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DOE OSTI2024

Question-answering system extracts information on injection drug use from clinical notes

Background. Injection drug use (IDU) can increase mortality and morbidity. Therefore, identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients’ electronic health records (EHR) is difficult because there is no other structured data available, such as International Classification of Disease (ICD) codes, and IDU is most often documented in unstructured free-text clinical notes. Although natural language processing can efficiently extract this information from unstructured data, there are no validated tools. Methods. Here, to address this gap in clinical information, we design a question-answering (QA) framework to extract information on IDU from clinical notes for use in clinical operations. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. We use 2323 clinical notes of 1145 patients curated from the US Department of Veterans Affairs (VA) Corporate Data Warehouse to construct the gold-standard dataset for developing and evaluating the QA model. We also demonstrate the QA model’s ability to extract IDU-related information from temporally out-of-distribution data. Results. Here, we show that for a strict match between gold-standard and predicted answers, the QA model achieves a 51.65% F1 score. For a relaxed match between the gold-standard and predicted answers, the QA model obtains a 78.03% F1 score, along with 85.38% Precision and 79.02% Recall scores. Moreover, the QA model demonstrates consistent performance when subjected to temporally out-of-distribution data. Conclusions. Our study introduces a QA framework designed to extract IDU information from clinical notes, aiming to enhance the accurate and efficient detection of people who inject drugs, extract relevant information, and ultimately facilitate informed patient care.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Structure prediction of epitaxial inorganic interfaces by lattice and surface matching with Ogre

We present a new version of the Ogre open source Python package with the capability to perform structure prediction of epitaxial inorganic interfaces by lattice and surface matching. In the lattice matching step, a scan over combinations of substrate and film Miller indices is performed to identify the domain-matched interfaces with the lowest mismatch. Subsequently, surface matching is conducted by Bayesian optimization to find the optimal interfacial distance and in-plane registry between the substrate and the film. For the objective function, a geometric score function is proposed based on the overlap and empty space between atomic spheres at the interface. The score function reproduces the results of density functional theory (DFT) at a fraction of the computational cost. The optimized interfaces are pre-ranked using a score function based on the similarity of the atomic environment at the interface to the bulk environment. Final ranking of the top candidate structures is performed with DFT. Ogre streamlines DFT calculations of interface energies and electronic properties by automating the construction of interface models. The application of Ogre is demonstrated for two interfaces of interest for quantum computing and spintronics, Al/InAs and Fe/InSb.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Simulating energy performance of buildings: a study using eQUEST and Energy Star ® portfolio manager

Commercial buildings consume significant energy in the United States and exhibit high potential for energy use reduction through retrofits. Benchmarking and energy simulation are well established tools in the industry to identify potential improvements and measure performance. Analysis to identify most sensitive retrofit parameters to energy performance can optimize investment and available energy savings. Presented study demonstrates methodology using a static model to determine sensitivity of building design and retrofit parameters with respect to energy performance. Calibrated simulation energy models (eQUEST) of two distribution centers (A, B) are presented. A fractional factorial analysis is conducted on retrofit parameters of efficiency measures targeting the highest energy consumers, and the results are benchmarked using Energy Star® Portfolio Manager. A custom Microsoft Excel® based simulation model is created to simulate occupancy levels, lighting, plug loads, and other equipment used in various spaces throughout the day. For Building A, efficient lighting was the most influential parameter for energy savings, carbon savings and benchmarking score; whereas, for Building B, HVAC efficiency was most influential for energy and demand controlled ventilation and economizers was most influential for benchmarking score. While retrofit projects can save energy and carbon emissions, variation in source-site ratios and state grid emissions, benchmarking scores may not always reflect equivalent improvement. State grid emissions factors, natural gas composition are difficult to model and hence not considered in this study. In conclusion, the synergistic analysis presented, emphasizes the importance of benchmarking and efficiency retrofits in promoting sustainable building practices to reduce energy consumption.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2025

Impacts of benchmarking choices on inferred model skill of the Arctic–Boreal terrestrial carbon cycle

Abstract Land surface models require continuous validation against observations to improve and reduce simulation uncertainty. However, inferred model performance can be heavily influenced by subjective choices made in the selection and application of observational data products. A key area often misrepresented by models is the Arctic–Boreal region, which is a potential tipping point region in Earth’s climate system due to large permafrost carbon stocks that are vulnerable to release with climate warming. We use the International Land Model Benchmarking (ILAMB) framework to evaluate how the model skill of TRENDY-v9 models varies based on the choice of observational-based benchmark and how benchmarks are applied in model evaluation. This analysis uses global datasets integrated into ILAMB and new, regionally-specific observational products from the Arctic–Boreal Vulnerability Experiment. Our results cover the overall time period of 1979–2019 and show that model scores can vary substantially depending on the data product applied, with higher model scores indicating better model performance against observations. The lowest model scores occur when benchmarked against regional, compared to global, datasets. We also evaluate observed and modeled functional relationships between ecosystem respiration and air temperature and between gross primary production and precipitation. Here, we find that the magnitude and shape of the responses are strongly impacted by the choice of observational dataset and the approach used to construct the functional relationship benchmark. These results suggest that model evaluation studies could conclude a false sense of model skill if only using a single benchmark data product or if not applying regional data products when performing a regional model analysis. Collectively, our findings highlight the influence of benchmarking choices on model evaluation and point to the need for benchmarking guidelines when assessing model skill.

Poe, Jeralyn (ORCID:0000000318495278)↗

DOE OSTI2021

VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families

Abstract Motivation Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets. Results In this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified. Availability and implementation The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Plasma phosphorylated tau217 strongly associates with memory deficits in the Alzheimer’s disease spectrum

Abstract Plasma phosphorylated tau (p-tau) biomarkers open unprecedented opportunities for identifying carriers of Alzheimer’s disease pathophysiology in early disease stages using minimally invasive techniques. Plasma p-tau biomarkers are believed to reflect tau phosphorylation and secretion. However, it remains unclear to what extent the magnitude of plasma p-tau abnormalities reflects neuronal network disturbance in the form of cognitive impairment. To address this question, we included 103 cognitively unimpaired elderly and 40 cognitively impaired, amyloid-β-positive individuals from the TRIAD cohort, in addition to 336 cognitively unimpaired and 216 cognitively impaired, amyloid-β-positive older adults from the BioFINDER-2 cohort. Participants had tau PET scans, amyloid PET scans or amyloid CSF, p-tau217, p-tau181 and p-tau231 blood measures, structural T1-MRI and cognitive assessments. In this cross-sectional study, we used regression models and correlation analyses to assess the relationship between plasma biomarkers and cognitive scores. Furthermore, we applied receiver operating characteristic curves to assess cognitive impairment across plasma biomarkers. Finally, we categorized participants into amyloid (A), p-tau (T1) and tau PET (T2) positive (+) or negative (−) profiles and ran non-parametric comparisons to assess differences across cognitive domains. We found that plasma p-tau217 was more associated with cognitive performance than p-tau181 and p-tau231 and that this relationship was particularly strong for memory scores (TRIAD: βp-tau217 = −0.53, βp-tau181 = −0.35 and βp-tau231 = −0.24; BioFINDER-2: βp-tau217 = −0.52, βp-tau181 = −0.24 and βp-tau231 = −0.29). Associations in amyloid-β-positive participants resembled these results, but other cognitive scores also showed strong associations in cognitively impaired individuals. Moreover, plasma p-tau217 outperformed plasma p-tau181 and plasma p-tau231 in identifying memory impairment (area under the curve values for TRIAD: p-tau217 = 0.86, p-tau181 = 0.77 and p-tau231 = 0.75; and for BioFINDER-2: p-tau217 = 0.86, p-tau181 = 0.76 and p-tau231 = 0.81) and in identifying executive function impairment only in the BioFINDER-2 cohort (p-tau217 = 0.82, p-tau181 = 0.76 and p-tau231 = 0.76). Lastly, we showed that subtle memory deficits were present in A+T1+T2− participants for plasma p-tau217 (P = 0.007) and plasma p-tau181 (P = 0.01) in the TRIAD cohort and for all biomarkers across cognitive domains in A+T1+T2− and A+T1+T2− individuals (P < 0.001 in all) in the BioFINDER-2 cohort. The A+T1+T2− individuals showed cognitive deficits in both cohorts (P < 0.001 in all). Together, our results suggest that plasma p-tau217 stands out as a biomarker capable of identifying memory deficits attributable to Alzheimer’s disease and that memory impairment certainly occurs in amyloid-β- and plasma p-tau-positive individuals who have no significant amounts of tau in the neocortex.

Neurosciences & Neurology↗

DOE OSTI2022

Disentangling Alzheimer’s disease neurodegeneration from typical brain ageing using machine learning

Abstract Neuroimaging biomarkers that distinguish between changes due to typical brain ageing and Alzheimer’s disease are valuable for determining how much each contributes to cognitive decline. Supervised machine learning models can derive multivariate patterns of brain change related to the two processes, including the Spatial Patterns of Atrophy for Recognition of Alzheimer’s Disease (SPARE-AD) and of Brain Aging (SPARE-BA) scores investigated herein. However, the substantial overlap between brain regions affected in the two processes confounds measuring them independently. We present a methodology, and associated results, towards disentangling the two. T1-weighted MRI scans of 4054 participants (48–95 years) with Alzheimer’s disease, mild cognitive impairment (MCI), or cognitively normal (CN) diagnoses from the Imaging-based coordinate SysTem for AGIng and NeurodeGenerative diseases (iSTAGING) consortium were analysed. Multiple sets of SPARE scores were investigated, in order to probe imaging signatures of certain clinically or molecularly defined sub-cohorts. First, a subset of clinical Alzheimer’s disease patients (n = 718) and age- and sex-matched CN adults (n = 718) were selected based purely on clinical diagnoses to train SPARE-BA1 (regression of age using CN individuals) and SPARE-AD1 (classification of CN versus Alzheimer’s disease) models. Second, analogous groups were selected based on clinical and molecular markers to train SPARE-BA2 and SPARE-AD2 models: amyloid-positive Alzheimer’s disease continuum group (n = 718; consisting of amyloid-positive Alzheimer’s disease, amyloid-positive MCI, amyloid- and tau-positive CN individuals) and amyloid-negative CN group (n = 718). Finally, the combined group of the Alzheimer’s disease continuum and amyloid-negative CN individuals was used to train SPARE-BA3 model, with the intention to estimate brain age regardless of Alzheimer’s disease-related brain changes. The disentangled SPARE models, SPARE-AD2 and SPARE-BA3, derived brain patterns that were more specific to the two types of brain changes. The correlation between the SPARE-BA Gap (SPARE-BA minus chronological age) and SPARE-AD was significantly reduced after the decoupling (r = 0.56–0.06). The correlation of disentangled SPARE-AD was non-inferior to amyloid- and tau-related measurements and to the number of APOE ε4 alleles but was lower to Alzheimer’s disease-related psychometric test scores, suggesting the contribution of advanced brain ageing to the latter. The disentangled SPARE-BA was consistently less correlated with Alzheimer’s disease-related clinical, molecular and genetic variables. By employing conservative molecular diagnoses and introducing Alzheimer’s disease continuum cases to the SPARE-BA model training, we achieved more dissociable neuroanatomical biomarkers of typical brain ageing and Alzheimer’s disease.

Hwang, Gyujoon↗

DOE OSTI2020

Efficacy of dalbavancin against MRSA biofilms in a rat model of orthopaedic implant-associated infection

Abstract Objectives The aim of this study was to evaluate the efficacy of dalbavancin against MRSA biofilm-related infection in orthopaedic implants in vivo. Methods One MRSA strain isolated from human osteomyelitis was used to promote biofilm formation on the surface of screws. The implants were inserted in the proximal tibia under general anaesthesia. Thirty-nine Wistar rats were divided into three groups [control group (no treatment), Group 1 (7 days of treatment) and Group 2 (14 days of treatment)]; both treatment groups were administered dalbavancin intraperitoneally and euthanized after treatment. cfu of bacteria present in both the tibia and the implant were quantified. The infection severity was assessed by histopathology and scored from 0 (no infection) to 4 (severe infection). Results The high number of cfu/g and cfu/mL present in the control group indicated a well-established infection. There was a significant reduction in cfu in rats treated with dalbavancin both in the tibia (2.8 × 105 cfu/g) and the implant (1.1 × 106 cfu/mL) in Group 1 (1.8 × 103 cfu/g and 2.4 × 105 cfu/mL, respectively) and in Group 2 (8.2 cfu/g and 8.2 × 103 cfu/mL, respectively). Most animals from the control group presented an infection scored as 3 (severe). At the end of the experiment, most rats from Groups 1 and 2 presented an infection scored as 2 (moderate) and 0 (no infection), respectively. Conclusions Although there was a marked decrease in cfu number, signs of biofilm-induced infection prevailed after 14 days of treatment. Further studies should be carried out to evaluate the potential of dalbavancin in the treatment of bone and orthopaedic implant-associated MRSA infections.

Silva, Vanessa↗

DOE OSTI2020

A catalogue of Locus Algorithm pointings for optimal differential photometry for 23 779 quasars

ABSTRACT This paper presents a catalogue of optimized pointings for differential photometry of 23 779 quasars extracted from the Sloan Digital Sky Survey (SDSS) Catalogue and a Score for each indicating the quality of the Field of View (FoV) associated with that pointing. Observation of millimagnitude variability on a time-scale of minutes typically requires differential observations with reference to an ensemble of reference stars. For optimal performance, these reference stars should have similar colour and magnitude to the target quasar. In addition, the greatest quantity and quality of suitable reference stars may be found by using a telescope pointing which offsets the target object from the centre of the FoV. By comparing each quasar with the stars which appear close to it on the sky in the SDSS Catalogue, an optimum pointing can be calculated, and a figure of merit, referred to as the ‘Score’ is calculated for that pointing. Highly flexible software has been developed to enable this process to be automated and implemented in a distributed computing paradigm, which enables the creation of catalogues of pointings given a set of input targets. Applying this technique to a sample of 40 000 targets from the fourth SDSS quasar catalogue resulted in the production of pointings and Scores for 23 779 quasars based on their magnitudes in the SDSS r-band. This catalogue is a useful resource for observers planning differential photometry studies and surveys of quasars to select those which have many suitable celestial neighbours for differential photometry.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Integrated Metrics for County-Level Resilience Ranking Using Entropy and TOPSIS

In the face of atypical weather events, power infrastructure failures, and limited resources for resilience investment, energy decision-makers need data-driven metrics to allocate resilience investments and maximize the reduction of power outage impacts. For state-level planning, for instance, ranking the resilience of each county is key to ensuring effective distribution of resources. In such cases, resilience for each spatial unit is multifaceted and is captured by a set of indicators (i.e., metrics) that can be combined into an overall score that reduces the complexity of power outage dynamics to a single decision metric. However, weighting of these indicators is often addressed by simplifying assumptions (i.e., equal weights) or semi-subjective methods that rely on user-defined weights that can introduce biases (e.g., weighted average score). Within the disaster risk reduction and resilience engineering community, a recurring challenge in multicriteria decision-making is the objective weighting of indicators for composite indices. To address this issue, we have leveraged a Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) combined with an entropy-based weighting approach to calculated the integrated scores. This method objectively determines the importance of each metric, better discerns between spatial units (i.e., counties), and offers a more reliable ranking of counties according to their relative resilience attributes. By improving methods for integrating resilience indicators, our approach helps planners and decision-makers prioritize resources more effectively for more efficient resilience investments.

Bhusal, Narayan [Oak Ridge National Laboratory (OR↗

DOE OSTI2021

Sentiment Analysis based Error Detection for Large-Scale Systems

Today's large-scale systems such as High Performance Computing (HPC) Systems are designed/utilized towards exascale computing, inevitably decreasing its reliability due to the increasing design complexity. HPC systems conduct extensive logging of their execution behaviour. In this paper, we leverage the inherent meaning behind the log messages and propose a novel sentiment analysis-based approach for the error detection in large-scale systems, by automatically mining the sentiments in the log messages. Our contributions are four-fold. (1) We develop a machine learning (ML) based approach to automatically build a sentiment lexicon, based on the system log message templates. (2) Using the sentiment lexicon, we develop an algorithm to detect system errors. (3) We develop an algorithm to identify the nodes and components with erroneous behaviors, based on sentiment polarity scores. (4) We evaluate our solution vs. other state-of-the-art machine/deep learning algorithms based on three representative supercomputers' system logs. Experiments show that our error detection algorithm can identify error messages with an average MCC score and f -score of 91% and 96% respectively, while state of the art ML/deep learning model (LSTM) obtains only 67% and 84%. To the best of our knowledge, this is the first work leveraging the sentiments embedded in log entries of large-scale systems for system health analysis.

error detection↗

DOE OSTI2021

FL-DISCO: Federated Generative Adversarial Network for Graph-based Molecule Drug Discovery: Special Session Paper

The outbreak of the global COVID-19 pandemic emphasizes the importance of collaborative drug discovery for high effectiveness; however, due to the stringent data regulation, data privacy becomes an imminent issue needing to be addressed to enable collaborative drug discovery. In addition to the data privacy issue, the efficiency of drug discovery is another key objective since infectious diseases spread exponentially and effectively conducting drug discovery could save lives. Advanced Artificial Intelligence (AI) techniques are promising to solve these problems: (1) Federated Learning (FL) is born to keep data privacy while learning data from distributed clients; (2) graph neural network (GNN) can extract structural properties of molecules whose underlying architecture is the connected atoms; and (3) generative adversarial network (GAN) can generate novel molecules while retaining the properties learned from the training data. In this work, we make the first attempt to build a holistic collaborative and privacy-preserving FL framework, namely FL- DISCO, which integrates GAN and GNN to generate molecular graphs. Experimental results demonstrate the effectiveness of FL- DISCO on: (1) IID data for ESOL and QM9, where FL-DISCO can generate highly novel compounds with high drug-likeliness, uniqueness and LogP scores compared to the baseline; (2) non- IID data for ESOL and QM9, where FL-DISCO generates 100% novel compounds with high validity and LogP scores compared to the baseline. We also demonstrate how different fractions of clients, generator and discriminator architectures affect our evaluation scores.

Manu, Daniel↗

DOE OSTI2021

Quantitative Evaluation of Autonomous Driving in CARLA

There has been a great deal of recent advancements in end-to-end imitation and reinforcement learning for self-driving vehicles. Despite this, there is a severe lack of standardized metrics for evaluating the performance of autonomous self-driving agents. Existing metrics are generally lacking in their ability to capture a wide range of driving behaviors and compare the severity of different failure cases. In this work, we introduce the Quantitative Evaluation for Driving metric, or QED, which assigns a quantitative score from 0-100 that captures the quality of driving for any driving agent. Our QED metric assesses different aspects of driving behavior including the ability to stay in the center of the lane, avoid weaving and erratic behavior, follow the speed limit, and avoid collisions, and it can be used under a wide range of driving scenarios. To show the effectiveness of our QED metric, we compare the scores generated by QED against scores assigned by human evaluators on a total of 30 different drivers and 6 different towns in the CARLA driving simulator. In ``easy'' evaluation scenarios, where it is relatively straightforward to distinguish better drivers from worse drivers, QED attains an average Pearson correlation of 0.96 and average Spearman correlation of 0.97 when compared against human evaluators. In ``hard'' evaluation scenarios, where it is far more ambiguous how to rank/score different types of bad driving behavior, QED attains an average Pearson correlation of 0.82 and average Spearman correlation of 0.75 when compared against human evaluators, which are both slighter higher than when we compare human evaluators against each other. While QED may not capture every characteristic that defines good driving, we consider it an important foundation for reproducibility and standardization in the community.

Gao, Shang↗

DOE OSTI2022

Automated Defect Detection and Localization in Photovoltaic Cells Using Semantic Segmentation of Electroluminescence Images

Not provided.

Energy & Fuels↗

DOE OSTI2022

Automated Shift Detection in Sensor-Based PV Power and Irradiance Time Series: Preprint

PV power and irradiance sensor-based measurements are prone to error, resulting in issues such as abrupt time series data shifts. These shifts, which are usually unintentional, may be caused by software or hardware configuration changes on a PV system, and do not reflect an actual change in overall system performance. Locating these shifts and segmenting the associated time series aids in more accurate future PV analysis. In this research, an offline changepoint detection (CPD) algorithm that automatically detects these abrupt data shifts in sensor-based time series is introduced. Data shift periods in 101 daily PV power and irradiance time series were labeled manually by two solar experts. These data streams represent sensor-based measurements, and display a variety of data shift behaviors. A changepoint detection algorithm was tuned using the 101 labeled data streams, with each model configuration's ability to detect labeled changepoints benchmarked using metrics such as F1-score, recall, and Rand Index. Best performing models on seasonality-corrected data streams include the Pruned Exact Linear (PELT) method, the Binary Segmentation method, and the Bottom-Up method, all scoring an average F1-score of 0.76 or greater at detecting labeled changepoints within a 30-day window for the labeled data sets. To promote further research in this space, we are releasing the labeled data shift sets on U.S. Department of Energy's (DOE) DuraMAT Data Hub, and the associated algorithm in the Python PVAnalytics package.

changepoint detection↗

DOE OSTI2025

Novel CHI3L1 ‐Associated Angiogenic Phenotypes Define Glioma Microenvironments: Insights From Multi‐Omics Integration

ABSTRACT The CHI3L1 signaling pathway significantly influences glioma angiogenesis, but its role in the tumor microenvironment (TME) remains elusive. We propose a novelCHI3L1‐associated vascular phenotype classification for glioma through integrative analyses of multiple datasets with bulk and single‐cell transcriptome, genomics, digital pathology, and clinical data. We investigated the biological characteristics, genomic alterations, therapeutic vulnerabilities, and immune profiles within these phenotypes through a comprehensive multi‐omics approach. We constructed the vascular‐related risk (VR) score based onCHI3L1‐associated vascular signatures (CAVS) identified by machine learning algorithms. Utilizing unsupervised consensus clustering, gliomas were stratified into three distinct vascular phenotypes: Cluster A, marked by high vascularization and stromal activation with a relatively low levels of tumor‐infiltrating lymphocytes (TILs); Cluster B, characterized by moderate vascularization and stromal activity, coupled with a high density of TILs; and Cluster C, defined by low vascularization and sparse immune cell infiltration. We observed that the CAVS effectively indicated glioma‐associated angiogenesis and immune suppression by single‐cell RNA‐seq analysis. Moreover, the high‐VR‐score group exhibited enhanced angiogenic activity, reduced immune response, resistance to immunotherapy, and poorer clinical outcomes. The VR score independently predicted glioma prognosis and, combined with a nomogram, provided a robust clinical decision‐making tool. Potential drug prediction based on transcription factors for high‐risk patients was also performed. Our study reveals thatCHI3L1‐associated vascular phenotypes shape distinct immune landscapes in gliomas, offering insights for optimizing therapeutic strategies to improve patient outcomes.

Oncology↗

DOE OSTI2020

“Figure‐of‐Eight” Suture‐Button Technique for Fixation of Displaced Anterior Cruciate Ligament Avulsion Fracture

Objective To assess the clinical results of the “figure‐of‐eight” suture‐button technique in the arthroscopic treatment of anterior cruciate ligament (ACL) tibial avulsion fractures. Methods This was a retrospective study reviewing data from September 2013 to June 2019. A total of 27 patients (13 males and 14 females) who underwent arthroscopic “figure‐of‐eight” suture‐button fixation for displaced ACL avulsion fractures were analyzed. The mean age of the patients in the sample was 15.8 years (10–29 years), with a mean follow‐up of 24 months (6–48 months). According to Meyers–McKeever classification, 11 patients were classified as type III and 16 as type IV. All patients were evaluated following the guidelines of the radiological union, the Lysholm knee scoring scale, and the International Knee Documentation Committee (IKDC). Results Fractures were united within 3 months after surgery in all 27 cases. During the last follow‐up, all the anterior drawer and Lachman tests were negative, except in 1 patient whose anterior drawer test was 1° positive. The range of motion was improved from 72.22° ± 27.92° before surgery to 137.78° ± 7.38° at the last follow‐up ( P < 0.05); the Lysholm score was improved from 45.81 ± 10.94 before surgery to 93.04 ± 5.66 at the last follow‐up ( P < 0.05); and the IKDC score was increased from 43.89 ± 11.16 before surgery to 90.26 ± 5.86 at the last follow‐up ( P < 0.05). In 1 patient, an inflammatory reaction was observed at the medial incision of the tibial tubercle; the symptoms disappeared with administration of antibiotics for 1 week. All patients returned to their preinjury physical activities at the last follow‐up. Conclusion The “figure‐of‐eight” suture‐button technique achieves a satisfactory clinical outcome and provides an effective method for the treatment of displaced ACL avulsion fractures.

Kuang, Shi‐da↗

DOE OSTI2023

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗