ArzEn-MultiGenre: An aligned parallel dataset of Egyptian Arabic song lyrics, novels, and subtitles, with English translations.

ArzEn-MultiGenre is a parallel dataset of Egyptian Arabic song lyrics, novels, and TV show subtitles that are manually translated and aligned with their English counterparts. The dataset contains 25,557 segment pairs that can be used to benchmark new machine translation models, fine-tune large language models in few-shot settings, and adapt commercial machine translation applications such as Google Translate. Additionally, the dataset is a valuable resource for research in various disciplines, including translation studies, cross-linguistic analysis, and lexical semantics. The dataset can also serve pedagogical purposes by training translation students and aid professional translators as a translation memory. The contributions are twofold: first, the dataset features textual genres not found in existing parallel Egyptian Arabic and English datasets, and second, it is a gold-standard dataset that has been translated and aligned by human experts.

Developing the Benchmark: Establishing a Gold Standard for the Evaluation of AI Caries Diagnostics.

Background/Objectives: The aim of this study was to establish a histology-based gold standard for the evaluation of artificial intelligence (AI)-based caries detection systems on proximal surfaces in bitewing images. Methods: Extracted human teeth were used to simulate intraoral situations, including caries-free teeth, teeth with artificially created defects and teeth with natural proximal caries. All 153 simulations were radiographed from seven angles, resulting in 1071 in vitro bitewing images. Histological examination of the carious lesion depth was performed twice by an expert. A total of thirty examiners analyzed all the radiographs for caries. Results: We generated in vitro bitewing images to evaluate the performance of AI-based carious lesion detection against a histological gold standard. All examiners achieved a sensitivity of 0.565, a Matthews correlation coefficient (MCC) of 0.578 and an area under the curve (AUC) of 76.1. The histology receiver operating characteristic (ROC) curve significantly outperformed the examiners' ROC curve (p < 0.001). All examiners distinguished induced defects from true caries in 54.6% of cases and correctly classified 99.8% of all teeth. Expert caries classification of the histological images showed a high level of agreement (intraclass correlation coefficient (ICC) = 0.993). Examiner performance varied with caries depth (p ≤ 0.008), except between E2 and E1 lesions (p = 1), while central beam eccentricity, gender, occupation and experience had no significant influence (all p ≥ 0.411). Conclusions: This study successfully established an unbiased dataset to evaluate AI-based caries detection on bitewing surfaces and compare it to human judgement, providing a standardized assessment for fair comparison between AI technologies and helping dental professionals to select reliable diagnostic tools.

Improving Sarcoma Outcomes: Target Trial Emulation to Compare the Impact of Unplanned and Planned Resections on the Outcome.

This study follows the Target Trial Emulation (TTE) framework to assess the impact of unplanned resections (UEs) and planned resections (PEs) of sarcomas on local recurrence-free survival (LRFS), metastasis-free survival (MFS), cancer-specific survival (CSS), and overall survival (OS). Sarcomas, malignant tumors with mesenchymal differentiation, present a significant clinical challenge due to their rarity, complexity, and the frequent occurrence of UEs, which complicates effective management. Our analysis utilized real-world-time data from the Swiss Sarcoma Network, encompassing 429 patients, to compare the impact of UEs and PEs, adjusting for known prognostic factors through a multivariable Cox regression model and propensity score weighting. Our findings reveal a significantly higher risk of local recurrence for UEs and a short-term follow-up period that showed no marked differences in MFS, CSS, and OS between the UE and PE groups, underlining the importance of optimal initial surgical management. Furthermore, tumor grade was validated as a critical prognostic factor, influencing outcomes irrespective of surgical strategy. This study illuminates the need for improved referral systems to specialized sarcoma networks to prevent UEs and advocates for the integration of TTE in sarcoma research to enhance clinical guidelines and decision-making in sarcoma care. Future research should focus on the prospective validations of these findings and the exploration of integrated care models to reduce the incidence of UEs and improve patient outcomes.

Brain-age prediction: Systematic evaluation of site effects, and sample age range and size.

Structural neuroimaging data have been used to compute an estimate of the biological age of the brain (brain-age) which has been associated with other biologically and behaviorally meaningful measures of brain development and aging. The ongoing research interest in brain-age has highlighted the need for robust and publicly available brain-age models pre-trained on data from large samples of healthy individuals. To address this need we have previously released a developmental brain-age model. Here we expand this work to develop, empirically validate, and disseminate a pre-trained brain-age model to cover most of the human lifespan. To achieve this, we selected the best-performing model after systematically examining the impact of seven site harmonization strategies, age range, and sample size on brain-age prediction in a discovery sample of brain morphometric measures from 35,683 healthy individuals (age range: 5-90 years; 53.59% female). The pre-trained models were tested for cross-dataset generalizability in an independent sample comprising 2101 healthy individuals (age range: 8-80 years; 55.35% female) and for longitudinal consistency in a further sample comprising 377 healthy individuals (age range: 9-25 years; 49.87% female). This empirical examination yielded the following findings: (1) the accuracy of age prediction from morphometry data was higher when no site harmonization was applied; (2) dividing the discovery sample into two age-bins (5-40 and 40-90 years) provided a better balance between model accuracy and explained age variance than other alternatives; (3) model accuracy for brain-age prediction plateaued at a sample size exceeding 1600 participants. These findings have been incorporated into CentileBrain (https://centilebrain.org/#/brainAGE2), an open-science, web-based platform for individualized neuroimaging metrics.

Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition.

Data-independent acquisition (DIA) techniques such as sequential window acquisition of all theoretical mass spectra (SWATH) acquisition have emerged as the preferred strategies for proteomic analyses. Our study optimized the SWATH-DIA method using a narrow isolation window placement approach, improving its proteomic performance. We optimized the acquisition parameter combinations of narrow isolation windows with different widths (1.9 and 2.9 Da) on a ZenoTOF 7600 (Sciex); the acquired data were analyzed using DIA-NN (version 1.8.1). Narrow SWATH (nSWATH) identified 5916 and 7719 protein groups on the digested peptides, corresponding to 400 ng of protein from mouse liver and HEK293T cells, respectively, improving identification by 7.52 and 4.99%, respectively, compared to conventional SWATH. The median coefficient of variation of the quantified values was less than 6%. We further analyzed 200 ng of benchmark samples comprising peptides from known ratios ofEscherichia coli, yeast, and human peptides using nSWATH. Consequently, it achieved accuracy and precision comparable to those of conventional SWATH, identifying an average of 95,456 precursors and 9342 protein groups across three benchmark samples, representing 12.6 and 9.63% improved identification compared to conventional SWATH. The nSWATH method improved identification at various loading amounts of benchmark samples, identifying 40.7% more protein groups at 25 ng. These results demonstrate the improved performance of nSWATH, contributing to the acquisition of deeper proteomic data from complex biological samples.

Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.

The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operon clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing strategies (PacBio circular consensus sequencing and two Nanopore approaches using unique molecular identifiers) and three tools for resolving amplicons sequence variants (ASVs) (USEARCH, VSEARCH, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essentially error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples, which enables us to identify previously undescribed microeukaryotic lineages.

Benchmarking for healthy food stores: protocol for a randomised controlled trial with remote Aboriginal and Torres Strait Islander communities in Australia to enhance adoption of health-enabling store policy and practice.

BACKGROUND: Aboriginal and Torres Strait Islander communities in remote Australia have initiated bold policies for health-enabling stores. Benchmarking, a data-driven and facilitated 'audit and feedback' with action planning process, provides a potential strategy to strengthen and scale health-enabling best-practice adoption by remote community store directors/owners. We aim to co-design a benchmarking model with five partner organisations and test its effectiveness with Aboriginal and Torres Strait Islander community stores in remote Australia. METHODS: Study design is a pragmatic randomised controlled trial with consenting eligible stores (located in very remote Northern Territory (NT) of Australia, primary grocery store for an Aboriginal community, and serviced by a Nutrition Practitioner with a study partner organisation). The Benchmarking model is informed by research evidence, purpose-built best-practice audit and feedback tools, and co-designed with partner organisation and community representatives. The intervention comprises two full benchmarking cycles (one per year, 2022/23 and 2023/24) of assessment, feedback, action planning and action implementation. Assessment of stores includes i adoption status of 21 evidence-and industry-informed health-enabling policies for remote stores, ii implementation of health-enabling best-practice using a purpose-built Store Scout App, iii price of a standardised healthy diet using the Aboriginal and Torres Strait Islander Healthy Diets ASAP protocol; and, iv healthiness of food purchasing using sales data indicators. Partner organisations feedback reports and co-design action plans with stores. Control stores receive assessments and continue with usual retail practice. All stores provide weekly electronic sales data to assess the primary outcome, change in free sugars (g) to energy (MJ) from all food and drinks purchased, baseline (July-December 2021) vs July-December 2023. DISCUSSION: We hypothesise that the benchmarking intervention can improve the adoption of health-enabling store policy and practice and reduce sales of unhealthy foods and drinks in remote community stores of Australia. This innovative research with remote Aboriginal and Torres Strait Islander communities can inform effective implementation strategies for healthy food retail more broadly. TRIAL REGISTRATION: ACTRN12622000596707, Protocol version 1.

Benchmarking computational variant effect predictors by their ability to infer human traits.

BACKGROUND: Computational variant effect predictors offer a scalable and increasingly reliable means of interpreting human genetic variation, but concerns of circularity and bias have limited previous methods for evaluating and comparing predictors. Population-level cohorts of genotyped and phenotyped participants that have not been used in predictor training can facilitate an unbiased benchmarking of available methods. Using a curated set of human gene-trait associations with a reported rare-variant burden association, we evaluate the correlations of 24 computational variant effect predictors with associated human traits in the UK Biobank and All of Us cohorts. RESULTS: AlphaMissense outperformed all other predictors in inferring human traits based on rare missense variants in UK Biobank and All of Us participants. The overall rankings of computational variant effect predictors in these two cohorts showed a significant positive correlation. CONCLUSION: We describe a method to assess computational variant effect predictors that sidesteps the limitations of previous evaluations. This approach is generalizable to future predictors and could continue to inform predictor choice for personal and clinical genetics.

Development and validation of the HMS-Sepsis mortality model.

BACKGROUND: When comparing outcomes after sepsis, it is essential to account for patient case mix to make fair comparisons. We developed a model to assess risk-adjusted 30-day mortality in the Michigan Hospital Medicine Safety's sepsis initiative (HMS-Sepsis). QUESTION: Can HMS-Sepsis registry data adequately predict risk of 30-day mortality? Do performance assessments using adjusted vs unadjusted data differ? STUDY DESIGN AND METHODS: Retrospective cohort of community-onset sepsis hospitalizations in HMS-Sepsis registry (4/2022-9/2023), with split derivation (70%) and validation (30%) cohorts. We fit a risk-adjustment model (HMS-Sepsis mortality model) incorporating acute physiology, demographic, and baseline health data and assessed model performance using c-statistics, Brier's scores, and comparisons of predicted vs observed mortality by deciles of risk. We compared hospital performance (1st quintile, middle quintiles, 5th quintile) using observed versus adjusted mortality to understand the extent to which risk-adjustment impacted hospital performance assessment. RESULTS: Among 17,514 hospitalizations from 66 hospitals during the study period, 12,260 (70%) were used for model derivation and 5,254 (30%) for model validation. 30-day mortality for the total cohort was 19.4%. The final model included 13 physiologic variables, two physiologic interactions, and 16 demographic and chronic health variables. The most significant variables were age, metastatic solid tumor, temperature, altered mental status, and platelet count. The model c-statistic was 0.82 for the derivation cohort, 0.81 for the validation cohort, and ≥0.78 for all subgroups assessed. Overall calibration error was 0.0% and mean calibration error across deciles of risk was 1.5%. Standardized mortality ratios yielded different assessments than observed mortality for 33.9% of hospitals. CONCLUSIONS: The HMS-Sepsis mortality model had strong discrimination, adequate calibration, and reclassified one-third of hospitals to a different performance category from unadjusted mortality. Based on its strong performance, the HMS-Sepsis mortality model can aid in fair hospital benchmarking, assessment of temporal changes, and observational causal inference analysis.

Benchmarking circularity in supply chains: A systematic literature review.

The challenges posed by unsustainable practices in today's economy underscore the urgent need for a transition toward a circular economy (CE) and a holistic supply chain (SC) perspective. Benchmarking plays a pivotal role in managing circular SCs, offering a metric to gauge progress. However, the lack of consensus on the optimal benchmarking approach hampers effective implementation of circular business practices. To address this gap, we conducted a systematic review of the literature, identifying 29 pertinent publications. The analysis revealed 30 unique attributes and sub-attributes for benchmarking circularity, which were clustered into five main attributes. The main attributes are goals, subjects, key performance indicators (KPIs), data sources, and evaluation methods, while the sub-attributes are organised as features of the main attributes and depicted as a feature model. Drawing from selected publications, we illustrated each feature with examples. Our model offers a comprehensive benchmarking reference for circularity and will be a valuable tool for managers in the transition toward circularity. Supply chains seeking to benchmark their transition to circularity can apply the reference model to ensure that their benchmarking strategy is consistent with state-of-the-art knowledge. By providing a generic circularity benchmarking approach that is valid for diverse economic sectors, our findings contribute to theoretical efforts to address the lack of generic frameworks for CE.

Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates.

BACKGROUND: Oxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However, even small levels of error can obscure the phylogenetic relationships between closely related isolates. Polishing tools have been developed to correct these errors, but it is uncertain if they obtain the accuracy needed for the high-resolution source tracking of foodborne illness outbreaks. RESULTS: We tested 132 combinations of assembly and short- and long-read polishing tools to assess their accuracy for reconstructing the genome sequences of 15 highly similar Salmonella enterica serovar Newport isolates from a 2020 onion outbreak. While long-read polishing alone improved accuracy, near perfect accuracy (99.9999% accuracy or ~ 5 nucleotide errors across the 4.8 Mbp genome, excluding low confidence regions) was only obtained by pipelines that combined both long- and short-read polishing tools. Notably, medaka was a more accurate and efficient long-read polisher than Racon. Among short-read polishers, NextPolish showed the highest accuracy, but Pilon, Polypolish, and POLCA performed similarly. Among the 5 best performing pipelines, polishing with medaka followed by NextPolish was the most common combination. Importantly, the order of polishing tools mattered i.e., using less accurate tools after more accurate ones introduced errors. Indels in homopolymers and repetitive regions, where the short reads could not be uniquely mapped, remained the most challenging errors to correct. CONCLUSIONS: Short reads are still needed to correct errors in nanopore sequenced assemblies to obtain the accuracy required for source tracking investigations. Our granular assessment of the performance of the polishing pipelines allowed us to suggest best practices for tool users and areas for improvement for tool developers.

Benchmarking predictive methods for small-angle X-ray scattering from atomic coordinates of proteins using maximum likelihood consensus data.

Stimulated by informal conversations at the XVII International Small Angle Scattering (SAS) conference (Traverse City, 2017), an international team of experts undertook a round-robin exercise to produce a large dataset from proteins under standard solution conditions. These data were used to generate consensus SAS profiles for xylose isomerase, urate oxidase, xylanase, lysozyme and ribonuclease A. Here, we apply a new protocol using maximum likelihood with a larger number of the contributed datasets to generate improved consensus profiles. We investigate the fits of these profiles to predicted profiles from atomic coordinates that incorporate different models to account for the contribution to the scattering of water molecules of hydration surrounding proteins in solution. Programs using an implicit, shell-type hydration layer generally optimize fits to experimental data with the aid of two parameters that adjust the volume of the bulk solvent excluded by the protein and the contrast of the hydration layer. For these models, we found the error-weighted residual differences between the model and the experiment generally reflected the subsidiary maxima and minima in the consensus profiles that are determined by the size of the protein plus the hydration layer. By comparison, all-atom solute and solvent molecular dynamics (MD) simulations are without the benefit of adjustable parameters and, nonetheless, they yielded at least equally good fits with residual differences that are less reflective of the structure in the consensus profile. Further, where MD simulations accounted for the precise solvent composition of the experiment, specifically the inclusion of ions, the modelled radius of gyration values were significantly closer to the experiment. The power of adjustable parameters to mask real differences between a model and the structure present in solution is demonstrated by the results for the conformationally dynamic ribonuclease A and calculations with pseudo-experimental data. This study shows that, while methods invoking an implicit hydration layer have the unequivocal advantage of speed, care is needed to understand the influence of the adjustable parameters. All-atom solute and solvent MD simulations are slower but are less susceptible to false positives, and can account for thermal fluctuations in atomic positions, and more accurately represent the water molecules of hydration that contribute to the scattering profile.

Cardiorenal effects of Angiotensin-converting enzyme inhibitors and Angiotensin receptor blockers in people underrepresented in trials: analysis of routinely collected data with emulation of a reference trial (ONTARGET).

Cardiovascular disease (CVD) is a leading cause of death globally. Angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARB), compared in the ONTARGET trial, each prevent CVD. However, trial results may not be generalisable and their effectiveness in underrepresented groups is unclear. Using trial emulation methods within routine-care data to validate findings, we explored generalisability of ONTARGET results. For people prescribed an ACEi/ARB in the UK Clinical Practice Research Datalink GOLD from 1/1/2001-31/7/2019, we applied trial criteria and propensity-score methods to create an ONTARGET trial-eligible cohort. Comparing ARB to ACEi, we estimated hazard ratios for the primary composite trial outcome (cardiovascular death, myocardial infarction, stroke, or hospitalisation for heart failure), and secondary outcomes. As the pre-specified criteria were met confirming trial emulation, we then explored treatment heterogeneity among three trial-underrepresented subgroups: females, those aged ≥75 years and those with chronic kidney disease (CKD). In the trial-eligible population (n=137,155), results for the primary outcome demonstrated similar effects of ARB and ACEi, (HR 0.97 [95% CI: 0.93, 1.01]), meeting the pre-specified validation criteria. When extending this outcome to trial-underrepresented groups, similar treatment effects were observed by sex, age and CKD. This suggests that ONTARGET trial findings are generalisable to trial-underrepresented subgroups.

American Heart Association Cardiogenic Shock Registry: Design and Implementation.

BACKGROUND: Cardiogenic shock is a morbid complication of heart disease that claims the lives of more than 1 in 3 patients presenting with this syndrome. Supporting a unique collaboration across clinical specialties, federal regulators, payors, and industry, the American Heart Association volunteers and staff have launched a quality improvement registry to better understand the clinical manifestations of shock phenotypes, and to benchmark the management patterns, and outcomes of patients presenting with cardiogenic shock to hospitals across the United States. METHODS: Participating hospitals will enroll consecutive hospitalized patients with cardiogenic shock, regardless of etiology or severity. Data are collected through individual reviews of medical records of sequential adult patients with cardiogenic shock. The electronic case record form was collaboratively designed with a core minimum data structure and aligned with Shock Academic Research Consortium definitions. This registry will allow participating health systems to evaluate patient-level data including diagnostic approaches, therapeutics, use of advanced monitoring and circulatory support, processes of care, complications, and in-hospital survival. Participating sites can leverage these data for onsite monitoring of outcomes and benchmarking versus other institutions. The registry was concomitantly designed to provide a high-quality longitudinal research infrastructure for pragmatic randomized trials as well as translational, clinical, and implementation research. An aggregate deidentified data set will be made available to the research community on the American Heart Association's Precision Medicine Platform. On March 31, 2022, the American Heart Association Cardiogenic Shock Registry received its first clinical records. At the time of this submission, 100 centers are participating. CONCLUSIONS: The American Heart Association Cardiogenic Shock Registry will serve as a resource using consistent data structure and definitions for the medical and research community to accelerate scientific advancement through shared learning and research resulting in improved quality of care and outcomes of shock patients.

Impact of Institutional Practices and Surgical Complexity on Sarcoma Surgery Costs: Driving Efficiency in Value-Based Healthcare.

BACKGROUND: Sarcomas present a unique challenge within healthcare systems due to their rarity and complex treatment requirements. This study explores the economic impact of sarcoma surgeries across three Swiss tertiary healthcare institutions, utilizing a consistent surgical approach by a single surgeon to eliminate variability in surgical expertise as a confounding factor. METHODS: By analyzing data from 356 surgeries recorded in a real-world-time data warehouse, this study assesses surgical and hospital costs relative to institutional characteristics and surgical complexity. RESULTS: Our findings reveal significant cost variations driven more by institutional resource management and pricing strategies than by surgical techniques. Surgical and total hospitalization costs were analyzed in relation to tumor dignity and complexity scores, showing that higher complexity and malignancy significantly increase costs. Interestingly, it was found that surgical costs accounted for only one-third of the total hospitalization costs, highlighting the substantial impact of non-surgical factors on the overall cost of care. CONCLUSIONS: The study underscores the need for standardized cost assessment practices and highlights the potential of predictive models in enhancing resource allocation and surgical planning. By advocating for value-based healthcare models and standardized treatment guidelines, this research contributes to more equitable and sustainable healthcare delivery for sarcoma patients. These insights affirm the necessity of including a full spectrum of care costs in value-based models to truly optimize healthcare delivery. These insights prompt a reevaluation of current policies and encourage further research across diverse geographical settings to refine cost management strategies in sarcoma treatment.

Optimizing in silico drug discovery: simulation of connected differential expression signatures and applications to benchmarking.

BACKGROUND: We present a novel simulation method for generating connected differential expression signatures. Traditional methods have struggled with the lack of reliable benchmarking data and biases in drug-disease pair labeling, limiting the rigorous benchmarking of connectivity-based approaches. OBJECTIVE: Our aim is to develop a simulation method based on a statistical framework that allows for adjustable levels of parametrization, especially the connectivity, to generate a pair of interconnected differential signatures. This could help to address the issue of benchmarking data availability for connectivity-based drug repurposing approaches. METHODS: We first detailed the simulation process and how it reflected real biological variability and the interconnectedness of gene expression signatures. Then, we generated several datasets to enable the evaluation of different existing algorithms that compare differential expression signatures, providing insights into their performance and limitations. RESULTS: Our findings demonstrate the ability of our simulation to produce realistic data, as evidenced by correlation analyses and the log2 fold-change distribution of deregulated genes. Benchmarking reveals that methods like extreme cosine similarity and Pearson correlation outperform others in identifying connected signatures. CONCLUSION: Overall, our method provides a reliable tool for simulating differential expression signatures. The data simulated by our tool encompass a wide spectrum of possibilities to challenge and evaluate existing methods to estimate connectivity scores. This may represent a critical gap in connectivity-based drug repurposing research because reliable benchmarking data are essential for assessing and advancing in the development of new algorithms. The simulation tool is available as a R package (General Public License (GPL) license) at https://github.com/cgonzalez-gomez/cosimu.

Efficiency and Security Evaluation of Lightweight Cryptographic Algorithms for Resource-Constrained IoT Devices.

The IoT has become an integral part of the technological ecosystem that we all depend on. The increase in the number of IoT devices has also brought with it security concerns. Lightweight cryptography (LWC) has evolved to be a promising solution to improve the privacy and confidentiality aspect of IoT devices. The challenge is to choose the right algorithm from a plethora of choices. This work aims to compare three different LWC algorithms: AES-128, SPECK, and ASCON. The comparison is made by measuring various criteria such as execution time, memory utilization, latency, throughput, and security robustness of the algorithms in IoT boards with constrained computational capabilities and power. These metrics are crucial to determine the suitability and help in making informed decisions on choosing the right cryptographic algorithms to strike a balance between security and performance. Through the evaluation it is observed that SPECK exhibits better performance in resource-constrained IoT devices.

3-dimensional surface geometry dataset of Scots pine and Norway spruce shoots from the Järvselja RAdiation transfer Model Intercomparison (RAMI) pine stand.

Conifer shoots exhibit intricate geometries at an exceptionally detailed spatial scale. Describing the complete structure of a conifer shoot, which contributes to a radiation scattering pattern, has been difficult, and the previous respective components of radiative transfer models for conifer stands were rather coarse. This paper presents a dataset aimed at models and applications requiring detailed 3D representations of needle shoots. The data collection was conducted in the Järvselja RAdiation transfer Model Intercomparison (RAMI) pine stand in Estonia. The dataset includes 3-dimensional surface information on 10 shoots of two conifer species present in the stand (5 shoots per species) - Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies L. Karst.). The samples were collected on 26th July 2022, and subsequently blue light 3D photogrammetry scanning technique was used to obtain their high-resolution 3D point cloud representations. For each of these samples, the dataset comprises of a photo of the sampled shoot and its obtained 3-dimensional surface reconstruction. Scanned shoots may replace previous, artificially generated models and contribute to the more realistic representation of 3D forest representations and, consequently, more accurate estimates of related parameters and processes by radiative transfer models.

Dyport: dynamic importance-based biomedical hypothesis generation benchmarking technique.

BACKGROUND: Automated hypothesis generation (HG) focuses on uncovering hidden connections within the extensive information that is publicly available. This domain has become increasingly popular, thanks to modern machine learning algorithms. However, the automated evaluation of HG systems is still an open problem, especially on a larger scale. RESULTS: This paper presents a novel benchmarking framework Dyport for evaluating biomedical hypothesis generation systems. Utilizing curated datasets, our approach tests these systems under realistic conditions, enhancing the relevance of our evaluations. We integrate knowledge from the curated databases into a dynamic graph, accompanied by a method to quantify discovery importance. This not only assesses hypotheses accuracy but also their potential impact in biomedical research which significantly extends traditional link prediction benchmarks. Applicability of our benchmarking process is demonstrated on several link prediction systems applied on biomedical semantic knowledge graphs. Being flexible, our benchmarking system is designed for broad application in hypothesis generation quality verification, aiming to expand the scope of scientific discovery within the biomedical research community. CONCLUSIONS: Dyport is an open-source benchmarking framework designed for biomedical hypothesis generation systems evaluation, which takes into account knowledge dynamics, semantics and impact. All code and datasets are available at: https://github.com/IlyaTyagin/Dyport .

Diagnosing patient flow issues in the emergency department: an Australasian hospital case study.

PURPOSE: This study investigates how a hospital can increase the flow of patients through its emergency department by using benchmarking and process improvement techniques borrowed from the manufacturing sector. DESIGN/METHODOLOGY/APPROACH: An in-depth case study of an Australasian public hospital utilises rigorous, multi-method data collection procedures with systems thinking to benchmark an emergency department (ED) value stream and identify the performance inhibitors. FINDINGS: High levels of value stream uncertainty result from inefficient processes and weak controls. Reduced patient flow arises from senior management's commitment to simplistic government targets, clinical staff that lack basic operations management skills, and fragmented information systems. High junior/senior staff ratios aggravate the lack of inter-functional integration and poor use of time and material resources, increasing the risk of a critical patient incident. RESEARCH LIMITATIONS/IMPLICATIONS: This research is limited to a single case; hence, further research should assess value stream maturity and associated performance enablers and inhibitors in other emergency departments experiencing patient flow delays. PRACTICAL IMPLICATIONS: This study illustrates how hospital managers can use systems thinking and a context-free performance benchmarking measure to identify needed interventions and transferable best practices for achieving seamless patient flow. ORIGINALITY/VALUE: This study is the first to operationalise the theoretical concept of the seamless healthcare system to acute care as defined by Parnaby and Towill (2008). It is also the first to use the uncertainty circle model in an Australasian public healthcare setting to objectively benchmark an emergency department's value stream maturity.