The Logic of Generalization From Systematic Reviews and Meta-Analyses of Impact Evaluations

Systematic reviews and meta-analyses are viewed as potent tools for generalized causal inference. These reviews are routinely used to inform decision makers about expected effects of interventions. However, the logic of generalization from research reviews to diverse policy and practice contexts is not well developed. Building on sampling theory, concerns about epistemic uncertainty, and principles of generalized causal inference, this article presents a pragmatic approach to generalizability assessment for use with systematic reviews and meta-analyses. This approach is applied to two systematic reviews and meta-analyses of effects of "evidence-based" psychosocial interventions for youth and families. Evaluations included in systematic reviews are not necessarily representative of populations and treatments of interest. Generalizability of results is limited by high risks of bias, uncertain estimates, and insufficient descriptive data from impact evaluations. Systematic reviews and meta-analyses can be used to test generalizability claims, explore heterogeneity, and identify potential moderators of effects. These reviews can also produce pooled estimates that are not representative of any larger sets of studies, programs, or people. Further work is needed to improve the conduct and reporting of impact evaluations and systematic reviews, and to develop practical approaches to generalizability assessment and guide applications of interventions in diverse policy and practice contexts.

An investigation of the effect of logical structures on Chinese preschool children's counterfactual reasoning development

Counterfactual reasoning helps people to learn from the past to prepare for the future. In contrast to English with counterfactual markers that directly signal counterfactual reasoning, Mandarin Chinese indicates counterfactual reasoning by counterfactuality enhancers, which enhance rather than directly signal entry into the counterfactual realm. There are more counterfactuality enhancers in subtractive than additive counterfactual premises. Hence, Chinese-speaking children might more readily interpret subtractive than additive counterfactual premises, leading to better performance on subtractive than additive counterfactual reasoning tasks. This difference between logical structures might be larger in Chinese than English, as English has counterfactual markers, which enable direct inference of counterfactuality regardless of logical structures. Consistent with these propositions, in two experiments, the present study found that Chinese preschool children's accuracy was significantly higher for subtractive than additive counterfactual reasoning. Also, the difference between logical structures was much larger compared to a previous study in UK children using a similar counterfactual reasoning task. Hence, the use of counterfactuality enhancers in Chinese might shape a developmental difference between subtractive and additive counterfactual reasoning. Parents and teachers may attend to this developmental pattern when scaffolding children's counterfactual reasoning growth.

DNA Logic Gates Integrated on DNA Substrates in Molecular Computing

Due to nucleic acid's programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. Pioneered by Milan Stojanovic, Boolean DNA logic gates created the foundation for the development of DNA computers. Similar to electronic computers, the field is evolving towards integrating DNA logic gates and circuits by positioning them on substrates to increase circuit density and minimize gate distance and undesired crosstalk. In this minireview, we summarize recent developments in the integration of DNA logic gates into circuits localized on DNA substrates. This approach of all-DNA integrated circuits (DNA ICs) offers the advantages of biocompatibility, increased circuit response, increased circuit density, reduced unit concentration, facilitated circuit isolation, and facilitated cell uptake. DNA ICs can face similar challenges as their equivalent circuits operating in bulk solution (bulk circuits), and new physical challenges inherent in spatial localization. We discuss possible avenues to overcome these obstacles.

Governing principles of transcriptional logic out of equilibrium

To survive, adapt, and develop, cells respond to external and internal stimuli by tightly regulating transcription. Transcriptional regulation involves the combinatorial binding of a repertoire of transcription factors to DNA, which often results in switch-like binary outputs akin to Boolean logic gates. Recent experimental studies have demonstrated that in eukaryotes, transcription factor binding to DNA often involves energy expenditure, thereby driving the system out of equilibrium. The governing principles of transcriptional logic operations out of equilibrium remain unexplored. Here, we employ a simple two-input, single-locus model of transcription that can accommodate both equilibrium and nonequilibrium mechanisms. Using this model, we find that nonequilibrium regimes can give rise to all the logic operations accessible in equilibrium. Strikingly, energy expenditure alters the regulatory function of the two transcription factors in a mutually exclusive manner. This allows for the emergence of new logic operations that are inaccessible in equilibrium. Overall, our results show that energy expenditure can expand the range of cellular decision-making without the need for more complex promoter architectures.

Exploring the decision-making process of female genital cosmetic procedures in Iranian women and constructing and validating a results-based logic model for a healthy public policy: a study protocol

BACKGROUND

Female genital cosmetic procedures have grown rapidly in most parts of the world. Professional organizations have issued warnings about the complications and long-term consequences of these practices. To be able to adopt the right health policies, it is necessary to know why women decide to perform these procedures. Therefore, the present study will be aim to discover the decision-making process involved in performing female genital cosmetic procedures for Iranian women and construct and validate a results-based logic model for healthy public policy.

METHODS

The present study was conducted in three phases. In the initial phase, a qualitative study will be conducted with the Corbin and Strauss ground theory approach. The participants in the study will be healthy women who desire or have undergone female genital cosmetic procedures without medical indications. In this phase, purposive and theoretical sampling will guide recruitment and data collection. The data will be collected via semi-structured interviews, field notes and observations of individual interactions. The data will be analysed using the approach of Corbin and Strauss (2015). MAXQDA 2007 software was used for managing the process of data analysis. In the second phase, the development of a results-based logic model for a healthy public policy is performed based on the findings of the first phase of the study, interviews with key informants and a review of the results of the literature in this field. Finally, validation of the designed program will be performed by the nominal group technique with the presence of a group of experts in the third phase.

DISCUSSION

The findings of this study, by identifying women's main concerns related to the studied phenomenon, the existing context, participants' reactions and the consequences of the adopted reactions, can be very important in designing a program that fits Iran's cultural characteristics. In this research, a program using a logical model will be presented that is suitable for policymakers, planners and healthcare service providers to be implemented in the social-cultural context of the study.

Latent Toehold-Mediated DNA Circuits Based on a Bulge-Loop Structure for Leakage Reduction and Its Application to Signal-Amplifying DNA Logic Gates

DNA circuits based on successive toehold-mediated DNA displacement reactions, particularly entropy-driven DNA circuit (EDC) systems, have attracted considerable attention as powerful enzyme-free tools for dynamic DNA nanotechnology. However, background leakage (noise signal) often occurs when the circuit is executed nonspecifically, even in the absence of the appropriate catalyst DNA (input). This study designed and developed a new latent toehold-mediated DNA circuit (LDC) system that relies on a bulge-loop structure as a latent toehold toward leakage reduction. Furthermore, the number (size) of nucleotides (nt) in the bulge-loop is found to play a significant role in the performance (i.e., leakage, signal, and kinetics) of LDC systems. In fact, the signal rate for the LDC systems increased as the number of nt in the bulge-loop increased from 4 to 8, whereas the leakage rate of the LDC systems with bulge-loops of 7 nt or less was low, but the leakage rate of the LDC system with a bulge-loop of 8 nt increased significantly. Note that the LDC system with the optimal bulge-loop (7 nt) was capable of not only reducing the leakage but also accelerating the circuit speed without any signal loss, unlike methods of reducing the leakage by reducing the signal reported previously for the conventional EDC systems. These facts indicate that the 7 nt bulge-loop acts as a "latent" toehold for the DNA circuit system. By using the amplification function of output signals with an accelerated circuit and reduced leakage, our LDC system with a 7 nt bulge-loop could be applied directly and successfully to signal-amplifying DNA logic gates such as OR and AND gates, and thus, sufficient output signals could be obtained even with a small amount of input. These findings reveal that our LDC systems with a bulge-loop structure can replace the conventional EDC system and have enormous potential in the field of DNA nanotechnology.

The effect of decisional styles on logic and belief

Classical theories of reasoning equate System 1 with biases and System 2 with correct responses. Refined theories of reasoning propose the parallel model to explain the two systems. The first purpose of the present article is to give a contribution to the debate on the parallel and default-interventionfist models: we hypothesized when logic and belief conflict both logical validity and belief judgments will be affected with greater level of response errors and/or longer response times. The second purpose of this article is to assess the relationship between decisional styles and performance in deductive reasoning. Seventy-two participants participated in the experiment and completed 64 modus ponens and modus tollens syllogistic reasoning tasks. Accordingly, we found that belief and logic judgments were affected by the conflict condition, both in easy syllogisms (i.e., modus ponens) and in complex syllogisms (i.e., modus tollens). Findings showed also that participants with a rational decision-making style were more strongly influenced by logic than belief, whereas those with an intuitive decision-making style were more strongly influenced by belief than logic.

Exploring the logic and conducting a comprehensive evaluation of AdipoRon-based adiponectin replacement therapy against hormone-related cancers-a systematic review

The potential benefits of adiponectin replacement therapy extend to numerous human diseases, with current research showing particular interest in its effectiveness against specific cancer forms, especially hormone-related. However, limitations in the pharmacological use of the intact protein have led to a focus on alternative options. AdipoRon is an extensively studied non-peptidic drug candidate for adiponectin replacement therapy. While researchers have explored the efficacy and therapeutic applications of AdipoRon in various disease conditions, their effects against cancer models advanced more, with no review regarding AdipoRon's efficacy against hormone-related cancers being published. The present systematic review aims to fill this gap. Preclinical evidence was compiled from PubMed, EMBASE, COCHRANE, and Google Scholar following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, and the manuscript's quality assessment was conducted using the Joanna Briggs Institute (JBI) Checklist Critical Appraisal Tool for Systematic Reviews' Quality. The included nine studies incorporated various cell and animal models of the pancreas, gynaecological system, and osteosarcoma cancers. AdipoRon demonstrated effectiveness against pancreatic cancer by activating p44/42 MAPK, mitochondrial dysfunction, and AMPK-mediated inhibition of ACC1. In gynaecological cancers, it exhibited promising anticancer effects through the activation of AMPK, potential inhibition of mTOR, and modulation of the SET1B/BOD1/AdipoR1 signaling cascade. Against osteosarcoma, AdipoRon worked by perturbing ERK1/2 signaling and reducing p70S6K phosphorylation. AdipoRon shows promise in preclinical studies, but human trials are crucial for clinical safety and effectiveness. Caution is needed due to potential off-target effects, especially in cancer therapy with multi-target approaches. Structural biology and computational methods can help predict these effects.

An intelligent ratiometric fluorescent assay based on MOF nanozyme-mediated tandem catalysis that guided by contrary logic circuit for highly sensitive sarcosine detection and smartphone-based portable sensing application

As the well-known test-indicator for early prostate cancer (PCa), sarcosine (SA) is closely related to the differential pathological process, which makes its accurate determination increasingly significant. Herein, we for the first time expanded the peroxidase (POD)-like property of facile-synthesized Zn-TCPP(Fe) MOF to fluorescent substrates and exploited it to ratiometric fluorescent (RF) sensing. By harnessing the effective catalytic oxidation of MOF nanozyme toward two fluorescent substrates (Scopoletin, SC; Amplex Red, AR) with contrary changes, and target-responsive (SA + SOx)/MOF/(SC + AR) tandem catalytic reaction, we constructed the first MOF nanozyme-based RF sensor for the quantitative determination of SA. Superior to previous works, the operation of this RF sensor is under the guidance of AND-(AND^NAND) contrary logic circuit. The dual-channel binary output changes (from 1/0 to 0/1) not only enable the intelligent logical recognition of SA, bringing strengthened reliability and accuracy, but also manifest the proof-of-concept discrimination of PCa individuals and healthy ones. Through recording the fluorescence alterations of SC (F465) and AR (F585), two segments of linear relationships between ratiometric values (F585/F465) and varied contents of SA are realized successfully. The LOD for SA could reach to as low as 39.98 nM, which outperforms all nanozyme-originated SA sensors reported till now. Moreover, this sensor also demonstrates high selectivity and satisfactory performance in human serum samples. Furthermore, the portable sensing of SA is realized under the assistance of smartphone-based RGB analysis, demonstrating the potential of point-of-care diagnostics of PCa in the future.

pH-dependent complex formation with TAR RNA and DNA: application towards logic gates

Nucleic acid-based logic gates have shown great potential in biotechnology, medicine as well as diagnostics. Herein, we have constructed pH-responsive logic devices by utilizing HIV-1 TAR hairpins in combination with a thiazole peptide that exhibits turn-on fluorescence upon interacting with TAR RNA or DNA. Based on this, INHIBIT-AND and YES-INHIBIT-AND logic gates were constructed in parallel. The pH alteration leads to conformational changes of the hairpin structure, enabling the construction of a multi-reset reusable logic system which could be developed for in vitro sensing of the HIV-1 viral RNA.

Preponderance of generalized chain functions in reconstructed Boolean models of biological networks

Boolean networks (BNs) have been extensively used to model gene regulatory networks (GRNs). The dynamics of BNs depend on the network architecture and regulatory logic rules (Boolean functions (BFs)) associated with nodes. Nested canalyzing functions (NCFs) have been shown to be enriched among the BFs in the large-scale studies of reconstructed Boolean models. The central question we address here is whether that enrichment is due to certain sub-types of NCFs. We build on one sub-type of NCFs, the chain functions (or chain-0 functions) proposed by Gat-Viks and Shamir. First, we propose two other sub-types of NCFs, namely, the class of chain-1 functions and generalized chain functions, the union of the chain-0 and chain-1 types. Next, we find that the fraction of NCFs that are chain-0 (also holds for chain-1) functions decreases exponentially with the number of inputs. We provide analytical treatment for this and other observations on BFs. Then, by analyzing three different datasets of reconstructed Boolean models we find that generalized chain functions are significantly enriched within the NCFs. Lastly we illustrate that upon imposing the constraints of generalized chain functions on three different GRNs we are able to obtain biologically viable Boolean models.

Neural flip-flops I: Short-term memory

The networks proposed here show how neurons can be connected to form flip-flops, the basic building blocks in sequential logic systems. The novel neural flip-flops (NFFs) are explicit, dynamic, and can generate known phenomena of short-term memory. For each network design, all neurons, connections, and types of synapses are shown explicitly. The neurons' operation depends only on explicitly stated, minimal properties of excitement and inhibition. This operation is dynamic in the sense that the level of neuron activity is the only cellular change, making the NFFs' operation consistent with the speed of most brain functions. Memory tests have shown that certain neurons fire continuously at a high frequency while information is held in short-term memory. These neurons exhibit seven characteristics associated with memory formation, retention, retrieval, termination, and errors. One of the neurons in each of the NFFs produces all of the characteristics. This neuron and a second neighboring neuron together predict eight unknown phenomena. These predictions can be tested by the same methods that led to the discovery of the first seven phenomena. NFFs, together with a decoder from a previous paper, suggest a resolution to the longstanding controversy of whether short-term memory depends on neurons firing persistently or in brief, coordinated bursts. Two novel NFFs are composed of two and four neurons. Their designs follow directly from a standard electronic flip-flop design by moving each negation symbol from one end of the connection to the other. This does not affect the logic of the network, but it changes the logic of each component to a logic function that can be implemented by a single neuron. This transformation is reversible and is apparently new to engineering as well as neuroscience.

Sea Anemone-like Nanomachine Based on DNA Strand Displacement Composed of Three Boolean Logic Gates: Diversified Input for Intracellular Multitarget Detection

Efficient and accurate acquisition of cellular biomolecular information is crucial for exploring cell fate, achieving early diagnosis, and the effective treatment of various diseases. However, current DNA biosensors are mostly limited to single-target detection, with few complex logic circuits for comprehensive analysis of three or more targets. Herein, we designed a sea anemone-like DNA nanomachine based on DNA strand displacement composed of three logic gates (YES-AND-YES) and delivered into the cells using gold nano bipyramid carriers. The AND gate activation depends on the trigger chain released by upstream DNA strand displacement reactions, while the output signal relies on the downstream DNAzyme structure. Under the influence of diverse inputs (including enzymes, miRNA, and metal ions), the interconnected logic gates simultaneously perform logical analysis on multiple targets, generating a unique output signal in the YES/NO format. This sensor can successfully distinguish healthy cells from tumor cells and can be further used for the diagnosis of different tumor cells, providing a promising platform for accurate cell-type identification.

Towards the development of a DNA automaton: modular RNA-cleaving deoxyribozyme logic gates regulated by miRNAs

Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects. Herein, we have developed six DNAzyme-based logic gates able to process YES, AND, and NOT Boolean logic. The novelty of this work lies in their additional functionalization with a common DNA scaffold for increased cooperativity in input recognition. Moreover, we explored hierarchical input binding to multi-input logic gates, which helped gate optimization. Additionally, we developed a new design of an allosteric hairpin switch used to implement NOT logic. All DNA logic gates achieved the desired true-to-false output signal when detecting a panel of miRNAs, known for their important role in malignancy regulation. This is the first example of DNAzyme-based logic gates having all input-recognizing elements integrated in a single DNA nanostructure, which provides new opportunities for building DNA automatons for diagnosis and therapy of human diseases.

Low-power and area-efficient memristor based non-volatile D latch and flip-flop: Design and analysis

In recent years, non-volatile memory elements have become highly appealing for memory applications to implement a new class of storage memory that could replace flash memories in sequential logic applications, with features such as compactness, low power, fast processing speed, high endurance, and retention. The memristor is one such non-volatile element that fits the fundamental blocks of sequential logic circuits, the latch and flip-flop; hence, in this article, a non-volatile latch architecture using memristor ratioed logic (MRL) inverter and CMOS components is focused, with an additional memristor as a memory element. A Verilog-A model was used to create the memristor element. The simulation findings validated the compact, low-voltage, and reliable design of the latch design. We evolved in technology enough to create a master-slave flip-flop and arrange it to function as a counter and a shift register. Power, number of elements, cell size, energy, programming time, and robustness are compared to comparable non-volatile topologies. The proposed non-volatile latch proves non-volatility and can store data with a 24% reduction in power consumption and a near 10% reduction in area.

Logic "AND Gate Circuit"-Based Gasdermin Protein Expressing Nanoplatform Induces Tumor-Specific Pyroptosis to Enhance Cancer Immunotherapy

Pyroptosis mediated by gasdermin protein has shown great potential in cancer immunotherapies. However, the low expression of gasdermin proteins and the systemic toxicity of nonspecific pyroptosis limit its clinical application. Here, we designed a synthetic biology strategy to construct a tumor-specific pyroptosis-inducing nanoplatform M-CNP/Mn@pPHS, in which a pyroptosis-inducing plasmid (pPHS) was loaded onto a manganese (Mn)-doped calcium carbonate nanoparticle and wrapped in a tumor-derived cell membrane. M-CNP/Mn@pPHS showed an efficient tumor targeting ability. After its internalization by tumor cells, the degradation of M-CNP/Mn@pPHS in the acidic endosomal environment allowed the efficient endosomal escape of plasmid pPHS. To trigger tumor-specific pyroptosis, pPHS was designed according to the logic "AND gate circuit" strategy, with Hif-1α and Sox4 as two input signals and gasdermin D induced pyroptosis as output signal. Only in cells with high expression of Hif-1α and Sox4 simultaneously will the output signal gasdermin D be expressed. Since Hif-1α and Sox4 are both specifically expressed in tumor cells, M-CNP/Mn@pPHS induces the tumor-specific expression of gasdermin D and thus pyroptosis, triggering an efficient immune response with little systemic toxicity. The Mn2+ released from the nanoplatform further enhanced the antitumor immune response by stimulating the cGAS-STING pathway. Thus, M-CNP/Mn@pPHS efficiently inhibited tumor growth with 79.8% tumor regression in vivo. We demonstrate that this logic "AND gate circuit"-based gasdermin nanoplatform is a promising strategy for inducing tumor-specific pyroptosis with little systemic toxicity.

Children dynamically update and extend the interface between number words and perceptual magnitudes

As adults, we represent and think about number, space, and time in at least two ways: our intuitive-but imprecise-perceptual representations, and the slowly learned-but precise-number words. With development, these representational formats interface, allowing us to use precise number words to estimate imprecise perceptual experiences. We test two accounts of this developmental milestone. Either slowly learned associations are required for the interface to form, predicting that deviations from typical experiences (e.g., presentation of a novel unit or unpracticed dimension) will disrupt children's ability to map number words to their perceptual experiences or children's understanding of the logical similarity between number words and perceptual representations allows them to flexibly extend this interface to novel experiences (e.g., units and dimensions they have not yet learned how to formally measure). 5-11-year-olds completed verbal estimation and perceptual sensitivity tasks across three dimensions: Number, Length, and Area. For verbal estimation, they were given novel units (i.e., a three-dot unit called one "toma" for Number, a 44 px long line called one "blicket" for Length, a 111 px2 blob called one "modi" for Area) and asked to estimate how many tomas/blickets/modies they saw when shown a larger set of dots, lines, and blobs. Children could flexibly link number words to novel units across dimensions, demonstrating positive estimation slopes, even for Length and Area, which younger children had limited experience with. This suggests that the logic of structure mapping can be dynamically utilized across perceptual dimensions, even without extensive experience.

The logic of protein post-translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments

Protein post-translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half-life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino-acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory switch, protein ubiquitylation as a degradation signal and histone modifications as a functional code. The contribution of crucial techniques for studying PTMs is also discussed. The central part of the essay explores shared chemical principles and catalytic strategies observed across diverse PTM systems, together with mechanisms of substrate selection, the reversibility of PTMs by erasers and the recognition of PTMs by reader domains. Similarities in the basic chemical mechanism are highlighted and their implications are discussed. The final part is dedicated to the evolutionary trajectories of PTM systems, beginning with their possible emergence in the context of rivalry in the prokaryotic world. Together, the essay provides a unified perspective on the diverse world of major protein modifications.

The Coding Logic of Interoception

Interoception, the ability to precisely and timely sense internal body signals, is critical for life. The interoceptive system monitors a large variety of mechanical, chemical, hormonal, and pathological cues using specialized organ cells, organ innervating neurons, and brain sensory neurons. It is important for maintaining body homeostasis, providing motivational drives, and regulating autonomic, cognitive, and behavioral functions. However, compared to external sensory systems, our knowledge about how diverse body signals are coded at a system level is quite limited. In this review, we focus on the unique features of interoceptive signals and the organization of the interoceptive system, with the goal of better understanding the coding logic of interoception.

Multimode adaptive logic gates based on temperature-responsive DNA strand displacement

Living organisms switch their intrinsic biological states to survive environmental turbulence, in which temperature changes are prevalent in nature. Most artificial temperature-responsive DNA nanosystems work as switch modules that transit between "ON-OFF" states, making it difficult to construct nanosystems with diverse functions. In this study, we present a general strategy to build multimode nanosystems based on a temperature-responsive DNA strand displacement reaction. The temperature-responsive DNA strand displacement was controlled by tuning the sequence of the substrate hairpin strands and the invading strands. The nanosystems were demonstrated as logic gates that performed a set of Boolean logical functions at specific temperatures. In addition, an adaptive logic gate was fabricated that could exhibit different logic functions when placed in different temperatures. Specifically, upon the same input strands, the logic gate worked as an XOR gate at 10 °C, an OR gate at 35 °C, an AND gate at 46 °C, and was reset at 55 °C. The design and fabrication of the multifunctional nanosystems would help construct advanced temperature-responsive systems that may be used for temperature-controlled multi-stage drug delivery and thermally-controlled multi-step assembly of nanostructures.

Survival processing occupies the central bottleneck of cognitive processing: A psychological refractory period analysis

Words judged for relevance in a survival situation are remembered better than words judged for relevance in a nonsurvival context. This survival processing effect has been explained by selective tuning of human memory during evolution to process and retain information specifically relevant for survival. According to the richness-of-encoding hypothesis the survival processing effect arises from a domain-general mechanism-namely, a particularly rich and distinct form of encoding. This form of information processing is effortful and requires limited cognitive capacities. In our experiment, we used the well-established psychological refractory period framework in conjunction with the effect propagation logic to assess the role of central cognitive resources for the survival processing effect. Our data demonstrate that the survival memory advantage indeed relies on the capacity-limited central stage of cognitive processing. Thus, rating words in the context of a survival scenario involves central processing resources to a greater amount than rating words in a nonsurvival control condition. We discuss implications for theories of the survival processing effect.

Debiasing thinking among non-WEIRD reasoners

Human reasoning has been shown to be biased in a variety of situations. While most studies have focused on samples of WEIRD participants (from Western Educated Industrialized Rich and Democratic societies), the sparse non-WEIRD data on the topic suggest an even stronger propensity for biased reasoning. This could be explained by a competence issue (people lack the ability to integrate logical knowledge into their reasoning) or a performance issue (people possess the logical knowledge but do not know it is relevant). We addressed this question using a debiasing paradigm with the base-rate task on a sample of non-industrialized people, the Himba of Namibia. After a short training, most participants were debiased, lending credence to the performance account. Debiasing was however to some extent boosted by schooling and living environment suggesting that competence also plays a role (in that more acquired knowledge allows for a higher training benefit). Results imply that debias interventions can be successfully employed to boost sound reasoning around the world.

DNA Logical Device Combining an Entropy-Driven Catalytic Amplification Strategy for the Simultaneous Detection of Exosomal Multiplex miRNAs In Situ

Exosomal miRNAs are considered promising biomarkers for cancer diagnosis, but their accuracy is severely compromised by the low content of miRNAs and the large amount of exosomal miRNAs released from normal cells. Here, we presented a dual-specific miRNA's logical recognition triggered by an entropy-driven catalysis (EDC)-enhanced system in exosomes for accurate detection of liver cancer-cell-derived exosomal miR-21 and miR-122. Taking advantage of the accurate analytical performance of the logic device, the excellent membrane penetration of gold nanoparticles, and the outstanding amplification ability of the EDC reaction, this method exhibits high sensitivity and selectivity for the detection of tumor-derived exosomal miRNAs in situ. Moreover, due to its excellent performance, this logic device can effectively distinguish liver cancer patients from healthy donors by determining the amount of cancer-cell-derived exosomal miRNAs. Overall, this strategy has great potential for analyzing various types of exosomes and provides a viable tool to improve the accuracy of cancer diagnosis.

Quality Control of Mass-Encoded Nanodevices by Compartmented DNA Origami Frames for Precision Information Coding and Logic Mapping

Encoded nanostructures afford an ideal platform carrying multi-channel signal components for multiplexed assay and information security. However, with the demand on exclusivity and reproducibility of coding signals, precise control on the structure and composition of nanomaterials featuring fully distinguishable signals remains challenging. By using the multiplexing capability of mass spectrometry (MS) and spatial addressability of DNA origami nanostructures, we herein propose a quality control methodology for constructing mass-encoded nanodevices (namely MNTs-TDOFs) in the scaffold of compartmented tetrahedral DNA origami frames (TDOFs), in which the arrangement and stoichiometry of four types of mass nanotags (MNTs) can be finely regulated and customized to generate characteristic MS patterns. The programmability of combinatorial MNTs and orthogonality of individual compartments allows further evolution of MNTs-TDOFs to static tagging agents and dynamic nanoprobes for labeling and sensing of multiple targets. More importantly, structure control at single TDOF level ensures the constancy of prescribed MS outputs, by which a high-capacity coding system was established for secure information encryption and decryption. In addition to the multiplexed outputs in parallel, the nanodevices could also map logic circuits with interconnected complexity and logic events of c-Met recognition and dimerization on cell surface for signaling regulation by MS interrogation.

A cost-effective, "mix & act" G-quadruplex/Cu (II) metal-nanozyme-based ratiometric fluorescent platform for highly sensitive and selective cysteine/bleomycin detection and multilevel contrary logic computing

Versatile nanozymes with fascinating catalytic properties provide inspiring and effective options for biosensing and pharmaceutical analysis. Herein, we report the first nanozyme-based ratiometric fluorescent platform for cysteine (Cys) and bleomycin (BLM) detection by harnessing the cost-effective and "mix & act" G-quadruplex/Cu(II) (G4/Cu) metal-nanozyme with satisfactory peroxidase-like activity, which was fully proven by circular dichroism (CD), electron paramagnetic resonance (EPR) spectra and reactive oxygen species (ROS) scavenging experiments. Based on the catalytic oxidation of G4/Cu metal-nanozyme toward two fluorescent substrates (Amplex Ultrared, AU; Scopoletin, Sc) with opposite responses in the presence of H2O2, and the specific interaction between Cu2+ and targets, we achieved the highly sensitive detection of Cys and BLM. Through recording the fluorescence changes of AU (emission at 590 nm, F590) and Sc (emission at 465 nm, F465), we obtained good linear relationships between ratiometric fluorescence values (F590/F465) and variable contents of targets, resulting in the competitive LODs of Cys (6.7 nM) and BLM (10 nM), respectively. Moreover, this platform presented high selectivity (without the need for masking agent) and acceptable performance in human serum samples. Furthermore, a library of DNA contrary logic pairs (CLPs) and multilevel concatenated circuits were fabricated based on the reverse dual-output of the above platform, enriching the building blocks of biocomputing. This work not only enlightened the design of affordable, "mix & act" type nanozyme-based ratiometric biosensors with high reliability, but also facilitated the pluralistic application of nucleic acid-templated nanozymes to innovative biocomputing.

Peptide-graphene logic sensing system for dual-mode detection of exosomes, molecular information processing and protection

Peptides with highly sequence-dependent recognition, assembly, and encoding abilities can perform functions similar to DNA or even better, such as biosensing, molecular information processing, coding, or storage. However, the combination of versatile peptides and 2D materials are rarely used for multipurpose integrated applications, including biosensing, information processing and security. Herein, peptide-graphene sensing system was comprehensively used for dual-signal sensing of tumor-derived exosomes (TDEs), logic computing, and information protection. The system used fluorescent-labeled CD63-binding peptide CP05 and graphene oxide (GO) to selectively detect CD63 and TDEs by fluorescence and resonance light scattering. From three levels such as matter, energy, and information analysis, the matter and energy changes in GO-CP05 peptide sensing system were transformed into valuable information, which achieve the dual-mode quantitative detection of TDEs and its marker CD63, and the actual serum analysis. This matter-energy interaction network was also informationized, and utilized for parallel and batch logic computing, two kinds of molecular crypto-steganography (based on peptide sequence and Boolean logic relationships), which facilitates development of intelligent sensing and advanced information technology. This work not only provides a new method for sensitive detection of important disease markers, but also provides ideas for integrating molecular sensing and informatization to open molecular digitization.

On peace and its logic

Glowacki argues that the human capacity for peace emerged 100,000 years ago, and that the logic of peace is such that the traits and technologies that enable peace are the same that are used to wage war. In my commentary I raise some concerns about these points as well as about Glowacki's understanding of peace.

Calibrating logics: How adolescents and young adults calibrate often-competing logics in their daily self-management of type 1 diabetes

Adolescents and young adults with type 1 diabetes must manage a demanding chronic condition in their daily lives, but adequate self-management remains a major challenge. In this article, we explore the logics invoked in shaping daily type 1 diabetes self-management among adolescents and young adults and propose an analytical view of self-management as a matter of 'calibrating logics'. Drawing on Annemarie Mol's concept of logic, our analysis of in-depth interviews with 21 adolescents and young adults with type 1 diabetes suggested that three main logics collectively shaped their self-management: biomedical, embodied and social. Biomedical logics appeared in the form of routinised insulin therapy, frequent blood glucose testing, and carbohydrate counting, all of which emphasise controlling blood glucose levels. Embodied logics emerged as refined practices such as 'thinking insulin units' and 'listening' to blood glucose fluctuations. Finally, social logics were at play when discreet or postponed self-management practices were used to adjust to social situations. While these logics may complement each other, study participants invoked how these logics often competed in daily life, generating tensions. We therefore propose viewing self-management as a matter of calibrating logics in which often-competing logics are at play. This can provide nuanced insights into the effort and challenges related to the daily self-management of type 1 diabetes for adolescents and young adults, in contrast to the prevailing dichotomy of adherence versus nonadherence to prescribed treatment regimens.

Simulating doctors' thinking logic for chest X-ray report generation via Transformer-based Semantic Query learning

Medical report generation can be treated as a process of doctors' observing, understanding, and describing images from different perspectives. Following this process, this paper innovatively proposes a Transformer-based Semantic Query learning paradigm (TranSQ). Briefly, this paradigm is to learn an intention embedding set and make a semantic query to the visual features, generate intent-compliant sentence candidates, and form a coherent report. We apply a bipartite matching mechanism during training to realize the dynamic correspondence between the intention embeddings and the sentences to induct medical concepts into the observation intentions. Experimental results on two major radiology reporting datasets (i.e., IU X-ray and MIMIC-CXR) demonstrate that our model outperforms state-of-the-art models regarding generation effectiveness and clinical efficacy. In addition, comprehensive ablation experiments fully validate the TranSQ model's innovation and interpretation. The code is available at https://github.com/zjukongming/TranSQ.

A Self-Similarity Logic May Shape the Organization of the Nervous System

From the morphological point of view, the nervous system exhibits a fractal, self-similar geometry at various levels of observations, from single cells up to cell networks. From the functional point of view, it is characterized by a hierarchical organization in which self-similar structures (networks) of different miniaturizations are nested within each other. In particular, neuronal networks, interconnected to form neuronal systems, are formed by neurons, which operate thanks to their molecular networks, mainly having proteins as components that via protein-protein interactions can be assembled in multimeric complexes working as micro-devices. On this basis, the term "self-similarity logic" was introduced to describe a nested organization where, at the various levels, almost the same rules (logic) to perform operations are used. Self-similarity and self-similarity logic both appear to be intimately linked to the biophysical evidence for the nervous system being a pattern-forming system that can flexibly switch from one coherent state to another. Thus, they can represent the key concepts to describe its complexity and its concerted, holistic behavior.

The mobius strip, the cell, and soft logic mathematics

The cell-cell signaling mechanisms that are the basis for all of physiology have been used to trace evolution back to the unicellular state, and beyond, to the "First Principles of Physiology". And since our physiology derives from the Cosmos based on Symbiogenesis, it has been hypothesized that the cell behaves like a functional Mobius Strip, having no 'inside or outside' cell membrane surface - it is continuous with the Cosmos, its history being codified from Quantum Entanglement to Newtonian Mechanics, affording the cell consciousness and unconsciousness/subconsciousness as a continuum for the first time. Similarly, Klein and Maimon have concluded that their 'Soft Logic' mathematics also constitutes a Mobius Strip, using both a real number axis, combined with a zero axis, numerically representing cognition. This is congruent with the cell as 'two-tiered' consciousness, the first tier being the real-time interface between the cell membrane and its environment; the second tier constituting integrated physiology, referencing the consciousness of the Cosmos. Thus, there is coherence between physiology, consciousness and mathematics for the first time.

A nicking enzyme-assisted allosteric strategy for self-resetting DNA switching circuits

The self-regulation of biochemical reaction networks is crucial for maintaining balance, stability, and adaptability within biological systems. DNA switching circuits, serving as basic units, play essential roles in regulating pathways, facilitating signal transduction, and processing biochemical reaction networks. However, the non-reusability of DNA switching circuits hinders its application in current complex information processing. Herein, we proposed a nicking enzyme-assisted allosteric strategy for constructing self-resetting DNA switching circuits to realize complex information processing. This strategy utilizes the unique cleavage ability of the nicking enzyme to achieve the automatic restoration of states. Based on this strategy, we implemented a self-resetting DNA switch. By leveraging the reusability of the DNA switch, we constructed a DNA switching circuit with selective activation characteristics and further extended its functionality to include fan-out and fan-in processes by expanding the number of functional modules and connection modes. Furthermore, we demonstrated the complex information processing capabilities of these switching circuits by integrating recognition, translation, and decision functional modules, which could analyze and transmit multiple input signals and realize parallel logic operations. This strategy simplifies the design of switching circuits and promotes the future development of biosensing, molecular computing, and nanomachines.

Establishing Tunable Genetic Logic Gates with Versatile Dynamic Performance by Varying Regulatory Parameters

Genetic logic gates can be employed in metabolic engineering and synthetic biology to regulate gene expression based on diverse inputs. Design of tunable genetic logic gates with versatile dynamic performance is essential for expanding the usability of these toolsets. Here, using the p-coumaric acid biosensor system as a proof-of-concept, we initially investigated the parameters influencing the buffer (BUF) genetic logic gates. Subsequently, integrating binding sequences from the p-coumaric acid biosensor system and tetR or lacI regulation systems into a constitutive promoter yielded AND genetic logic gates. Additionally, characterized antisense RNAs (asRNAs) or single guide RNAs (sgRNAs) with various repression efficiencies were combined with BUF gates to construct a suite of p-coumaric acid-triggered NOT genetic logic gates. Finally, the designed BUF and NOT gates were combined to construct bifunctional genetic circuits that were subjected to orthogonality evaluation. The genetic logic gates established in this study can serve as valuable tools in future applications of metabolic engineering and synthetic biology.

Strengthening students’ well-being and nutritional balance in Grand Est (France): “Lycéen Bouge” program intervention logic

Introduction

As part of a national health policy to fight excess weight and obesity, the “Lycéen Bouge” program aims to fight against social inequalities in health among adolescents by improving their well-being and nutritional balance. The aim of this article is to present the intervention logic of this program and to identify the key functions that are essential for the project to function properly and to be transferable.

Method

Data was collected through interviews with project officers, observation sessions in several high schools. A documentary analysis was also carried out. The data was then analyzed thematically, in a collaborative process with the project leader, in order to develop the program logic model.

Results

The analysis and development of the logic model identified the program’s objectives and components, as well as six key functions. The key functions identified concern the format and co-construction of activities, local partnerships, high-school volunteering, social skills training and project length.

Conclusion

In some respects, the program differs from the literature and the evidence and could therefore draw on it for improvement. These include the involvement of beneficiaries and the implementation of a comprehensive approach and a gender-sensitive approach, which would make it possible to reach more students.

Constructing the "home-side" of a scientific legacy: Mary Everest Boole, pedagogy, and domesticity

The Victorian writer Mary Everest Boole (1832-1916) developed an idiosyncratic pedagogical treatment of arithmetic, algebra, and logic. Her pedagogy favored active, child-directed learning, and is now generally admired as ahead of its time, though it must be deciphered through fairly eccentric delivery. A recurring theme in Mrs. Boole's prolific writing is the misunderstood legacy of her late husband, the renowned mathematician and logician George Boole (1815-1864). As existing literature has shown, she worked to promote a morally and religiously charged understanding of his work. More fundamentally, she presented an all-encompassing pedagogical perspective on Mr. Boole's life and work. Across her voluminous publications, Mrs. Boole filtered everything-mathematics, logic, religion, morality, and homelife-through the lens of pedagogy. She used this expansive conception of teaching to span the gulf between professional and domestic work, thereby claiming a privileged domestic perspective on her husband's intellectual output and enlisting his legacy as a resource for her own writing. The Booles' entangled careers show how particular ways of practicing domesticity could shape and be shaped by mathematical identities and ideas.

Implicit and explicit processing on base rate neglect problems

Base rate reasoning as assessed on Base rate neglect (BRN) Tasks has been studied extensively, with a sizable body of findings indicating that both logical (base rate) and belief-based (case description) processing contribute to responses on the task. Various task conditions have been found to influence which type of processing controls responding. The present study compares two instructional sets, one which requires responding in terms of the base rate information and one which requires responding in accordance with the case description. This manipulation allows for a distinction between explicit processing (set-consistent) and implicit processing (set-inconsistent and potentially interfering). We also manipulated the extremity of the base rates employed in the task and the extremity of the stereotypes contained in the case description. We argue that extremity effects should be present in implicit, but not explicit, processing, suggesting that these effects are the result of limitations in the control of set-inconsistent processing. The results generally supported the predictions. In addition, a proclivity for analytical thinking, as measured by actively open-minded thinking (AOT), was associated with less interference of belief-based processing on logical responding, but greater interference of logical processing on belief-based responding.

Accuracy and Response Time for Modus Ponens Syllogisms Vary by Controversial Topic and Categorical Emotion

Researchers have documented differential effects of emotion on cognitive processes, debating whether emotion may increase or decrease the response time and accuracy of logical thinking. The current study proposed that differences may be due to variability occurring across topic and categorical emotions, such that assessment of several basic emotional responses in the context of performing logical reasoning tasks may provide an initial indication of these differences. Utilizing modus ponens syllogisms composed of controversial statements, the current study evoked a variety of emotional responses and tested the accuracy of participants' basic logical thinking. Results indicated that logical skills were largely preserved despite the topic and emotion, nonetheless, accuracy varied across syllogism type (controversial vs. control), with increased accuracy on controversial syllogisms. Syllogisms rated as evoking no emotion were answered more accurately than those that evoked any emotion, with disgust and anger associated with less accuracy than no emotion and gladness associated with increased accuracy. Response times also differed across syllogism type, emotion, and emotion intensity.

The Intransitive Logic of Directed Cycles and Flipons Enhances the Evolution of Molecular Computers by Augmenting the Kolmogorov Complexity of Genomes

Cell responses are usually viewed as transitive events with fixed inputs and outputs that are regulated by feedback loops. In contrast, directed cycles (DCs) have all nodes connected, and the flow is in a single direction. Consequently, DCs can regenerate themselves and implement intransitive logic. DCs are able to couple unrelated chemical reactions to each edge. The output depends upon which node is used as input. DCs can also undergo selection to minimize the loss of thermodynamic entropy while maximizing the gain of information entropy. The intransitive logic underlying DCs enhances their programmability and impacts their evolution. The natural selection of DCs favors the persistence, adaptability, and self-awareness of living organisms and does not depend solely on changes to coding sequences. Rather, the process can be RNA-directed. I use flipons, nucleic acid sequences that change conformation under physiological conditions, as a simple example and then describe more complex DCs. Flipons are often encoded by repeats and greatly increase the Kolmogorov complexity of genomes by adopting alternative structures. Other DCs allow cells to regenerate, recalibrate, reset, repair, and rewrite themselves, going far beyond the capabilities of current computational devices. Unlike Turing machines, cells are not designed to halt but rather to regenerate.

Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits

DNA logic nanodevices are powerful tools for both molecular computing tasks and smart bioanalytical applications. Nevertheless, the hour-level operation time and high cost caused by the frequent redesign/reconstruction of gates, tedious strand-displacement reaction, and expensive labeled probes (or tool enzymes) in previous works are ineluctable drawbacks. Herein, we report an ultrafast and cost-effective system for engineering concurrent DNA logic nanodevices (CDLNs) by combining polythymine CuNCs with SYBR Green I (SG I) as universal dual-output producers. Particularly, benefiting from the concomitant minute-level quick response of both unlabeled illuminators and the exquisite strand-displacement-free design, all CDLNs including contrary logic pairs (YES∧NOT, OR∧NOR, and Even∧Odd number classifier), noncontrary ones (IDE∧IMP, OR∧NAND), and concatenated circuits are implemented in just 10 min via a "one-stone-two-birds" method, resulting in only 1/12 the operation time and 1/4 the cost needed in previous works, respectively. Moreover, all of them share the same threshold value, and the dual output can be easily visualized by the naked eye under a portable UV lamp, indicating the universality and practicality of this system. Furthermore, by exploiting the "positive/negative cross-verification" advantages of concurrent contrary logic, the smart in vitro analysis of the polyadenine strand and its polymerase is realized, providing novel molecular tools for the early diagnosis of cancer-related diseases.

Nanoclusters with specific DNA overhangs: modifying configurability, engineering contrary logic pairs and the parity generator/checker for error detection

The most promising alternative for next-generation molecular computers is biocomputing, which uses DNAs as its primary building blocks to perform a Boolean operation. DNA nanoclusters (NCs) have emerged as promising candidates for biosensing applications due to their unique self-assembly properties and programmability. It has been demonstrated that adding DNA overhangs to DNA NCs improves their adaptability in identifying specific biomolecular interactions. A recent proposal in DNA computing is the concept of "contrary logic pairs (CLPs)" executed by employing a DNA hybrid architecture as a universal platform. We have designed thymine overhang-modified DNA-templated NCs (T-Au/Ag NCs). These NCs serve as a chemosensing ensemble platform, where the presence of HgII ions mediates the formation of M-Au/Ag NCs. The resulting NCs exhibit the capability to drive elementary CLPs (YES, NOT, OR, NOR, INH and IMP) as well as complex logic operations (XOR and XNOR). Additionally, they can be utilized for advanced non-arithmetic DNA logic devices like a parity generator (pG) and a parity checker (pC) for "error detection". Bit errors are an unavoidable and common occurrence during any computing. A cascade of XOR operations was used to evaluate these errors by introducing the pG and pC at the transmitting (TX) and receiving (RX) ends in binary transmission, respectively, which has devastating implications for reliable logic circuits, especially in advanced logic computation. Moreover, an even/odd natural number from 0 to 9 distinguishable pC was designed based on a dual-source responsive computing platform. This work offers inspiring avenues for a cost-effective strategy to construct highly-intelligent DNA computing devices by enhancing the multi-input responsive single DNA platform concept.

The Amplified DNA Logic Gates Based on Aptamer-Receptor Recognition for Cell Detection and Bioimaging

A powerful and accurate method for identifying and isolating cells would be of great importance due to its sensitivity, gentleness and effectiveness. Here, we designed a receptor-based DNA logic device that allows Boolean logic analysis of multiple cells. For ease of expression, the molecules on the cell surface that can bind to the aptamer are referred to as "receptors". This DNA logic device sends signals based on cell surface sgc8c and sgc4f receptor expression by performing NOT, NOR, AND and OR logic operations, and amplifies and evaluates the signals using HCR. Meanwhile, the release of ICG from the endopore of HMSNs is controlled by affecting structural changes in the DNA logic device. This approach can accurately identify and treat multiple cells on demand based on the presence or absence of cell-specific receptors, facilitating the development of personalized medicine.

A design logic for sequential segmentation across organisms

Multitudes of organisms display metameric compartmentalization of their body plan. Segmentation of these compartments happens sequentially in diverse phyla. In several sequentially segmenting species, periodically active molecular clocks and signaling gradients have been found. The clocks are proposed to control the timing of segmentation, while the gradients are proposed to instruct the positions of segment boundaries. However, the identity of the clock and gradient molecules differs across species. Furthermore, sequential segmentation of a basal chordate, Amphioxus, continues at late stages when the small tail bud cell population cannot establish long-range signaling gradients. Thus, it remains to be explained how a conserved morphological trait (i.e., sequential segmentation) is achieved by using different molecules or molecules with different spatial profiles. Here, we first focus on sequential segmentation of somites in vertebrate embryos and then draw parallels with other species. Thereafter, we propose a candidate design principle that has the potential to answer this puzzling question.

Don't you see the possibilities? Young preschoolers may lack possibility concepts

Preschoolers struggle to solve problems when they have to consider what might and might not happen. Instead of planning for all open possibilities, they simulate one possibility and treat it as the fact of the matter. Why? Are scientists asking them to solve problems that outstrip their executive capacity? Or do children lack the logical concepts needed to take multiple conflicting possibilities into account? To address this question, task demands were eliminated from an existing measure of children's ability to think about mere possibilities. One hundred nineteen 2.5- to 4.9-year-olds were tested. Participants were highly motivated but could not solve the problem. Bayesian analysis revealed strong evidence that reducing task demands while holding reasoning demands constant did not change performance. Children's struggles with the task cannot be explained by these task demands. Results are consistent with the hypothesis that children struggle because they cannot deploy possibility concepts that allow them to mark representations as merely possible. RESEARCH HIGHLIGHTS: Preschoolers are surprisingly irrational when faced with problems that ask them to consider what might and might not be the case. These irrationalities could arise from deficits in children's logical reasoning capacities or from extraneous task demands. This paper describes three plausible task demands. A new measure is introduced that preserves logical reasoning demands while eliminating all three extraneous task demands. Eliminating these task demands does not change performance. These task demands are not likely a cause of children's irrational behavior.

Multifunctional dumbbell probes-based logic circuits: microRNAs logic detection and tumor cells identification

BACKGROUND

The powerful logic processing capability of DNA logic circuits over multiple input signals perfectly meets the demands of multi-biomarker-based clinical diagnostics. As important biomarkers for cancer diagnosis and treatment, the orthogonal differential expression of microRNAs (miRNAs) in different diseases and different cancer cells makes the precise logical detection of multiple miRNAs particularly critical.

RESULTS

Therefore, we constructed two fundamental "AND" and "OR" logic gates and one "AND-OR" logic gate on the basis of our proposed multifunctional dumbbell probes. These logic gates allowed for the logical profiling of multiple cancer-associated miRNAs. In addition, by making simple adjustments to the functional modules of multifunctional dumbbell probes, the three logic gates we proposed could be easily transformed without the use of sophisticated probe design. Remarkably, these logic gates, in particular the "AND-OR" logic gate, were able to compute several miRNAs simultaneously, demonstrating excellent cell identification capabilities.

SIGNIFICANCE

Overall, this work provided a new idea for accurately distinguishing multiple cell types and showed great application prospects.

Deciphering RNA splicing logic with interpretable machine learning

Machine learning methods, particularly neural networks trained on large datasets, are transforming how scientists approach scientific discovery and experimental design. However, current state-of-the-art neural networks are limited by their uninterpretability: Despite their excellent accuracy, they cannot describe how they arrived at their predictions. Here, using an "interpretable-by-design" approach, we present a neural network model that provides insights into RNA splicing, a fundamental process in the transfer of genomic information into functional biochemical products. Although we designed our model to emphasize interpretability, its predictive accuracy is on par with state-of-the-art models. To demonstrate the model's interpretability, we introduce a visualization that, for any given exon, allows us to trace and quantify the entire decision process from input sequence to output splicing prediction. Importantly, the model revealed uncharacterized components of the splicing logic, which we experimentally validated. This study highlights how interpretable machine learning can advance scientific discovery.

A DNA Logic Circuit Equipped with a Biological Amplifier Loaded into Biomimetic ZIF-8 Nanoparticles Enables Accurate Identification of Specific Cancers In Vivo

DNA logic circuits (DLC) enable the accurate identification of specific cell types, such as cancer cells, but they face the challenges of weak output signals and a lack of competent platforms that can efficiently deliver DLC components to the target site in the living body. To address these issues, we rationally introduced a cascaded biological amplifier module based on the Primer Exchange Reaction inspired by electronic circuit amplifier devices. As a paradigm, three abnormally expressed Hela cell microRNAs (-30a, -17, and -21) were chosen as "AND" gate inputs. DLC response to these inputs was boosted by the amplifier markedly enhancing the output signal. More importantly, the encapsulation of DLC and amplifier components into ZIF-8 nanoparticles resulted in their efficient delivery to the target site, successfully distinguishing the Hela tumor subtype from other tumors in vivo. Thus, we envision that this strategy has great potential for clinical cancer diagnosis.

Creating theory: Encouragement for using creativity and deduction in qualitative nursing research

Texts about theory in nursing often refer to theory construction by using inductive methods in a rigid way. In this paper, it is instead argued that theories are created, which is in line with most philosophers of science. Theory creation is regarded as a creative process that does not follow a specific method or logic. As in any creative endeavour, the inspiration for theory creation can come from many sources, including previous research and existing theory. The main idea put forward is that deductive qualitative research approaches should play a key role in theory creation. Furthermore, there is a need to differentiate between theory creation and theory justification. A model that emphasizes the creative aspects of theory creation and theory justification using qualitative approaches is presented. The model suggests that knowledge development is a deductive trial-and-error process where theory creation is followed by testing. Scientific theory creation and justification are presented as an iterative process that is deductive in that a testable hypothesis is derived from the theory. If the hypothesis is falsified, then the theory needs modification or might be altogether wrong. Several factors can block the creative process, both in theory development and in finding ways to test a theory in the justification phase. Some of these blockers are the idea of 'building blocks' and the inductive view of science often brought forward in nursing. Other blockers include striving for consensus and adherence to existing nursing philosophies and existing theories. Research and knowledge development are creative processes, and following predefined methods is not enough to ensure scientific rigour in qualitative nursing research.

Integration of DNA-RNA-triplex-based regulation of transcription into molecular logic gates

In recent years, increasing numbers of noncoding RNA molecules were identified as possible components of endogenous DNA-RNA hybrid triplexes involved in gene regulation. Triplexes are potentially involved in complex molecular signaling networks that, if understood, would allow the engineering of biological computing components. Here, by making use of the enhancing and inhibiting effects of such triplexes, we demonstrate in vitro the construction of triplex-based molecular gates: 'exclusive OR' (XOR), 'exclusive NOT-OR' (XNOR), and a threshold gate, via transcription of a fluorogenic RNA aptamer. Precise modulation was displayed by the biomolecular-integrated systems over a wide interval of transcriptional outputs, ranging from drastic inhibition to significant enhancement. The present contribution represents a first example of molecular gates developed using DNA-RNA triplex nanostructures.

Aligning the logics of inquiry and action to address the biodiversity crisis

Despite an abundance of research reaffirming biodiversity's importance to the health of the planet and society, species continue to go extinct at an alarming rate. Why has continued research on the value of biodiversity not had the intended effect and what can be done about it? We considered biodiversity loss as a public value failure and the result of a misalignment between the logic of inquiry (which guides scientists) and the logic of action (which guides practitioners). We drew lessons from our own research to propose the creation of a national biodiversity strategy designed to link the logic of inquiry with the logic of action and coordinate the production of actionable conservation science and informed conservation action.