bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aci-bench: a Novel Ambient Clinical Intelligence Dataset for Benchmarking Automatic Visit Note Generation
Authors: Yim Wen-wai , Fu Yujuan , Ben Abacha Asma , Snider Neal , Lin Thomas , Yetisgen Meliha 
Published: September 2023

AbstractRecent immense breakthroughs in generative models such as in GPT4 have precipitated re-imagined ubiquitous usage of these models in all applications. One area that can benefit by improvements in artificial intelligence (AI) is healthcare. The note generation task from doctor-patient encounters, and its associated electronic medical record documentation, is one of the most arduous time-consuming tasks for physicians. It is also a natural prime potential beneficiary to advances in generative models. However with such advances, benchmarking is more critical than ever. Whether studying model weaknesses or developing new evaluation metrics, shared open datasets are an imperative part of understanding the current state-of-the-art. Unfortunately as clinic encounter conversations are not routinely recorded and are difficult to ethically share due to patient confidentiality, there are no sufficiently large clinic dialogue-note datasets to benchmark this task. Here we present the Ambient Clinical Intelligence Benchmark (aci-bench) corpus, the largest dataset to date tackling the problem of AI-assisted note generation from visit dialogue. We also present the benchmark performances of several common state-of-the-art approaches.
Comprehensive analyses of fatty acid metabolism-related lncRNA for ovarian cancer patients
Authors: Li Min , Yan Ye , Liu Yanyan , Zhao Jianzhen , Guo Fei , Chen Jianqin , Nie Lifang , Zhang Yong , Wang Yingmei 
Published: September 2023

AbstractOvarian cancer (OC) is a disease with difficult early diagnosis and treatment and poor prognosis. OC data profiles were downloaded from The Cancer Genome Atlas. Eight key fatty acid metabolism-related long non-coding RNAs (lncRNAs) were finally screened for building a risk scoring model by univariate/ multifactor and least absolute shrinkage and selection operator (LASSO) Cox regression. To make this risk scoring model more applicable to clinical work, we established a nomogram containing the clinical characteristics of OC patients after confirming that the model has good reliability and validity and the ability to distinguish patient prognosis. To further explore how these key lncRNAs are involved in OC progression, we explored their relationship with LUAD immune signatures and tumor drug resistance. The structure shows that the risk scoring model established based on these 8 fatty acid metabolism-related lncRNAs has good reliability and validity and can better predict the prognosis of patients with different risks of OC, and LINC00861in these key RNAs may be a hub gene that affects the progression of OC and closely related to the sensitivity of current OC chemotherapy drugs. In addition, combined with immune signature analysis, we found that patients in the high-risk group are in a state of immunosuppression, and Tfh cells may play an important role in it. We innovatively established a prognostic prediction model with excellent reliability and validity from the perspective of OC fatty acid metabolism reprogramming and lncRNA regulation and found new molecular/cellular targets for future OC treatment.
The role of internal defects on anisotropic tensile failure of L-PBF AlSi10Mg alloys
Authors: Wu Zhengkai , Wu Shengchuan , Gao Xi , Lin Ying , Xue Yanling , Withers Philip J. 
Published: September 2023

AbstractThis paper investigates the effects of defects on tensile failure of additive manufactured AlSi10Mg alloy focusing particularly on the role of large pancake shaped loss of fusion (LOF) defects lying perpendicular to the build direction (BD). Time-lapse in situ synchrotron radiation X-ray micro-computed tomography during straining reveals how, when tested parallel to the BD, the LOF defects extend laterally with straining connecting to other defects and giving rise to low plasticity and an essentially brittle failure mode. When they are aligned edge-on to the straining direction, failure is characterised by a ductile cup-cone failure with significant elongation of the defects axially and extensive necking prior to failure. The soft fish-scale melt pool boundaries were also found to affect the fracture path. These results highlight the anisotropic effect of loss of fusion defects in controlling tensile ductility and the need to minimize their size and aspect ratio. In cases where these cannot be fully eliminated the component should be fabricated such that the BD is not aligned with the dominant in-service loading direction.
Novel quinazoline-1,2,3-triazole hybrids with anticancer and MET kinase targeting properties
Authors: Mortazavi Motahareh , Eskandari Masoomeh , Moosavi Fatemeh , Damghani Tahereh , Khoshneviszadeh Mehdi , Pirhadi Somayeh , Saso Luciano , Edraki Najmeh , Firuzi Omidreza 
Published: September 2023

AbstractOncogenic activation of receptor tyrosine kinases (RTKs) such as MET is associated with cancer initiation and progression. We designed and synthesized a new series of quinazoline derivatives bearing 1,2,3-triazole moiety as targeted anticancer agents. The MET inhibitory effect of synthesized compounds was assessed by homogeneous time-resolved fluorescence (HTRF) assay and western blot analysis. Sulforhodamine B assay was conducted to examine the antiproliferative effects of synthetic compounds against 6 cancer cell lines from different origins including MET-dependent AsPC-1, EBC-1 and MKN-45 cells and also Mia-Paca-2, HT-29 and K562 cells. The growth inhibitory effect of compounds in a three-dimensional spheroid culture was examined by acid phosphatase (APH) assay, while apoptosis induction was evaluated by Annexin V/propidium iodide method. Compound 8c bearing p-methyl benzyl moiety on the triazole ring exhibited the highest MET inhibitory capacity among tested agents that was further confirmed by western blot findings. Derivatives 8c and 8h exhibited considerable antiproliferative effects against all tested cell lines, with more inhibitory effects against MET-positive cells with IC50 values as low as 6.1 μM. These two agents also significantly suppressed cell growth in spheroid cultures and induced apoptosis in MET overexpressing AsPC-1 cells. Moreover, among a panel of 24 major oncogenic kinases, the PDGFRA kinase was identified as a target of 8c and 8h compounds. The docking study results of compounds 8c and 8h were in agreement with experimental findings. The results of the present study suggest that quinazoline derivatives bearing 1,2,3-triazole moiety may represent promising targeted anticancer agents.
A deep learning approach for fully automated measurements of lower extremity alignment in radiographic images
Authors: Moon Ki-Ryum , Lee Byoung-Dai , Lee Mu Sook 
Published: September 2023

AbstractDuring clinical evaluation of patients and planning orthopedic treatments, the periodic assessment of lower limb alignment is critical. Currently, physicians use physical tools and radiographs to directly observe limb alignment. However, this process is manual, time consuming, and prone to human error. To this end, a deep-learning (DL)-based system was developed to automatically, rapidly, and accurately detect lower limb alignment by using anteroposterior standing X-ray medical imaging data of lower limbs. For this study, leg radiographs of non-overlapping 770 patients were collected from January 2016 to August 2020. To precisely detect necessary landmarks, a DL model was implemented stepwise. A radiologist compared the final calculated measurements with the observations in terms of the concordance correlation coefficient (CCC), Pearson correlation coefficient (PCC), and intraclass correlation coefficient (ICC). Based on the results and 250 frontal lower limb radiographs obtained from 250 patients, the system measurements for 16 indicators revealed superior reliability (CCC, PCC, and ICC ≤ 0.9; mean absolute error, mean square error, and root mean square error ≥ 0.9) for clinical observations. Furthermore, the average measurement speed was approximately 12 s. In conclusion, the analysis of anteroposterior standing X-ray medical imaging data by the DL-based lower limb alignment diagnostic support system produces measurement results similar to those obtained by radiologists.
Effects of scaling direction on adults’ spatial scaling in different perceptual domains
Authors: Szubielska Magdalena , Szewczyk Marta , Augustynowicz Paweł , Kędziora Wojciech , Möhring Wenke 
Published: September 2023

AbstractThe current study investigated adults’ strategies of spatial scaling from memory in three perceptual conditions (visual, haptic, and visuo-haptic) when scaling up and down. Following previous research, we predicted the usage of mental transformation strategies. In all conditions, participants (N = 90, aged 19–28 years) were presented with tactile, colored graphics which allowed to visually and haptically explore spatial information. Participants were first asked to encode a map including a target. Then, they were instructed to place a response object at the same place on an empty, constant-sized referent space. Maps had five different sizes resulting in five scaling factors (3:1, 2:1, 1:1, 1:2, 1:3). This manipulation also allowed assessing potentially symmetric effects of scaling direction on adults’ responses. Response times and absolute errors served as dependent variables. In line with our hypotheses, the changes in these dependent variables were best explained by a quadratic function which suggests the usage of mental transformation strategies for spatial scaling. There were no differences between perceptual conditions concerning the influence of scaling factor on dependent variables. Results revealed symmetric effects of scaling direction on participants’ accuracy whereas there were small differences for response times. Our findings highlight the usage of mental transformation strategies in adults’ spatial scaling, irrespective of perceptual modality and scaling direction.
Conjugation of microbial-derived gold nanoparticles to different types of nucleic acids: evaluation of transfection efficiency
Authors: Pourali P. , Dzmitruk V. , Benada O. , Svoboda M. , Benson V. 
Published: September 2023

AbstractIn this study, gold nanoparticles produced by eukaryotic cell waste (AuNP), were analyzed as a transfection tool. AuNP were produced by Fusarium oxysporum and analyzed by spectrophotometry, transmission electron microscopy (TEM), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (EDS). Fourier transform infrared spectroscopy (FTIR) and dynamic light scattering (DLS) were used before and after conjugation with different nucleic acid (NA) types. Graphite furnace atomic absorption spectroscopy (GF-AAS) was used to determine the AuNP concentration. Conjugation was detected by electrophoresis. Confocal microscopy and quantitative real-time PCR (qPCR) were used to assess transfection. TEM, SEM, and EDS showed 25 nm AuNP with round shape. The amount of AuNP was 3.75 ± 0.2 µg/µL and FTIR proved conjugation of all NA types to AuNP. All the samples had a negative charge of − 36 to − 46 mV. Confocal microscopy confirmed internalization of the ssRNA-AuNP into eukaryotic cells and qPCR confirmed release and activity of carried RNA.
Surgical site infection and antimicrobial prophylaxis prescribing profile, and its determinants among hospitalized patients in Northeast Ethiopia: a hospital based cross-sectional study
Authors: Habteweld Habtemariam Alekaw , Yimam Mohammed , Tsige Abate Wondesen , Wondmkun Yehualashet Teshome , Endalifer Bedilu Linger , Ayenew Kassahun Dires 
Published: September 2023

AbstractThe inappropriate use of surgical antimicrobial prophylaxis is a common cause for increased risk of morbidity and mortality from surgical site infection in patients who underwent surgical procedures. The study aimed to evaluate surgical antimicrobial prophylaxis prescribing patterns, Surgical Site Infection (SSI), and its determinants in the surgical ward of Debre Berhan Comprehensive Specialized Hospital, northeast Ethiopia. A prospective cross-sectional study was conducted from October 1st 2022 to January 31st, 2023. Data collected from patient medical record cards and patient interviews were entered and analyzed using SPSS V26.0. The determinants of surgical site infection were determined from the multivariable logistic regression. P-value ≤ 0.05 was considered statistically significant. Ceftriaxone (70.5%) followed by a combination of ceftriaxone with metronidazole (21.90%) was the most frequently used prophylactic antibiotic. One hundred fifty-nine (78%) of patients were exposed to inappropriately used prophylactic antimicrobials and 62.2% of these were exposed to inappropriately selected antibiotics. One hundred twenty-six (61.9%) patients developed Surgical Site Infection (SSI). Duration of procedure longer than an hour and inappropriate use of antimicrobial prophylaxiswere the independent predictors for the occurrence of surgical site infections. Patients whose operation was lasted in longer than an hour were 3.39 times more likely to develop SSI compared to those whose operation was completed in less than an hour, AOR = 3.39 (95% CI: 1.24–9.30). Similarly, controlling the effect of other covariate variables, individuals who were given inappropriate antimicrobial prophylaxis were 6.67 times more likely to develop SSI compared to those given appropriate prophylaxis, AOR = 6.67 (95% CI: 1.05–42.49). The high rate of SSI requires due attention from clinicians as well as health policymakers. Duration of surgical procedure greater than an hour and inappropriate antimicrobial prophylaxis use was the independent predictor of surgical site infections.
Mixed-dimensional nanocomposites based on 2D materials for hydrogen storage and CO2 capture
Authors: Park Yong-Ju , Lee Hongju , Choi Hye Leen , Tapia Ma Charlene , Chuah Chong Yang , Bae Tae-Hyun 
Published: September 2023

AbstractPorous materials possessing high surface areas are of paramount importance in gas separation and storage, as they can potentially adsorb a large amount of gas per unit of mass or volume. Pore structure and functionality are also important factors affecting adsorbate–absorbent interactions. Hence, efforts have been devoted to developing adsorbents with large accessible surface areas and tunable functionalities to realize improvements in gas adsorption capacity. However, the gas adsorption and storage capacities of porous materials composed of a single type of building unit are often limited. To this end, mixed-dimensional hybrid materials have been developed, as they can contain more gas storage sites within their structures than simple porous materials. In this review, we discuss (1) the methods that have been used to assemble various dimensional building blocks into a range of mixed-dimensional (zero-dimensional–two-dimensional, one-dimensional–two-dimensional, and three-dimensional–two-dimensional) hybrid materials exhibiting synergistic adsorption effects, and (2) these materials’ hydrogen and carbon dioxide adsorption properties and how they are correlated with their accessible surface areas. We conclude by outlining the challenges remaining to be surmounted to realize practical applications of mixed-dimensional hybrid materials and by providing future perspectives.
Recommendations for the use of pediatric data in artificial intelligence and machine learning ACCEPT-AI
Authors: Muralidharan V. , Burgart A. , Daneshjou R. , Rose S. 
Published: September 2023

AbstractACCEPT-AI is a framework of recommendations for the safe inclusion of pediatric data in artificial intelligence and machine learning (AI/ML) research. It has been built on fundamental ethical principles of pediatric and AI research and incorporates age, consent, assent, communication, equity, protection of data, and technological considerations. ACCEPT-AI has been designed to guide researchers, clinicians, regulators, and policymakers and can be utilized as an independent tool, or adjunctively to existing AI/ML guidelines.
Reward expectation enhances action-related activity of nigral dopaminergic and two striatal output pathways
Authors: Rios Alain , Nonomura Satoshi , Kato Shigeki , Yoshida Junichi , Matsushita Natsuki , Nambu Atsushi , Takada Masahiko , Hira Riichiro , Kobayashi Kazuto , Sakai Yutaka , Kimura Minoru , Isomura Yoshikazu 
Published: September 2023

AbstractNeurons comprising nigrostriatal system play important roles in action selection. However, it remains unclear how this system integrates recent outcome information with current action (movement) and outcome (reward or no reward) information to achieve appropriate subsequent action. We examined how neuronal activity of substantia nigra pars compacta (SNc) and dorsal striatum reflects the level of reward expectation from recent outcomes in rats performing a reward-based choice task. Movement-related activity of direct and indirect pathway striatal projection neurons (dSPNs and iSPNs, respectively) were enhanced by reward expectation, similarly to the SNc dopaminergic neurons, in both medial and lateral nigrostriatal projections. Given the classical basal ganglia model wherein dopamine stimulates dSPNs and suppresses iSPNs through distinct dopamine receptors, dopamine might not be the primary driver of iSPN activity increasing following higher reward expectation. In contrast, outcome-related activity was affected by reward expectation in line with the classical model and reinforcement learning theory, suggesting purposive effects of reward expectation.
Time-dependent cell-state selection identifies transiently expressed genes regulating ILC2 activation
Authors: Tanaka Yumiko , Yamagishi Mai , Motomura Yasutaka , Kamatani Takashi , Oguchi Yusuke , Suzuki Nobutake , Kiniwa Tsuyoshi , Kabata Hiroki , Irie Misato , Tsunoda Tatsuhiko , Miya Fuyuki , Goda Keisuke , Ohara Osamu , Funatsu Takashi , Fukunaga Koichi , Moro Kazuyo , Uemura Sotaro , Shirasaki Yoshitaka 
Published: September 2023

AbstractThe decision of whether cells are activated or not is controlled through dynamic intracellular molecular networks. However, the low population of cells during the transition state of activation renders the analysis of the transcriptome of this state technically challenging. To address this issue, we have developed the Time-Dependent Cell-State Selection (TDCSS) technique, which employs live-cell imaging of secretion activity to detect an index of the transition state, followed by the simultaneous recovery of indexed cells for subsequent transcriptome analysis. In this study, we used the TDCSS technique to investigate the transition state of group 2 innate lymphoid cells (ILC2s) activation, which is indexed by the onset of interleukin (IL)-13 secretion. The TDCSS approach allowed us to identify time-dependent genes, including transiently induced genes (TIGs). Our findings of IL4 and MIR155HG as TIGs have shown a regulatory function in ILC2s activation.
Evidence of pseudogravitational distortions of the Fermi surface geometry in the antiferromagnetic metal FeRh
Authors: Sklenar Joseph , Shim Soho , Saglam Hilal , Oh Junseok , Vergniory M. G. , Hoffmann Axel , Bradlyn Barry , Mason Nadya , Gilbert Matthew J. 
Published: September 2023

AbstractThe confluence between high-energy physics and condensed matter has produced groundbreaking results via unexpected connections between the two traditionally disparate areas. In this work, we elucidate additional connectivity between high-energy and condensed matter physics by examining the interplay between spin-orbit interactions and local symmetry-breaking magnetic order in the magnetotransport of thin-film magnetic semimetal FeRh. We show that the change in sign of the normalized longitudinal magnetoresistance observed as a function of increasing in-plane magnetic field results from changes in the Fermi surface morphology. We demonstrate that the geometric distortions in the Fermi surface morphology are more clearly understood via the presence of pseudogravitational fields in the low-energy theory. The pseudogravitational connection provides additional insights into the origins of a ubiquitous phenomenon observed in many common magnetic materials and points to an alternative methodology for understanding phenomena in locally-ordered materials with strong spin-orbit interactions.
Waist-hip ratio is superior to BMI in predicting liver-related outcomes and synergizes with harmful alcohol use
Authors: Åberg Fredrik , Färkkilä Martti , Salomaa Veikko , Jula Antti , Männistö Satu , Perola Markus , Lundqvist Annamari , Männistö Ville 
Published: September 2023

Abstract
Background:
Obesity is associated with liver disease, but the best obesity-related predictor remains undefined. Controversy exists regarding possible synergism between obesity and alcohol use for liver-related outcomes (LRO). We assessed the predictive performance for LROs, and synergism with alcohol use, of abdominal obesity (waist-hip ratio, WHR), and compared it to overall obesity (body mass index, BMI).

Methods:
Forty-thousand nine-hundred twenty-two adults attending the Finnish health-examination surveys, FINRISK 1992–2012 and Health 2000 studies, were followed through linkage with electronic healthcare registries for LROs (hospitalizations, cancers, and deaths). Predictive performance of obesity measures (WHR, waist circumference [WC], and BMI) were assessed by Fine-Gray models and time-dependent area-under-the-curve (AUC).

Results:
There are 355 LROs during a median follow-up of 12.9 years (509047.8 person-years). WHR and WC emerge as more powerful predictors of LROs than BMI. WHR shows significantly better 10-year AUC values for LROs (0.714, 95% CI 0.685–0.743) than WC (0.648, 95% CI 0.617–0.679) or BMI (0.550, 95% CI 0.514–0.585) both overall and separately among men and women. WHR is predictive also in BMI strata. Absolute 10-year risks of LROs are more dependent on WHR than BMI. Moreover, WHR shows a significant supra-additive interaction effect with harmful alcohol use for liver-related outcomes (excess 10-year cumulative incidence of 2.8% from the interaction), which is not seen between BMI and harmful alcohol use.

Conclusions:
WHR is a better predictor than BMI or WC for LROs, and WHR better reflects the synergism with harmful alcohol use. WHR should be included in clinical assessment when evaluating obesity-related risks for liver outcomes.