Browse Articles

Is Ockham’s razor losing its edge? New perspectives on the principle of model parsimony

The preference for simple explanations, known as the parsimony principle, has long guided the development of scientific theories, hypotheses, and models. Yet recent years have seen a number of successes in employing highly complex models for scientific inquiry (e.g., for 3D protein folding or climate forecasting). In this paper, we reexamine the parsimony principle in light of these scientific and technological advancements. We review recent developments, including the surprising benefits of modeling with more parameters than data, the increasing appreciation of the context-sensitivity of data and misspecification of scientific models, and the development of new modeling tools. By integrating these insights, we reassess the utility of parsimony as a proxy for desirable model traits, such as predictive accuracy, interpretability, effectiveness in guiding new research, and resource efficiency. We conclude that more complex models are sometimes essential for scientific progress, and discuss the ways in which parsimony and complexity can play complementary roles in scientific modeling practice.

The unskilled-and-unaware problem and performance feedback in monotonous, easily accustomed, and repetitive work

Abstract The current research examined whether people predict their performance on monotonous, easily accustomed, and repetitive (MEAR) tasks accurately and confirm the effects of performance feedback on their MEAR work predictions. Considering typing on the keyboard as an MEAR task in modern society, 128 university students were asked to type a 12-digit number displayed on each monitor within 5 minutes, explaining that there would be 75 typing problems and participants would receive 20 yen per correct answer. Additionally, participants were informed that they could earn money by reaching a self-determined performance target, with the condition that if they did not reach their self-set goal, they would not receive any earnings. The main findings were as follows: Regardless of the performance levels of typing on keyboards, only 23% of the participants reached the goal, indicating that the absence of performance feedback led to individuals’ overestimation of performance. In contrast, providing feedback significantly improved performance predictions: 76% of the participants reached the goal with feedback on their own performance, 70% with feedback on others’ performance, and 88% with feedback on both their own and others’ performance information. Specifically, the effects between one’s own and others’ performance feedback did not vary at statistically significant levels.

Fatty acid metabolism and the oxidative stress response support bacterial predation

Despite growing awareness of their importance in soil ecology, the genetic and physiological traits of bacterial predators are still relatively poorly understood. In the course of a Myxococcus xanthus predator evolution experiment, we identified a class of genotypes leading to enhanced predation against diverse species. RNA-seq analysis demonstrated that this phenotype is linked to the constitutive activation of a predation-specific program. Functional analysis of the mutations accumulated across the evolutionary time in a two-component system and Acyl-CoA-manipulating enzymes revealed the critical roles of fatty acid metabolism and antioxidant gene induction. The former likely adapts the predator to metabolites derived from the prey while the latter protects predatory cells from reactive oxygen species generated by prey cells under stress and released upon lysis during predation. These findings reveal interesting parallels between bacterial predator–prey dynamics and pathogen–host cell interactions.

Yiqi Juanshen decoction alleviates renal interstitial fibrosis by targeting the LOXL2/PI3K/AKT pathway to suppress EMT and inflammation

The present and future of peer review: Ideas, interventions, and evidence

What is wrong with the peer review system? Is peer review sustainable? Useful? What other models exist? These are central yet contentious questions in today’s academic discourse. This perspective critically discusses alternative models and revisions to the peer review system. The authors highlight possible changes to the peer review system, with the goal of fostering further dialog among the main stakeholders, including producers and consumers of scientific research. Neither our list of identified issues with the peer review system nor our discussed resolutions are complete. A point of agreement is that fair assessment and efficient change would require more comprehensive and rigorous data on the various aspects of the peer review system.

Study of evolution for 3D structured surface with nano-balls and walls-like features with thickness variation for WO3 thin films made by spray deposition

Dialogues about the practice of science

Integrating radiological and clinical data for clinically significant prostate cancer detection with machine learning techniques

Discourse on measurement

Measurement literacy is required for strong scientific reasoning, effective experimental design, conceptual and empirical validation of measurement quantities, and the intelligible interpretation of error in theory construction. This discourse examines how issues in measurement are posed and resolved and addresses potential misunderstandings. Examples drawn from across the sciences are used to show that measurement literacy promotes the goals of scientific discourse and provides the necessary foundation for carving out perspectives and carrying out interventions in science.

Author Correction: Short tandem repeats delineate gene bodies across eukaryotes

Benefits of Gardenia jasminoides Ellis’s floral volatile components on human emotions and moods

PgpP is a broadly conserved phosphatase required for phosphatidylglycerol lipid synthesis

The cytoplasmic membrane of bacteria is composed of a phospholipid bilayer made up of a diverse set of lipids. Phosphatidylglycerol (PG) is one of the principal constituents and its production is essential for growth in many bacteria. All the enzymes required for PG biogenesis in Escherichia coli have been identified and characterized decades ago. However, it has remained poorly understood how gram-positive bacteria perform the terminal step in the pathway that produces this essential lipid. In E. coli, this reaction is mediated by three functionally redundant phosphatases that convert phosphatidylglycerophosphate (PGP) into PG. Here, we show that homologs of these enzymes in Bacillus subtilis are not required for PG synthesis. Instead, we identified a previously uncharacterized B. subtilis protein, YqeG (renamed PgpP), as an essential enzyme required for the conversion of PGP into PG. Expression of B. subtilis or Staphylococcus aureus PgpP in E. coli lacking all three Pgp enzymes supported the growth of the strain. Furthermore, depletion of PgpP in B. subtilis led to growth arrest, reduced membrane lipid staining, and accumulation of PGP. PgpP is broadly conserved among Firmicutes and Cyanobacteria. Homologs are also present in yeast mitochondria and plant chloroplasts, suggesting that this widely distributed enzyme has an ancient origin. Finally, evidence suggests that PgpP homologs are essential in many gram-positive pathogens and thus the enzyme represents an attractive target for antibiotic development.

Cooperative mechanisms of oxide ion conduction in tellurites with secondary bond interactions and Grotthuss-like processes

Abstract Oxide-ion conducting materials are gaining considerable attention in various applications ranging from oxide fuel cells to oxygen permeation membranes. The oxide ion migration mechanisms are the basis for designing oxide-ion conducting materials. Here, enlightened by proton diffusion in hydrogen-bond networks, we report the coordination polyhedra cooperative mechanism with similar Grotthuss process of oxide ion migration in tellurites. Bi2Te2O7 and Bi2Te4O11 were selected due to their abundance of secondary bonds similar to hydrogen bonds and show high oxide ionic conductivity as mixed electronic and ionic conductors. Neutron total scattering experiments with reverse Monte Carlo simulations indicated that the oxide ion migration in those two tellurites is a synergetic effect of mutual transition between Te-O secondary bonds and covalent bonds assisted by Te-O polyhedra rotation. This detailed investigation of the cooperative mechanism with similar Grotthuss process at the atomic scale provides a direction for optimization and discovering oxide ion conducting materials.

A novel aggregated coefficient ranking based feature selection strategy for enhancing the diagnosis of breast cancer classification using machine learning

Abstract Effective Breast cancer (BC) analysis is crucial for early prognosis, controlling cancer recurrence, timely medical intervention, and determining appropriate treatment procedures. Additionally, it plays a significant role in optimizing mortality rates among women with breast cancer and increasing the average lifespan of patients. This can be achieved by performing effective critical feature analysis of the BC by picking superlative features through significant ranking-based Feature Selection (FS). Various authors have developed strategies relying on single FS, but this approach may not yield excellent results and could lead to various consequences, including time and storage complexity issues, inaccurate results, poor decision-making, and difficult interpretation of models. Therefore, critical data analysis can facilitate the development of a robust ranking methodology for effective feature selection. To solve these problems, this paper suggests a new method called Aggregated Coefficient Ranking-based Feature Selection (ACRFS), which is based on tri chracteristic behavioral criteria. This strategy aims to significantly improve the ranking for an effective Attribute Subset Selection (ASSS). The proposed method utilized computational problem solvers such as chi-square, mutual information, correlation, and rank-dense methods. The work implemented the introduced methodology using Wisconsin-based breast cancer data and applied the Synthetic Minority Oversampling Technique (SMOTE) to the obtained data subset. Later, we employed models such as decision trees, support vector machines, k-nearest neighbors, random forests, stochastic gradient descent, and Gaussian naive bayes to determine the type of cancer. The classification metrics such as accuracy, precision, recall, F1 score, kappa score, and Matthews coefficient were utilized to evaluate the effectiveness of the suggested ACRFS approach. The proposed method has demonstrated superior outcomes with fewer features and a minimal time complexity.

Bubble coalescence principle in saline water

Bubbles present in saline water typically exhibit a prolonged lifetime, making them attractive for various engineering processes. Herein, we unveil a transition from delayed bubble coalescence to rapid bursting within about one millisecond in salty solutions. The key aspect in understanding this transition lies in the combined influences of surface deformation and ion surface excess instead of characterizing the ions alone. Only with a sufficiently deformed region trapped between the colliding bubble and fluid surfaces can the coalescence inhibition effect be maintained to cause the bouncing behavior. Thus, we quantify a consistent upper limit of ion transfer content required for instant coalescence under different salty conditions. Furthermore, we present numerical ranges associated with different bubble behaviors in terms of E o , R e , and W e and determine the critical values to predict bubble dynamics. Our findings shed light on the bubble coalescence principle in saline water and allow access to the regulation of coalescence time based on the requirement of technological applications.

Lipoic acid-boronophenylalanine-derived multifunctional vesicles for cancer chemoradiotherapy

Sphingosine kinase 1 promotes M2 macrophage infiltration and enhances glioma cell migration via the JAK2/STAT3 pathway

Discrete coordination nanochains based on photoluminescent dyes reveal intrachain exciton migration dynamics

First detection and phylogenetic analysis of Trypanosoma species in European wolves and bears: discovery of novel haplotypes

The misalignment of incentives in academic publishing and implications for journal reform

For most researchers, academic publishing serves two goals that are often misaligned—knowledge dissemination and establishing scientific credentials. While both goals can encourage research with significant depth and scope, the latter can also pressure scholars to maximize publication metrics. Commercial publishing companies have capitalized on the centrality of publishing to the scientific enterprises of knowledge dissemination and academic recognition to extract large profits from academia by leveraging unpaid services from reviewers, creating financial barriers to research dissemination, and imposing substantial fees for open access. We present a set of perspectives exploring alternative models for communicating and disseminating scientific research. Acknowledging that the success of new publishing models depends on their impact on existing approaches for assigning academic credit that often prioritize prestigious publications and metrics such as citations and impact factors, we also provide various viewpoints on reforming academic evaluation.