, holding promise for accelerating discovery, enhancing reproducibility, and overcoming the traditional impediments to scientific progress. This article evaluates the scope of automation within scientific practice and assesses recent approaches. Furthermore, it discusses different perspectives to the following questions: where do the greatest opportunities lie for automation in scientific practice?; What are the current bottlenecks of automating scientific practice?; and What are significant ethical and practical consequences of automating scientific practice? By discussing the motivations behind automated science, analyzing the hurdles encountered, and examining its implications, this article invites researchers, policymakers, and stakeholders to navigate the rapidly evolving frontier of automated scientific practice.

Identifying the color and absorption band properties of Fe oxides in Danxia red beds by the visible diffuse reflectance spectrum

Environmental variability across space and time drives the recolonization pattern of a historically persecuted large carnivore

Wildlife populations are not static. Intrinsic and extrinsic factors affect individuals, which lead to spatiotemporal variation in population density and range. Yet, dynamics in density and their drivers are rarely documented, due in part to the inherent difficulty of studying long-term population-level phenomena at ecologically meaningful scales. We studied the spatiotemporal density dynamics in a recolonizing large carnivore population, the wolverine Gulo gulo , across the Scandinavian Peninsula over nine years. We fitted open-population spatial capture-recapture models to noninvasive genetic sampling data collected across Norway and Sweden to estimate annual density surfaces and their drivers. This approach allowed us to model sex-specific changes in wolverine density and the effect of landscape-level environmental determinants over time. Our results revealed that, as wolverines successfully recolonized many parts of their historical range in Scandinavia, the relationship with spatial determinants of density has changed over time. We also found support for sex-specific responses of the Scandinavian wolverine to the environmental determinants of density and differences in the temporal dynamics of their relationships, indicating disproportionate recolonization ability and anthropogenic pressures. We observed significant changes in the relationship of female wolverine density with several determinants during the study period, suggesting still ongoing expansion of female wolverines whereas males might have already reached the range limits. These findings show that the Scandinavian wolverine population is still recovering from centuries of persecution and severe range contraction. Our study sheds light on the dynamics and challenges of recolonizing large carnivores in human-dominated landscapes across time and space.

Computer-aided cholelithiasis diagnosis using explainable convolutional neural network

Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria

Heterocytes, specialized cells for nitrogen fixation in cyanobacteria, are surrounded by heterocyte glycolipids (HGs), which contribute to protection of the nitrogenase enzyme from oxygen. Diverse HGs preserve in the sediment and have been widely used as evidence of past nitrogen fixation, and structural variation has been suggested to preserve taxonomic information and reflect paleoenvironmental conditions. Here, by comprehensive HG identification and screening of HG biosynthetic gene clusters throughout cyanobacteria, we reconstruct the convergent evolutionary history of HG structure, in which different clades produce the same HGs. We find that rudimentary HG biosynthetic machinery was already present in cyanobacteria before the emergence of heterocytes for functions unrelated to nitrogen fixation and identify HG analogs produced by specific and distantly related nonheterocytous cyanobacteria. These structurally less complex molecules represent precursors of HGs, suggesting that HGs arose after a genomic reorganization and expansion of ancestral biosynthetic machinery, enabling the rise of cyanobacterial heterocytes in an increasingly oxygenated atmosphere. Our results open a chapter in the potential use of diagenetic products of HGs and HG analogs as fossils for reconstructing the evolution of multicellularity and division of labor in cyanobacteria.

Dairy calves provided with environmental enrichment are more active, playful and have fewer feeding interruptions

Abstract Concerns for farm animal welfare have led to the use of environmental enrichment to stimulate natural behaviours and promote positive emotions. In cattle, the provision of brushes is sometimes recommended but their use in calves and the effects they may have are not well established. The use of precision technologies enables the collection of detailed behavioural data that can be used as welfare indicators. Here we use ultra-wideband location sensors to measure activity and play, along with automatic milk feeders to measure feeding. We assessed the effects of stationary brushes on the behaviour of 226 dairy calves for up to 72 days. Half of the calves had access to the brushes for half of the experimental period. Using a mixed-effects linear model we showed that when brushes were present calves had significantly higher activity, fed slower, had fewer interruptions in their meals and spent less time around the feeder, suggesting reduced competition. Furthermore, calves that had access to brushes during the trial were more active and playful, even on days when the brushes were not available, compared to the control group. This finding indicates for the first time that enrichment may have a lasting effect on calf behaviour and welfare.

Electric transportation and electroreception in hummingbird flower mites

Electric fields in terrestrial environments are used by caterpillars to detect their predators, as foraging cues by pollinators, and facilitate ballooning by spiders. This study shows that electric fields facilitate transportation and detection of hummingbirds in a guild of tropical phoretic mites. Hummingbird flower mites feed on nectar and pollen and complete their life cycle inside flowers. Mites colonize new flowers by hitching rides on hummingbird beaks. Flower mites emerge from hummingbird nostrils and disembark when the beak touches a flower. We tested whether flower mites are attracted to unmodulated electrostatic, or to modulated electric fields with amplitudes and frequencies in the range of those previously reported for hummingbirds. In a laboratory setup, mites were only attracted to modulated electric fields. In a choice experiment between positive or negative polarities, mites almost instantaneously chose positive charges, but only when the field was modulated. Mites display questing behavior, moving their front legs toward an electrostatic source. In experiments where we removed one or both front leg tarsi, we show that modulated fields are detected by sensory structures present in the front legs. We also show that flower mites use electrostatic attraction to bridge the gap to the beaks of hummingbirds, for a few milliseconds becoming one of the fastest terrestrial organisms. Our results confirm that hummingbird flower mites evolved an additional sensory modality — electroreception — to quickly detect hummingbirds and use electrostatics to facilitate transportation onto their hosts.

Navajo Sandstone concretions record extended magnetic chronology

Alternative models of funding curiosity-driven research

Funding of curiosity-driven science is the lifeblood of scientific and technological innovation. Various models of funding allocation became institutionalized in the 20th century, shaping the present landscape of research funding. There are numerous reasons for scientists to be dissatisfied with current funding schemes, including the imbalance between funding for curiosity-driven and mission-directed research, regional and country disparities, path-dependency of who gets funded, gender and race disparities, low inter-reviewer reliability, and the trade-off between the effort and time spent on writing or reviewing proposals and doing research. We discuss possible alternative models for dealing with these issues. These alternatives include incremental changes such as placing more weight on the proposals or on the investigators and representative composition of panel members, along with deeper reforms such as distributed or concentrated funding and partial lotteries in response to low inter-reviewer reliability. We also consider radical alternatives to current funding schemes: the removal of political governance and the introduction of international competitive applications to a World Research Council alongside national funding sources. There is likely no single best way to fund curiosity-driven research; we examine arguments for and against the possibility of systematically evaluating alternative models empirically.

Removal of iron and manganese from acidic aqueous solution by pyrite and pyrite-calcium sulfite

Efficient, scalable, and near-nucleotide-resolution profiling of protein occupancy in the genome with deaminases

Dynamic multiday seizure cycles and evolving rhythms in a tetanus toxin rat model of epilepsy

Chronic stress–induced cholesterol metabolism abnormalities promote ESCC tumorigenesis and predict neoadjuvant therapy response

Recent studies have demonstrated that chronic stress can enhance the development of multiple human diseases, including cancer. However, the role of chronic stress in esophageal carcinogenesis and its underlying molecular mechanisms remain unclear. This study uncovered that dysregulated cholesterol metabolism significantly promotes esophageal carcinogenesis under chronic stress conditions. Our findings indicate that the persistent elevation of glucocorticoids induced by chronic stress stimulates cholesterol uptake, contributing to esophageal carcinogenesis. The activated glucocorticoid receptor (GCR) enrichment at the promoter region of High Mobility Group Box 2 (HMGB2) facilitates its transcription. As a transcription coactivator, HMGB2 enhances Sterol Regulatory Element Binding Transcription Factor 1 (SREBF1) transcription and regulates cholesterol metabolism through LDL particle uptake into cells via Low Density Lipoprotein Receptor (LDLR). These results emphasize the significant impact of chronic stress on esophageal carcinogenesis and establish cholesterol metabolism disorder as a crucial link between chronic stress and the development of ESCC. The implications suggest that effectively managing chronic stress may serve as a viable strategy for preventing and treating ESCC.

CRIP1 inhibits cutaneous melanoma progression through TFAM-mediated mitochondrial biogenesis

New evidence for early Indian Ocean trade routes into the South African interior

The rise and spread of ancient Indian Ocean Rim (IOR) trade networks profoundly impacted southern Africa. Control over this trade played a critical role in the rise and maintenance of complex societies of the second millennium CE such as Mapungubwe and Great Zimbabwe. While the African origins of this trade lie in the first millennium CE, understanding its earliest phases and subsequent development in the far south has been hampered by a general paucity of research. The recovery of Persian Gulf ceramic sherds and Asian glass beads from the Letaba region of northeastern South Africa demonstrates that communities up to 400 km inland were already part of IOR trade by the 10th century. Although glass beads have been found at several late first millennium CE sites throughout the region, glazed wares are much rarer by comparison. In southern Africa, archaeological sites with Persian Gulf ceramics largely date to between the 9th and 10th centuries with a distribution limited to the Limpopo River’s main tributaries. This distribution poses new questions about early IOR trade routes into the southern African interior and suggests Xai-Xai in southern Mozambique as a possible entry point for early IOR trade.

Panoramic radiographic features for machine learning based detection of mandibular third molar root and inferior alveolar canal contact

How should the advancement of large language models affect the practice of science?

Large language models (LLMs) are being increasingly incorporated into scientific workflows. However, we have yet to fully grasp the implications of this integration. How should the advancement of large language models affect the practice of science? For this opinion piece, we have invited four diverse groups of scientists to reflect on this query, sharing their perspectives and engaging in debate. Schulz et al. make the argument that working with LLMs is not fundamentally different from working with human collaborators, while Bender et al. argue that LLMs are often misused and overhyped, and that their limitations warrant a focus on more specialized, easily interpretable tools. Marelli et al. emphasize the importance of transparent attribution and responsible use of LLMs. Finally, Botvinick and Gershman advocate that humans should retain responsibility for determining the scientific roadmap. To facilitate the discussion, the four perspectives are complemented with a response from each group. By putting these different perspectives in conversation, we aim to bring attention to important considerations within the academic community regarding the adoption of LLMs and their impact on both current and future scientific practices.

Identification of a comprehensive set of transcriptional regulators involved in the long-term survivability of Escherichia coli in soil

14-3-3 promotes sarcolemmal expression of cardiac Ca _V 1.2 and nucleates isoproterenol-triggered channel superclustering

The L-type Ca 2+ channel (Ca V 1.2) is essential for cardiac excitation–contraction coupling. To contribute to the inward Ca 2+ flux that drives Ca 2+ -induced-Ca 2+ -release, Ca V 1.2 channels must be expressed on the sarcolemma; thus the regulatory mechanisms that tune Ca V 1.2 expression to meet contractile demand are an emerging area of research. A ubiquitously expressed protein called 14-3-3 has been proposed to affect Ca 2+ channel trafficking in nonmyocytes; however, whether 14-3-3 has similar effects on Ca V 1.2 in cardiomyocytes is unknown. 14-3-3 preferentially binds phospho-serine/threonine residues to affect many cellular processes and is known to regulate cardiac ion channels including Na V 1.5 and the human ether-à-go-go–related gene (hERG) potassium channel. Altered 14-3-3 expression and function have been implicated in cardiac pathologies including hypertrophy. Accordingly, we tested the hypothesis that 14-3-3 interacts with Ca V 1.2 in a phosphorylation-dependent manner and regulates cardiac Ca V 1.2 trafficking and recycling. Confocal imaging, proximity ligation assays, superresolution imaging, and coimmunoprecipitation revealed a population of 14-3-3 colocalized and closely associated with Ca V 1.2. The degree of 14-3-3/Ca V 1.2 colocalization increased upon stimulation of β -adrenergic receptors with isoproterenol. Notably, only the 14-3-3-associated Ca V 1.2 population displayed increased cluster size with isoproterenol, revealing a role for 14-3-3 as a nucleation factor that directs Ca V 1.2 superclustering. Isoproterenol-stimulated augmentation of sarcolemmal Ca V 1.2 expression, Ca 2+ currents, and Ca 2+ transients in ventricular myocytes were strengthened by 14-3-3 overexpression and attenuated by 14-3-3 inhibition. These data support a model where 14-3-3 interacts with Ca V 1.2 in a phosphorylation-dependent manner to promote enhanced trafficking/recycling, clustering, and activity during β -adrenergic stimulation.

Production of novel theranostic nano-vector based on superparamagnetic iron oxide nanoparticles/miR-497 targeting colorectal cancer

Abstract Colorectal cancer (CRC) is a serious public health concern worldwide. Immune checkpoint inhibition medication is likely to remain a crucial part of CRC clinical management. This study aims to create new super paramagnetic iron oxide nano-carrier (SPION) that can effectively transport miRNA to specific CRC cell lines. In addition, evaluate the efficiency of this nano-formulation as a therapeutic candidate for CRC. Bioinformatics tools were used to select a promising tumor suppressor miRNA (mir-497-5p). Green route, using Fusarium oxyporium fungal species, manipulated for the synthesis of SPION@Ag@Cs nanocomposite as a carrier of miR-497-5p. That specifically targets the suppression of PD1/PDL1 and CTLA4pathways for colorectal therapy. UV/visible and FTIR spectroscopy, Zeta potential and MTT were used to confirm the allocation of the miR-497 on SPION@Ag@Cs and its cytotoxicity against CRC cell lines. Immunofluorescence was employed to confirm transfection of cells with miR-497@NPs, and the down- regulation of CTLA4 in HT29, and Caco2 cell lines. On the other hand, PDL1 showed a significant increase in colorectal cell lines (HT-29 and Caco-2) in response to mir497-5p@Nano treatment. The data suggest that the mir-497 -loaded SPION@Ag@Cs nano-formulation could be a good candidate for the suppression of CTLA4in CRC human cell lines. Consequently, the targeting miR-497/CTLA4 axis is a potential immunotherapy treatment strategy for CRC.