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Impact of non-reciprocal interactions on colloidal self-assembly with tunable anisotropy.

Non-reciprocal (NR) effective interactions violating Newton's third law occur in many biological systems, but can also be engineered in synthetic, colloidal systems. Recent research has shown that such NR interactions can have tremendous effects on the overall collective behavior and pattern formation, but can also influence aggregation processes on the particle scale. Here, we focus on the impact of non-reciprocity on the self-assembly of a colloidal system (originally passive) with anisotropic interactions whose character is tunable by external fields. In the absence of non-reciprocity, that is, under equilibrium conditions, the colloids form square-like and hexagonal aggregates with extremely long lifetimes yet no large-scale phase separation [Kogler et al., Soft Matter 11, 7356 (2015)], indicating kinetic trapping. Here, we study, based on Brownian dynamics simulations in 2D, an NR version of this model consisting of two species with reciprocal isotropic, but NR anisotropic interactions. We find that NR induces an effective propulsion of particle pairs and small aggregates ("active colloidal molecules") forming at the initial stages of self-assembly, an indication of the NR-induced non-equilibrium. The shape and stability of these initial clusters strongly depend on the degree of anisotropy. At longer times, we find, for weak NR interactions, large (even system-spanning) clusters where single particles can escape and enter at the boundaries, in stark contrast to the small rigid aggregates appearing at the same time in the passive case. In this sense, weak NR shortcuts the aggregation. Increasing the degree of NR (and thus, propulsion), we even observe large-scale phase separation if the interactions are weakly anisotropic. In contrast, systems with strong NR and anisotropy remain essentially disordered. Overall, the NR interactions are shown to destabilize the rigid aggregates interrupting self-assembly and phase separation in the passive case, thereby helping the system to overcome kinetic barriers.

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Predicting Promoters in Multiple Prokaryotes with Prompt.

Promoters are important cis-regulatory elements for the regulation of gene expression, and their accurate predictions are crucial for elucidating the biological functions and potential mechanisms of genes. Many previous prokaryotic promoter prediction methods are encouraging in terms of the prediction performance, but most of them focus on the recognition of promoters in only one or a few bacterial species. Moreover, due to ignoring the promoter sequence motifs, the interpretability of predictions with existing methods is limited. In this work, we present a generalized method Prompt (Promoters in multiple prokaryotes) to predict promoters in 16 prokaryotes and improve the interpretability of prediction results. Prompt integrates three methods including RSK (Regression based on Selected k-mer), CL (Contrastive Learning) and MLP (Multilayer Perception), and employs a voting strategy to divide the datasets into high-confidence and low-confidence categories. Results on the promoter prediction tasks in 16 prokaryotes show that the accuracy (Accuracy, Matthews correlation coefficient) of Prompt is greater than 80% in highly credible datasets of 16 prokaryotes, and is greater than 90% in 12 prokaryotes, and Prompt performs the best compared with other existing methods. Moreover, by identifying promoter sequence motifs, Prompt can improve the interpretability of the predictions. Prompt is freely available at https://github.com/duqimeng/PromptPrompt , and will contribute to the research of promoters in prokaryote.

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Measuring the operational performance of an artificial intelligence-based blood tube-labeling robot, NESLI.

Laboratory testing, crucial for medical diagnosis, has 3 phases: preanalytical, analytical, and postanalytical. This study set out to demonstrate whether automating tube labeling through artificial intelligence (AI) support enhances efficiency, reduces errors, and improves outpatient phlebotomy services. The NESLI tube-labeling robot (Labenko Informatics), which uses AI models for tube selection and handling, was used for the experiments. The study evaluated the NESLI robot's operational performance, including labelling time, technical problems, tube handling success, and critical stock alerts. The robot's label readability was also tested on various laboratory devices. This research will contribute to the field's understanding of the potential impact of automated tube-labeling systems on laboratory processes in the preanalytical phase. NESLI demonstrated high performance in labeling processes, achieving a success rate of 99.2% in labeling parameters and a success rate of 100% in other areas. For nonlabeling parameters, the average labeling time per tube was measured at 8.96 seconds, with a 100% success rate in tube handling and critical stock warnings. Technical issues were promptly resolved, affirming the NESLI robot's effectiveness and reliability in automating the tube-labeling processes. Robotic systems using AI, such as NESLI, have the potential to increase process efficiency and reduce errors in the preanalytical phase of laboratory testing. Integration of such systems into comprehensive information systems is crucial for optimizing phlebotomy services and ensuring timely and accurate diagnostics.

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Quantum chemical package Jaguar: A survey of recent developments and unique features.

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.

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Use of Standardized Nursing Terminologies to Capture Social Determinants of Health Data: An Integrative Review.

Addressing social determinants of health in nursing care is important for improving health outcomes and reducing health inequities. Using standardized nursing terminologies to capture this information generates sharable data that can be used to achieve these goals and create new knowledge. The purpose of this integrative review was to examine use of standardized nursing terminologies for collecting social determinants of health data in nursing research and practice. The CINAHL, MEDLINE, and Web of Science databases were searched using the terms "social determinants of health" [and] "nursing" [and] "standardized terminology" or names for each of the 12 American Nurses Association-approved terminologies. Limiters included peer-reviewed and English language. After removal of duplicates, 120 articles were found and screened for relevance and quality using a three-step process. This yielded a final sample of seven articles. Article data were extracted and analyzed for themes. In all articles, retrospective, observational, or secondary analysis research designs were used to analyze previously collected data from large, deidentified datasets or research studies. The Omaha System was the only standardized nursing terminology represented in the sample. All operational definitions of social determinants of health included behavioral items. In most studies, a social determinants of health index score was calculated, and data were analyzed using descriptive statistics and visualization methods. Results reported across the articles were diverse; some themes were identified. This review revealed published literature on this topic is limited. More quality improvement and multisite studies that examine the use of standardized nursing terminologies by nurses to collect and use social determinants of health data are needed.

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