This dataset contains the underlying data and analysis files associated with the review article “One clip, many genomes: how genome state may shape the use of tandem HMG-box proteins in organellar nucleoids” by Mari Takusagawa and Yoshiki Nishimura. The deposited files support the phylogenetic and structure-based analyses presented in Figs. 2 and 3 of the article. The dataset includes: HMG-box amino-acid sequences, the MAFFT alignment, maximum-likelihood phylogenetic trees, IQ-TREE reports, and approximately unbiased (AU) test outputs underlying Fig. 2; numerical structural-similarity matrices, AlphaFold Database predicted-aligned-error matrices, and protein biophysical properties underlying Fig. 3; AlphaFold3 input specifications, predicted TFAM–DNA and HLP–DNA models, and associated confidence summaries; and the Python script and tabulated results used to estimate DNA bend angles from the predicted models. The TFAM and HLP modelling jobs used the same 30-bp DNA sequence. The bend-angle analysis fits principal axes to the outer thirds of the two DNA arms while excluding the bent apex. These computational models and analyses are provided to support inspection and reproducibility. AlphaFold3 model geometry is predictive and should not be interpreted as experimental evidence for HLP-mediated DNA bending or HBD1-mediated DNA bridging. No supplementary figures or supplementary tables are included in this deposit. A detailed description of the files, software versions and directory structure is provided in README.txt. The CC BY 4.0 licence applies to the authors’ original compilation, analyses and documentation. Third-party source data and prediction outputs remain subject to the terms of their respective providers.
Mari Takusagawa, Yoshiki Nishimura· Zenodo (CERN European Organi...· 0 citations
This repository contains the reproducibility package for the study “PGR-Guard: Cross-Layer Detection and Prevention of IT-to-OT Cyberattacks in Small Power-Generation Facilities.” The study introduces PGR-Guard, an applied cybersecurity framework designed to detect and interrupt multi-stage attack progression from information technology environments into operational technology and cyber-physical processes. The framework correlates five security layers: identity activity, network behavior, operational technology protocol activity, controller state, and physical-process context. The repository includes the synthetic/emulated dataset, Python source code, holdout evaluation results, confidence intervals, scenario-level detection results, ablation analysis, statistical significance tests, threshold-selection results, and publication figures used in the manuscript. The evaluation models ten representative attack scenarios, including password spraying, valid-account compromise, internal reconnaissance, IT-to-OT traversal, engineering workstation access, PLC discovery, unauthorized controller reads and writes, controller task modification, and operational disruption. The experiments compare PGR-Guard with signature-based intrusion detection, OT-only anomaly detection, and an independent multi-sensor baseline. On the separated holdout evaluation set, PGR-Guard achieved approximately 0.990 precision, 0.879 recall, 0.931 F1 score, 2.55-second mean time to detection, 97.8% attack interruption rate, and 99.7% Cyber-Physical Prevention Rate (CPPR). The package contains: reproduce_pgr_guard.py — end-to-end reproducibility script PGR_Guard_synthetic_trials.csv — trial-level synthetic/emulated dataset holdout performance and confidence-interval files attack-scenario detection results ablation-study results statistical significance analyses threshold-selection results publication figures data dictionary and software requirements Important data provenance note: the included dataset is generated from a controlled synthetic/emulated OT cybersecurity model. It does not contain telemetry from the 2026 UK power-generation cyber incident, a real utility, a physical power-generation facility, or a physical PLC testbed. The results should therefore be interpreted as controlled emulation results rather than real-world operational measurements. Fixed random seeds are included in the source code to support reproducibility. The repository is intended to support independent verification, extension, and comparison of cross-layer IT-to-OT cyberattack detection methods.
Halil Dursunoglu· Zenodo (CERN European Organi...· 0 citations
This study aims to investigate the causality mechanisms linking managerial style and organizational discipline to employee work effectiveness through the mediation of work expectation fulfillment. Focusing on PT Bank Rakyat Indonesia (Persero) Tbk Pekalongan Branch, this research outlines performance optimization challenges within a dynamic state-owned banking ecosystem. The inquiry emphasizes aligning leadership and rule compliance to foster a productive work climate. The inclusion of work expectation fulfillment clarifies psychological pathways transforming structural drivers into sustainable staff operational achievements, while addressing integration gaps between managerial orientation and internal banking regulatory compliance. An exploratory-explanatory quantitative approach was applied to test the proposed structural hypotheses. From a population of 180 employees, a sample of 120 respondents was drawn using purposive sampling based on specific operational qualification criteria. Primary data were collected via a structured Likert-scale questionnaire validated for validity and reliability. Measurement model evaluation and causal relationship testing were comprehensively analyzed using SmartPLS software. Variance-based Structural Equation Modeling (PLS-SEM) was selected to estimate direct and indirect paths simultaneously. Empirical findings confirm that managerial style and organizational discipline positively and significantly influence employee work effectiveness, both directly and indirectly through work expectation fulfillment. Work expectation fulfillment acts as a solid mediating variable transmitting leadership and rule compliance impacts onto performance achievement. Practical implications emphasize the necessity for management to prioritize aligning adaptive managerial supervision, fair regulatory enforcement, and psychological contract fulfillment to realize optimal, sustainable operational effectiveness.
OBJECTIVE
To prospectively evaluate whether modifying DSL version 5-based hearing aid (HA) fittings by adjusting gain on HA fitting software so that measured functional gain (FG) approached a one-third gain (1/3G) target could provide appropriate fitting outcomes in patients with sensorineural hearing loss.
METHODS
Twenty-four patients (48 ears) with bilateral sensorineural hearing loss underwent initial HA fitting using the DSL version 5 prescription formula. FG was measured at 250-4000 Hz, and HA gain was adjusted on HA fitting software so that FG approached the target 1/3 G. Speech discrimination scores at 65 and 80 dB SPL were evaluated after a two-week trial period using the 67-S Japanese monosyllable word list. Based on speech discrimination test results, ears were classified as well-fitting or non-well-fitting. FG values were compared between the two groups.
RESULTS
Twenty-one patients (42 ears) completed the study. Thirty-one ears (73%) were classified as well-fitting. Although HA gain was adjusted toward the target 1/3 G, measured FG values at 250 and 500 Hz remained lower than the target values. In well-fitting ears, low-frequency FG values were lower than the target 1/3 G, whereas FG at 2000 Hz was close to the target value. In contrast, non-well-fitting ears showed low-frequency FG values closer to the target 1/3 G, whereas FG values at 2000 and 4000 Hz remained below the target values.
CONCLUSIONS
Although HAs adjusted toward a 1/3 G target did not achieve the intended FG values, particularly at low frequencies, relatively favorable fitting outcomes were obtained in approximately three-quarters of the ears. In well-fitting ears, low-frequency FG remained below the target 1/3 G, whereas FG in the mid-frequency range around 2000 Hz was close to the target value. These findings provide a basis for future prospective studies to clarify how these FG characteristics should be applied to optimize HA adjustment.
PURPOSE
This study aimed to develop and validate OcuTOP, a novel handheld corneal topography device designed to overcome the limitations of conventional desktop systems. By incorporating software-based misalignment correction, OcuTOP seeks to provide accurate corneal curvature measurements without need for bulky mechanical alignment mechanisms. Validation was performed using a reference surface with known geometry to assess device accuracy and robustness.
METHODS
The OcuTOP device (75 g; 85 × 60 × 60 mm) was evaluated using a reference button with a known curvature (43.3 D). Controlled misalignments were introduced in longitudinal (Z: 42.5-43.5 mm), lateral (X: ±2 mm), and vertical (Y: ±2 mm) directions, generating 243 test cases. Images acquired by the device were analysed using neural network algorithms to estimate misalignment parameters, which were subsequently used to correct axial and tangential curvature maps and estimate button diameter, analogous to white-to-white corneal diameter.
RESULTS
OcuTOP demonstrated strong agreement with reference curvature values across all misalignment conditions (P for K1 & K2 = 0.365, 0.385 at Z = 42.5 mm; 0.606, 0.907 at Z = 43.0 mm; 0.297, 0.462 at Z = 43.5 mm). Even at maximum displacement (±2 mm in X and Y), central curvature predictions remained within 2% of true values, with mean astigmatism artifacts limited to <0.2 D at the apex of the surface. However, the errors in estimating curvature values increased progressively towards the periphery. Neural network estimation of Z distance achieved a mean error of 0.06 ± 0.05 mm, with no significant influence on the ability of the device to estimate curvature. WTW predictions were also consistent, with a mean value of 11.66 mm, differing by <1.5% from the reference diameter.
CONCLUSIONS
OcuTOP's software-based correction reliably compensates for translational and longitudinal misalignments, showing promising results for future studies enabling accurate corneal surface measurements without mechanical stabilisation.
Vimal Manoharan Nair, Ya-Bo Ye, Yuanwan Lou et al.· Contact lens & anterior eye...· 0 citations
This paper traces the historical development of frequentist sample size estimation from its philosophical origins to its present-day complexity. Preliminary concepts were identified by Christiaan Huygens' work on expected value and Jacob Bernoulli's law of large numbers, which first linked sample size and estimation accuracy. The 18th and 19th centuries brought major advances in probability theory through the work of Pierre-Simon de Laplace, Carl Friedrich Gauss and Siméon-Denis Poisson, yet explicit sample size planning remained uncommon. The early 20th century saw the emergence of methods for sample size calculations based on Jerzy Neyman and Egon Pearson's hypothesis testing framework and Sir Ronald Aylmer Fisher's experimental design principles. While Donald Mainland and Austin Bradford Hill referred indirectly to these as early as the 1930s, it took many decades before their explicit use became common. After the Second World War, contributions from figures such as Abraham Wald further embedded sample size planning with sequential methodologies. From the 1970s onward, standardised formulas, regulatory requirements, reporting standards such as CONSORT and statistical software consolidated frequentist sample size estimation as a routine component in applied research. In the 21st century, simulation-based, adaptive and Bayesian approaches, together with open-source computational ecosystems, have expanded the scope and accessibility of sample size methods. In contemporary research, sample size estimation has evolved into a multifaceted discipline; its methodological sophistication is contingent upon the underlying objective, illustrating the persistent divergence between explanatory inference and decision-oriented design.
K. Thorlund, Christian Gluud· Journal of the Royal Society...· 0 citations
Retrieval-Augmented Generation (RAG) grounds Large Language Model (LLM) outputs in external knowledge, but RAG systems usually trust whatever they retrieve, creating a Security-Reliability Gap: high semantic relevance does not guarantee factual truth. Adversaries exploit this through knowledge poisoning, inserting malicious documents to cause targeted misinformation. We propose an Evaluation Agent, middleware that combines Natural Language Inference (NLI) factual verification, a five-signal poison detector with relevance-weighted aggregation, and a Trust Index T = 0.4 F + 0.35 C + 0.25 (1 - P ) with a non-linear dampener for high-contamination contexts. On TruthfulQA with Llama 3.3 70B, the agent reaches 91% accuracy and 100% precision, with 100% recall on instruction injection, while in-place edits, such as entity swaps, remain hard to detect. Across three LLMs the Trust Index stays discriminative, with a Receiver Operating Characteristic Area Under the Curve (ROC-AUC) of 0.73 to 0.81; generation style matters more than model size, and per-LLM threshold calibration restores baseline competitive accuracy, whereas a weaker FEVER result shows that cross-dataset generalization requires domain-specific calibration. In a software-engineering use case, a secure-coding assistant over guidance from the Open Worldwide Application Security Project (OWASP) Top 10 and the Common Weakness Enumeration (CWE), the agent reliably blocks instruction injection of unsafe advice (F1 92%), while contradiction and subtle semantic weakening remain hard. Throughout, the agent measures detection of poisoned context before generation, not whether the LLM adopts the injected misinformation. We release the proposed approach, attack generator, and experimental artifacts at the link: https://github.com/GPT-Laboratory/TrustworthyRAG.
Balkrishna Giri, M. Hasan, Jussi Rasku et al.· 0 citations
Generative artificial intelligence (GAI) is becoming more incorporated into software engineering functions like code creation, debugging, requirement analysis, testing, and sharing knowledge. This research looks at how GAI affects software teams in terms of productivity and quality of the output in Agile environments. The research design used is quantitative, cross-sectional survey type using a questionnaire prepared for this research. The data used consists of 35 responses, with 34 usable cases in analyzing 30 Likert items. The measuring instrument consists of six concepts: use of GAI, efficiency of the software team, quality of the software output, GAI in Agile, team collaboration, and communication, and overall impact perceived. The descriptive results show positive feelings about the six concepts. The values on the mean for the different concepts varied from 3.54 to 3.78 on a scale of five, with GAI being the concept that received the highest mean (M = 3.78, SD = 0.47) while productivity was the one that received the lowest (M = 3.54, SD = 0.69). The instrument has a high level of internal consistency with α = 0.799 for the entire scale of 30 items. In terms of specific items, productivity, quality, and team collaboration had acceptable reliability, whereas GAI had low internal consistency and Agile and general have the upper limit of reliability therefore, construct-level findings should be interpreted cautiously. Pearson correlation analysis showed statistically significant positive associations between overall perceived impact and software output quality (r = 0.365, p = 0.034) and team collaboration and communication (r = 0.371, p = 0.031). Productivity was positively associated with overall impact but did not reach the conventional 0.05 significance level (r = 0.312, p = 0.073). In a multiple regression model, the five dimensions explained 23.5% of the variance in overall perceived impact (R² = 0.235); however, the overall model was not statistically significant (F(5, 28) = 1.719, p = 0.163). These findings support a cautious interpretation: respondents generally perceive GAI positively, but the present small sample does not provide strong evidence for broad causal claims.
ABDALMENAM KHALIF MASAUD ABUSWAH, ABDARRAHMAN KHALIF ALI ABOUSOWA, ZIAD OMAR SALEM WAREG· Al-Farooq Journal of Science...· 0 citations
The findings of the present study indicated that potential complications such as delayed union, nonunion, and osteomyelitis in the intramedullary nailing method are approximately comparable to those of the external fixator method.
Reza Noktesanj, Ali Nami, F. Amani et al.· journal of Health Research a...· 0 citations
Simulation of tillage operations is critical for precision management of soil-tool interactions, facilitating the conservation of soil structure. Improper use of machinery during land preparation in agriculture may lead to soil structure destruction. This paper aimed to analyze the effect of deep tillage on soil structure and the measured and simulated tillage resistance of the subsoiler cum rotary mixing implement. Soil bin measurements were collected using a motorized trolley with resistance sensors and a soil profilometer. A 3D geometry of the implement was created using PTC Creo Parametric 3D Modelling software, and the soil bed was modeled by discrete element (DE) particles using EDEM software. Accurate calibration of the DE model parameters was achieved by reproducing the soil bin. The cohesion between the particles was created by adding a cohesion resistance to the normal contact resistances to simulate the actual cohesive soil. It was found that the shape of the rotary blades significantly impacts the measured tillage resistance, the formed soil profile, and the simulations. The relative error of 0.4%, 4.9% and 4.2% was obtained for horizontal resistance, vertical resistance and soil profile respectively. The horizontal resistance showed the best regression results of 0.9997 $$\:{R}^{2}$$ at a $$\:NRMSE$$ of 0.04, followed by the soil furrow with 0.9936 $$\:{R}^{2}$$ and $$\:NRMSE$$ of 0.23 and vertical resistance with 0.9 $$\:{R}^{2}$$ and a $$\:NRMSE$$ of 0.27. The unpaired T-Test showed no statistically significant difference $$\:(p>0.05)$$ between simulation and experimental results. Regardless of tillage depth, soil layers cannot be destroyed with the proper blades on rotary tillers. DEM can be used as an accurate, consistent, and fast method of effectively predicting the final soil condition and resistances needed for tillage operations.
N. Makange, Chang-Ying Ji· Discover Soil· 0 citations
Abstract Background Total skin electron therapy (TSET) is a standard treatment for cutaneous T‐cell lymphoma. Due to the complex patient positioning and irregular body contours, robust in‐vivo dosimetry (IVD) is essential to verify dose uniformity. While thermoluminescent dosimeters (TLDs) are traditional standard, their utility is hindered by labor‐intensive, manual processing. Purposes This study evaluates the clinical implementation of a Gafchromic™ EBT4 film‐based IVD system integrated with a bespoke, open‐source analysis platform for automated batch‐processing. To address the inherent orientation dependence and loss of film orientation frequently encountered when preparing small‐format IVD films with a manual paper cutter, we developed an orthogonal dual‐scan protocol. By averaging pixel values from two perpendicular scans for both calibration and clinical measurement, this protocol effectively mitigates orientation‐dependent uncertainties and ensures dosimetric robustness. Methods The film‐based IVD system was clinically assessed in five TSET treatments and compared to six treatments utilizing TLD‐based IVD. Dosimetric accuracy was evaluated by comparing normalized fractional doses to the prescription. Statistical analysis was performed using the Mann‐Whitney U test with the Benjamini‐Hochberg procedure to control the false discovery rate across 20 anatomical sites. Workflow efficiency was quantified by the total time required for data readout and analysis per patient. Results The EBT4 film‐based IVD demonstrated dosimetric accuracy comparable to the TLDs, with mean fractional doses of 102.7% ± 9.6% and 100.4% ± 9.7%, respectively (p = 0.25). Clinical implementation of the film‐based approach significantly enhanced efficiency, reducing the total processing time from approximately 50 min to 15 min per treatment. Conclusions The proposed EBT4 film‐based IVD system, supported by open‐source software and an orthogonal dual‐scan protocol, offers a robust, cost‐effective, and time‐efficient alternative to traditional TLDs. This approach streamlines the clinical workflow without compromising dosimetric accuracy, making it a viable solution for TSET and broader radiotherapy IVD applications.
Zhexuan Zhang, Lan Lu, G. Videtic et al.· Journal of Applied Clinical...· 0 citations
AIMS
Safe prescribing and effective medication review during acute hospitalization depends on accurate information about liver and kidney function because these organs are responsible for the elimination of most medications. While estimates for kidney function are widely used, comparable markers of hepatic drug-metabolizing capacity are not routinely available. We evaluated the clinical relevance of pharmacogenomic (PGx) information for key pharmacogenes implicated in medication elimination in older adults presenting to the emergency department.
METHODS
Fourteen pharmacogenes were analysed using the Personal Medicine Profile™ test. GeneYouIn PillCheck™ software performed genotype-to-phenotype translations, identified drug-gene interactions (DGIs) and generated a clinical decision report based on each patient's actual medication use.
RESULTS
Among 125 acutely admitted older medical patients (median age 78.3 years; 10 medications; 7 chronic diseases), PGx testing identified 88 DGIs across 63 patients (50.4%). Of these, 46.5% were considered by clinical experts to be clinically relevant for the individual patient, affecting 33 patients (26.4%) in the total study population. Frequently implicated pharmacogenes included CYP2C19 (25.0%), SLCO1B1 (25.0%), CYP2D6 (20.5%), CYP2C9 (14.8%) and OPRM1 (6.8%), and frequently implicated medications included losartan (13.6%), pantoprazole (12.5%), simvastatin (12.5%), atorvastatin (11.4%) and metoprolol (11.4%).
CONCLUSION
With more than one-quarter of acutely admitted older medical patients having one or more clinically relevant DGIs, these findings suggest that PGx information may have meaningful clinical utility for improving prescribing practices in acute care. However, interpretation in this population requires careful consideration of other factors such as nutritional status and inflammation that may modify pharmacogene activity.
L. W. Christensen, A. K. Boas, Emilie Clausen et al.· British Journal of Clinical...· 0 citations
A USAF cadet and a Lincoln Laboratory researcher found AI chatbots can help nontechnical service members produce viable software applications for their unique problems.
