Implementation of a Technical Peer Review Process: Principles, Policy, and Cultural Change
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Alvarez, Francisco↗
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Weak baselines and reporting biases lead to overoptimism in machine learning for fluid-related partial differential equations
One of the most promising applications of machine learning in computational physics is to accelerate the solution of partial differential equations (PDEs). The key objective of machine-learning-based PDE solvers is to output a sufficiently accurate solution faster than standard numerical methods, which are used as a baseline comparison. Here, we first perform a systematic review of the ML-for-PDE-solving literature. Out of all of the articles that report using ML to solve a fluid-related PDE and claim to outperform a standard numerical method, we determine that 79% (60/76) make a comparison with a weak baseline. Second, we find evidence that reporting biases are widespread, especially outcome reporting and publication biases. We conclude that ML-for-PDE-solving research is overoptimistic: weak baselines lead to overly positive results, while reporting biases lead to under-reporting of negative results. To a large extent, these issues seem to be caused by factors similar to those of past reproducibility crises: researcher degrees of freedom and a bias towards positive results. We call for bottom-up cultural changes to minimize biased reporting as well as top-down structural reforms to reduce perverse incentives for doing so.
97 MATHEMATICS AND COMPUTING↗
Building and Sustaining a Community Resource for Best Practices in Scientific Software: The Story of BSSw.io
The development of scientific software—a cornerstone of long-term collaboration and scientific progress—parallels the development of other types of software but still poses distinct challenges, especially in high-performance computing. Although web searches yield numerous resources on software engineering, there is still a scarcity specifically for scientific software development. Here, this article introduces the Better Scientific Software site (https://bssw.io), a platform that hosts a community of researchers, developers, and practitioners who share their experiences and insights on scientific software development. Since 2017, this collaborative hub has gained traction within the scientific computing community, attracting a growing number of readers and contributors eager to share ideas and elevate their software development practices. In sharing the BSSw.io site’s story, we hope to encourage further growth of the BSSw.io community through both readership and contributors, with a long-term goal of fostering culture change by increasing emphasis on best practices in scientific software.
97 MATHEMATICS AND COMPUTING↗
Shifting institutional culture to develop climate solutions with Open Science
To address our climate emergency, “we must rapidly, radically reshape society”—Johnson & Wilkinson, All We Can Save. In science, reshaping requires formidable technical (cloud, coding, reproducibility) and cultural shifts (mindsets, hybrid collaboration, inclusion). We are a group of cross-government and academic scientists that are exploring better ways of working and not being too entrenched in our bureaucracies to do better science, support colleagues, and change the culture at our organizations. We share much-needed success stories and action for what we can all do to reshape science as part of the Open Science movement and 2023 Year of Open Science.
54 ENVIRONMENTAL SCIENCES↗
Gender in Mineral Names
Minerals are the fundamental constituents of Earth, and mineral names appear in scientific literature for disciplines including geology, chemistry, materials science, biology, and medicine, among others. Choosing a name is the full responsibility of the authors of new mineral proposals submitted to the International Mineralogical Association (IMA). Scientific nomenclature and its traditions have evolved over time and, consequently, mineral names track changes in the landscape of mineralogy with respect to language, technology, and culture. To evaluate these changes, the namesake information for all 5896 minerals approved by the IMA or ‘grandfathered’ into use as of December 2022 was recorded and categorized within a workable database. The compiled information yields diverse insights into the intersection of science and culture and could also be used to project future trends. In this study, we used the name database to investigate gender diversity among mineral eponyms. More than half (c. 54%) of all mineral species are named after people, the identities of whom are largely a reflection of the people that have historically been involved, in one way or another, in the geosciences and in the mining industry. Of the 2738 people with minerals named for them, approximately 6.1% are (interpreted to be) women. Nearly all minerals named for women were named during the last sixty years, although the rate of growth in the year-on-year percentage of women among new mineral namesakes has slowed since about 1985. If current and historical trends hold, our model predicts that women will not comprise more than about 10.35% of newly established mineral namesakes in future years. The representation of women among mineral namesakes also differs starkly among countries. For example, Russians comprise 43.11% of women with minerals named for them, but account for only 15.12% of all eponyms. However, there are additional disparities beyond the proportions of namesakes. For scientists who were alive when a mineral was named for them, women were an average of 3.74 years older than men when evaluated over the same timespan (1954–2022). These results demonstrate that gender-based disparities are imprinted into current mineral nomenclature and indicate that gender parity among new mineral namesakes is impossible without unprecedented changes in the upstream demographics that are most likely to affect naming trends.
58 GEOSCIENCES↗
YAP1 Dysfunction Promotes Molecular Properties Linked to Breast Cancer Susceptibility
YAP1 is a cotranscription factor that promotes malignant and stem cell properties in cancer. We previously found that YAP1 dysregulation is associated with aging in human mammary epithelia. With increased age, YAP1 expression changes in luminal epithelial cells, the prospective breast cancer cell of origin. Because age is a significant risk factor for breast cancer, we tested whether YAP1 dysregulation acted early in cancer progression by conferring cellular states associated with increased cancer susceptibility. In this study, we find that with increased age and genetic risk for developing cancer, human breast tissues showed significantly increased YAP1 expression, and cultured primary human mammary epithelial cells (HMEC) showed significantly increased expression of both YAP1 and its transcriptional targets. Increased YAP1 expression in cultured HMEC induced gene expression changes associated with increased cancer susceptibility, such as genes associated with stem cell states, increased telomerase activity, breast cancer progression, and increased age and genetic breast cancer risk. Furthermore, overexpression of YAP1 in post-stasis HMEC—finite lifespan cells that have bypassed a retinoblastoma-mediated senescence barrier—promoted properties related to increased growth potential. We found that YAP1 dysregulation in finite epithelial cells allows for access to gene programs and functions that are typically thought to be restricted to stem cells. We hypothesize that YAP1 acts early in breast cancer progression, long before the development of a tumor, to impose cancer-susceptible molecular states.
YAP1↗
Uncertain Pathways to a Future Safe Climate
Abstract Global climate change is often thought of as a steady and approximately predictable physical response to increasing forcings, which then requires commensurate adaptation. But adaptation has practical, cultural and biological limits, and climate change may pose unanticipated global hazards, sudden changes or other surprises–as may societal adaptation and mitigation responses. These poorly known factors could substantially affect the urgency of mitigation as well as adaptation decisions. We outline a strategy for better accommodating these challenges by making climate science more integrative, in order to identify and quantify known and novel physical risks including those arising from interactions with ecosystems and society. We need to do this even–or especially–when they are highly uncertain, and to explore risks and opportunities associated with mitigation and adaptation responses by engaging across disciplines. We argue that upcoming climate assessments need to be more risk‐aware, and suggest ways of achieving this. These strategies improve the chances of anticipating potential surprises and identifying and communicating “safe landing” pathways that meet UN Sustainable Development Goals and guide humanity toward a better future.
Sherwood, S. C.↗
Sac1 links phosphoinositide turnover to cryptococcal virulence
Cryptococcus neoformans is an environmentally acquired fungal pathogen that causes over 140,000 deaths per year. Cryptococcal infection occurs when infectious particles are deposited into the lung, where they encounter host phagocytic cells. C. neoformans may be engulfed by these phagocytes, an important step of infection that leads to outcomes ranging from termination of infection to cryptococcal dissemination. To study this critical process, we screened approximately 4,700 cryptococcal gene deletion mutants for altered uptake, using primary mouse and human phagocytic cells. Among the hits of these two screens, we identified 93 mutants with perturbed uptake in both systems, as well as others with differences in uptake by only one cell type. We further screened the hits for changes in thickness of the capsule, a protective polysaccharide layer around the cell which is an important cryptococcal virulence factor. The combination of our three screens yielded 45 mutants, including one lacking the phosphatidylinositol-4-phosphate phosphatase Sac1. In this work, we implicate Sac1 in both host cell uptake and capsule production. We found that sac1 mutants exhibit lipid trafficking defects, reductions in secretory system function, and changes in capsule size and composition. Many of these changes occur specifically in tissue culture media, highlighting the role of Sac1 phosphatase activity in responding to the stress of host-like conditions. Overall, these findings show how genome-scale screening can identify cellular factors that contribute to our understanding of cryptococcal biology and demonstrate the role of Sac1 in determining fungal virulence.
59 BASIC BIOLOGICAL SCIENCES↗
Molecular Imaging of Microbially Induced Corrosion of Synthetic Archeological Glasses by a Rhizosphere Bacterium
Microbially induced corrosion (MIC) focuses on the degradation of solid materials, such as glass or metal. Soil microbes are often associated with the corrosion of foreign objects in the rhizosphere. Paenibacillus polymyxa SCE2, a facultative anaerobic bacterium in soil, is of the same genus as bacteria found near nuclear waste disposal sites. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used for imaging surface changes induced by P. polymyxa SCE2 cultured on two synthetic glass coupons to represent natural analogs of materials that were studied in relation to the vitrification of nuclear waste. Multimodal imaging was used to verify bacterial coverage across the glass surface after long-term growth. ToF-SIMS spectral analysis showed detection of glass component ions, such as silicon oxide (m/z – 59.96 SiO 2 – ) and aluminum oxide (m/z – 101.95 Al 2 O 3 – ), and biofilm’s extracellular polymeric substance (EPS) components, such as pentadecanoic acid (m/z – 241.22 C 15 H 29 O 2 – ) and sterol lipids (m/z – 311.16 C 20 H 23 O 3 – ). ToF-SIMS spectral, imaging, and depth profiling analyses showed that the glass rich in silica and other light elements (“granite glass”) had more “corrosion related” peaks than the glass that was less silica-rich and contained more iron (“dike glass”). Furthermore, these surface and interface compositional and spatial differences observed in the mass spectra and imaging were attributed to bacterial metabolism and an electron transfer mechanism influenced by morphological and compositional differences between the two types of glasses. ToF-SIMS is effective in studying microbial effects, bringing new molecular insights into MIC in a broader context of materials degradation.
Amorphous materials↗
Assessment of the Effect of Deleting the African Swine Fever Virus Gene R298L on Virus Replication and Virulence of the Georgia2010 Isolate
African swine fever (ASF) is a lethal disease of domestic pigs that is currently challenging swine production in large areas of Eurasia. The causative agent, ASF virus (ASFV), is a large, double-stranded and structurally complex virus. The ASFV genome encodes for more than 160 proteins; however, the functions of most of these proteins are still in the process of being characterized. The ASF gene R298L, which has previously been characterized as able to encode a functional serine protein kinase, is expressed late in the virus infection cycle and may be part of the virus particle. There is no description of the importance of the R298L gene in basic virus functions such as replication or virulence in the natural host. Based on its evolution, it is proposed that there are four different phenotypes of R298L of ASFV in nature, which may have potential implications for R298L functionality. We report here that a recombinant virus lacking the R298L gene in the Georgia 2010 isolate, ASFV-G-∆R298L, does not exhibit significant changes in its replication in primary cultures of swine macrophages. In addition, when experimentally inoculated in pigs, ASFV-G-∆R298L induced a fatal form of the disease similar to that caused by the parental virulent ASFV-G. Therefore, deletion of R298L does not significantly affect virus replication and virulence in domestic pigs of the ASFV Georgia 2010 isolate.
Virology↗
Optimized Illuminance Operation-A Light-Driven Dilution Strategy to Improve Microalgae Biomass Productivity
Periodic dilution is a necessary operation to avoid light limitation due to self-shading as the culture grows dense. However, environmental conditions are constantly changing in outdoor cultivation systems, making it difficult to determine the optimal dilution rate. To address this challenge, this study evaluated a dilution approach based on light penetration to optimize illuminance (OptiLum) in the culture. Biomass concentration was controlled via sensor-feedback directed dilution to ensure that light reaching the bottom of the culture was maintained above the compensation intensity. Under replicated outdoor pond conditions, by keeping the entire culture within a net-positive photosynthetic zone, the OptiLum operation improved the biomass productivities of two top-performing strains, Picochlorum celeri and Tetraselmis striata, by 95 % and 86 %, respectively, compared to conventional semi-continuous batch cultivation. The dilution rate varied daily and was dynamically adjusted based on the light status within the culture, which is concurrently influenced by weather, culture density, and growth rate. The techno-economic analysis showed that the OptiLum operation could reduce biomass production cost by as much as 24 % and 33 % for P. celeri and T. striata, respectively, assuming a low-cost dewatering approach with initial gravity settling of biomass can be realized for both strains. However, a more costly two-stage dewatering strategy, comprising only membranes and centrifuges, may be necessary for non-settling strains, such as P. celeri, which would alternatively increase production costs by 23 % for the OptiLum case. The results demonstrated that the proposed OptiLum operation is a promising approach to improve biomass productivity and lower production cost via weather-responsive and self-adjusting dilution.
09 BIOMASS FUELS↗
Women in Nuclear Security: The United Arab Emirates Story
Historically in the United Arab Emirates, security personnel stationed at nuclear sites were typically men with military or policing backgrounds. Although these groups bring important, transferrable skills and experience to the nuclear security mission, some Emirati stakeholders recognize the increased benefit of a greater diversity of voices and backgrounds within the nuclear security team hierarchy. By recruiting from a wider range of disciplines and encouraging gender diversity, the security team could develop broader insight into security challenges, and a greater variety of perspectives could bring forth more innovative solutions. When aligning a diverse, multinational workforce with a common mission, all members of a security organization must fundamentally change their individual approaches to the work; the entire staff must be on the same page. This can be particularly challenging for some people who find it difficult to transition from a framework of beliefs because of past experiences based on prescriptive, exclusionary, hierarchical thought. Also, national cultural values are learned early, held deeply, and change slowly over the course of generations, and inherent biases rooted in these values can create barriers to the collective progress of a team. Creating a more open, diverse, and transparent culture for the team by accepting a unique, egalitarian, professional nuclear security culture that all members adhere to can be a challenging task for some. In this article, I share my experiences related to professional roadblocks, personal challenges, and lessons learned, particularly those regarding the empowerment of women in science and engineering, while developing and establishing the United Arab Emirates nuclear security program. I also discuss the support (and underrepresentation) of women, including those currently in critical leadership positions, and their careers in nuclear security.
Barakah Nuclear Power Plant↗
Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation
ABSTRACT Mycobacterium tuberculosis(Mtb) is the causative agent of tuberculosis (TB), the leading cause of infectious disease-related deaths worldwide. TB infections present on a spectrum from active to latent disease. In the human host,Mtbfaces hostile environments, such as nutrient deprivation, hypoxia, and low pH. Under these conditions,Mtbcan enter a dormant, but viable, state characterized by a lack of cell replication and increased resistance to antibiotics. DormantMtbposes a major challenge to curing infections and eradicating TB globally. We subjectedMtbmc 2 6020 (ΔlysAand ΔpanCD), a double auxotrophic strain, to carbon starvation (CS), a culture condition that induces growth stasis and mimics environmental conditions associated with dormancyin vivo. We provide a detailed analysis of the proteome in CS compared to replicating samples. We observed extensive proteomic reprogramming, with 36% of identified proteins significantly altered in CS. Many enzymes involved in oxidative phosphorylation and lipid metabolism were retained or more abundant in CS. The cell wall biosynthetic machinery was present in CS, although numerous changes in the abundance of peptidoglycan, arabinogalactan, and mycolic acid biosynthetic enzymes likely result in pronounced remodeling of the cell wall. Many clinically approved anti-TB drugs target cell wall biosynthesis, and we found that these enzymes were largely retained in CS. Lastly, we compared our results to those of other dormancy models and propose that CS produces a physiologically distinct state of stasis compared to hypoxia inMtb. IMPORTANCE Tuberculosis is a devastating human disease that kills over 1.2 million people a year. This disease is caused by the bacterial pathogenMycobacterium tuberculosis(Mtb).Mtbexcels at surviving in the human host by entering a non-replicating, dormant state. The current work investigated the proteomic changes thatMtbundergoes in response to carbon starvation, a culture condition that models dormancy. The authors found broad effects of carbon starvation on the proteome, with the relative abundance of 37% of proteins significantly altered. Protein changes related to cell wall biosynthesis, metabolism, and drug susceptibility are discussed. Proteins associated with a carbon starvation phenotype are identified, and results are compared to other dormancy models, including hypoxia.
Microbiology↗
Direct effects of prolonged TNF-α and IL-6 exposure on neural activity in human iPSC-derived neuron-astrocyte co-cultures
Cognitive impairment is one of the many symptoms reported by individuals suffering from long-COVID and other post-viral infection disorders such as myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). A common factor among these conditions is a sustained immune response and increased levels of inflammatory cytokines. Tumor necrosis factor alpha (TNF-α) and interleukin-6 (IL-6) are two such cytokines that are elevated in patients diagnosed with long-COVID and ME/CFS. In this study, we characterized the changes in neural functionality, secreted cytokine profiles, and gene expression in co-cultures of human iPSC-derived neurons and primary astrocytes in response to prolonged exposure to TNF-α and IL-6. We found that exposure to TNF-α produced both a concentration-independent and concentration-dependent response in neural activity. Burst duration was significantly reduced within a few days of exposure regardless of concentration (1 pg/mL – 100 ng/mL) but returned to baseline after 7 days. Treatment with low concentrations of TNF-α (e.g., 1 and 25 pg/mL) did not lead to changes in the secreted cytokine profile or gene expression but still resulted in significant changes to electrophysiological features such as interspike interval and burst duration. Conversely, treatment with high concentrations of TNF-α (e.g., 10 and 100 ng/mL) led to reduced spiking activity, which may be correlated to changes in neural health, gene expression, and increases in inflammatory cytokine secretion (e.g., IL-1β, IL-4, and CXCL-10) that were observed at higher TNF-α concentrations. Prolonged exposure to IL-6 led to changes in bursting features, with significant reduction in the number of spikes in bursts across a wide range of treatment concentrations (i.e., 1 pg/mL–10 ng/mL). In combination, the addition of IL-6 appears to counteract the changes to neural function induced by low concentrations of TNF-α, while at high concentrations of TNF-α the addition of IL-6 had little to no effect. Conversely, the changes to electrophysiological features induced by IL-6 were lost when the cultures were co-stimulated with TNF-α regardless of the concentration, suggesting that TNF-α may play a more pronounced role in altering neural function. These results indicate that increased concentrations of key inflammatory cytokines associated with long-COVID can directly impact neural function and may be a component of the cognitive impairment associated with long-COVID and other post-viral infection disorders.
60 APPLIED LIFE SCIENCES↗
Modernizing the Nuclear Industry and New Ways of Working
Nuclear energy is recognized as the most feasible energy source towards achieving nation-wide net-zero goals (COP 208, MIT). Additionally, the demand for reliable, consistent energy supply is soaring with the construction of energy hungry data centers and AI tools. This means the construction of new nuclear and the continuation of current nuclear are a high national priority. However, this leaves the nuclear industry with a workforce challenge. The rising demand for nuclear power is threatened by an underpopulated workforce. There exist a few contributors to the decreased workforce such as skewed workforce demographics resulting in large-scale workforce retirement. Also, some plants have observed difficulty hiring and retaining skill sets that typically comprise the nuclear power workforce – specifically skilled craftsman. Those who are graduating with desirable skills are seeking employment in sectors that are more modern and culturally more aligned with younger generational values. Lastly, within the nuclear sector, skilled employees will be a competitive commodity as advanced plants come online offering work environments that incorporate modern technologies, skill sets, and opportunities for career advancement. These factors emphasize the need for legacy plants to modernize with a focus on the workplace environment and culture that meets younger generations’ skills, cultural expectations, and desire for advancement opportunities. Nuclear plants are actively engaged in deploying advancements that improve the management of systems, structures, and components as well as process improvements and technologies that can reduce the costs of operation and maintenance. However, the advancements must also be analyzed, reviewed and deployed in a manner that considers the impact on how people within the organization collaborate, communicate, make decisions, and solve problems. Neglecting to consider the cultural impact of modernization risks poor adoption, unrealized opportunities, or insignificant change toward helping attract new employees. The traditional way of working is not necessarily the way new generations want to engage with their employer. For instance, in a survey performed by North American Young Generation in Nuclear the top three reasons for younger nuclear employees to seek other job opportunities was seeking better work-life balance, a lack of advancement opportunities, and work culture and leadership style differences (Smyth et al. 2022). Integrated Operations for Nuclear (ION) is an approach for the nuclear industry to create long-term strategic modernization plans and analyze each advancement for the impact on people and processes and measure how those impacts flow up to support high-level, long-term plant goals and requirements. One principle of ION is to replace the current labor-centric operation style in legacy nuclear plants with data-centric collaborative operation styles. This paper will explain how transitioning operations to leverage centralized skills and responsibility, multi-skilled teams, and collaborative decision making can flatten the hierarchical structure in plants, enable greater individual efficacy while also offering more experiences and advancement opportunities to staff. Adopting the ION way of working shifts the industry mind-set towards more networked, collaborative, and modern way of working that will attract skilled, next-generation workers to operate the legacy nuclear fleet.
99 - GENERAL AND MISCELLANEOUS↗
Purple non-sulfur bacteria for biotechnological applications
Abstract In this review, we focus on how purple non-sulfur bacteria can be leveraged for sustainable bioproduction to support the circular economy. We discuss the state of the field with respect to the use of purple bacteria for energy production, their role in wastewater treatment, as a fertilizer, and as a chassis for bioplastic production. We explore their ability to serve as single-cell protein and production platforms for fine chemicals from waste materials. We also introduce more Avant-Garde technologies that leverage the unique metabolisms of purple bacteria, including microbial electrosynthesis and co-culture. These technologies will be pivotal in our efforts to mitigate climate change and circularize the economy in the next two decades. One-sentence summary Purple non-sulfur bacteria are utilized for a range of biotechnological applications, including the production of bio-energy, single cell protein, fertilizer, bioplastics, fine chemicals, in wastewater treatment and in novel applications like co-cultures and microbial electrosynthesis.
Morrison, Hailee M. (ORCID:0000000225121824)↗
Impact of salinity on morphology, growth, and pigment profiles of Scenedesmus obliquus HTB1 under ambient air and elevated CO 2 (10 %) conditions
Certain microalgal species, such as Scenedesmus obliquus strain HTB1, thrive under high CO 2 concentrations, making them promising for carbon sequestration to mitigate climate change. Isolated from the Baltimore Inner Harbor, HTB1 grows faster with 10 % CO 2 than with ambient air. To investigate its responses to salinity and elevated CO 2 , two experiments were conducted. In the first, HTB1 was cultured at seven different salinities (0, 17.5, 20, 22.5, 25, 27.5, and 30 ppt) (parts per thousand) under ambient air. Higher salinity caused cell shrinkage, color changes from green to pale white, reduced pigments like zeaxanthin, lutein, and chlorophyll b, but increased canthaxanthin. Growth declined significantly above 22.5 ppt. The second experiment compared HTB1's response to salinity (0, 10, 20 ppt) under air and 10 % CO 2 . Cultures under 10 % CO 2 showed minimal color changes, while those under air shifted from green to brown, with salinity having less inhibitory effects on growth under elevated CO 2 . Interestingly, lutein and canthaxanthin levels rose with salinity in 10 % CO 2 . These findings indicate that elevated CO 2 mitigates salt stress in HTB1, reducing its impact on growth and promoting adaptive pigment changes. This study sheds light on how salinity and CO 2 interact to influence HTB1's morphology, growth, and pigment composition, enhancing our understanding of its resilience and potential applications.
20 FOSSIL-FUELED POWER PLANTS↗
Hepatocellular Metabolic Profile: Understanding Post-Thawing Metabolic Shift in Primary Hepatocytes In Vitro
Primary human hepatocytes (PHHs) are widely used as in vitro models for liver function and drug metabolism studies, yet their metabolic stability post-thawing remains an open question. To better characterize early metabolic changes, we conducted a time-course experiment using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze metabolic shifts in PHHs cultured in suspension. Unexposed and exposed (acetaminophen-treated) samples were evaluated, and TITAN analysis was applied to determine the time point of maximal metabolic change at both individual metabolite and global metabolic profile levels. Our results indicate that the majority of metabolic shifts occur within the first five hours post-thawing. In the early culture time points, substantial metabolic overlap was observed between unexposed and exposed cells, suggesting a conserved biological response likely related to cellular recovery. However, at later time points, metabolite profiles diverged, with acetaminophen treatment-specific metabolic changes emerging, potentially reflecting differences in homeostatic restoration versus hepatotoxic responses. Our study highlights the importance of considering early post-thawing metabolic dynamics in experimental design and offers insights for optimizing hepatocyte culture protocols to better replicate in vivo physiological conditions.
59 BASIC BIOLOGICAL SCIENCES↗