bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated identification of fall-related injuries in unstructured clinical notes
Authors: Ge Wendong , Godeiro Coelho Lilian M , Donahue Maria A , Rice Hunter J , Blacker Deborah , Hsu John , Newhouse Joseph P , Hernandez-Diaz Sonia , Haneuse Sebastien , Westover Brandon , Moura Lidia M V R 
Published: July 2024

Abstract
Fall-related injuries (FRIs) are a major cause of hospitalizations among older patients, but identifying them in unstructured clinical notes poses challenges for large-scale research. In this study, we developed and evaluated natural language processing (NLP) models to address this issue. We utilized all available clinical notes from the Mass General Brigham health-care system for 2100 older adults, identifying 154 949 paragraphs of interest through automatic scanning for FRI-related keywords. Two clinical experts directly labeled 5000 paragraphs to generate benchmark-standard labels, while 3689 validated patterns were annotated, indirectly labeling 93 157 paragraphs as validated-standard labels. Five NLP models, including vanilla bidirectional encoder representations from transformers (BERT), the robustly optimized BERT approach (RoBERTa), ClinicalBERT, DistilBERT, and support vector machine (SVM), were trained using 2000 benchmark paragraphs and all validated paragraphs. BERT-based models were trained in 3 stages: masked language modeling, general boolean question-answering, and question-answering for FRIs. For validation, 500 benchmark paragraphs were used, and the remaining 2500 were used for testing. Performance metrics (precision, recall, F1 scores, area under the receiver operating characteristic curve [AUROC], and area under the precision-recall [AUPR] curve) were employed by comparison, with RoBERTa showing the best performance. Precision was 0.90 (95% CI, 0.88-0.91), recall was 0.91 (95% CI, 0.90-0.93), the F1 score was 0.91 (95% CI, 0.89-0.92), and the AUROC and AUPR curves were [both??] 0.96 (95% CI, 0.95-0.97). These NLP models accurately identify FRIs from unstructured clinical notes, potentially enhancing clinical-notes–based research efficiency.
Ground-truth validation of uni- and multivariate lesion inference approaches
Authors: Zavaglia Melissa , Malherbe Caroline , Schlaadt Sebastian , Nachev Parashkev , Hilgetag Claus C 
Published: July 2024

Abstract
Lesion analysis aims to reveal the causal contributions of brain regions to brain functions. Various strategies have been used for such lesion inferences. These approaches can be broadly categorized as univariate or multivariate methods. Here we analysed data from 581 patients with acute ischaemic injury, parcellated into 41 Brodmann areas, and systematically investigated the inferences made by two univariate and two multivariate lesion analysis methods via ground-truth simulations, in which we defined a priori contributions of brain areas to assumed brain function. Particularly, we analysed single-region models, with only single areas presumed to contribute functionally, and multiple-region models, with two contributing regions that interacted in a synergistic, redundant or mutually inhibitory mode. The functional contributions could vary in proportion to the lesion damage or in a binary way. The analyses showed a considerably better performance of the tested multivariate than univariate methods in terms of accuracy and mis-inference error. Specifically, the univariate approaches of Lesion Symptom Mapping as well as Lesion Symptom Correlation mis-inferred substantial contributions from several areas even in the single-region models, and also after accounting for lesion size. By contrast, the multivariate approaches of Multi-Area Pattern Prediction, which is based on machine learning, and Multi-perturbation Shapley value Analysis, based on coalitional game theory, delivered consistently higher accuracy and specificity. Our findings suggest that the tested multivariate approaches produce largely reliable lesion inferences, without requiring lesion size consideration, while the application of the univariate methods may yield substantial mis-localizations that limit the reliability of functional attributions.
Catalytic combustion of toluene over Co3O4 loaded on ZrSn1−xFexO4−δ
Authors: Nunotani Naoyoshi , Tanaka Takumi , Imanaka Nobuhito 
Published: July 2024

Abstract
Toluene is one of the volatile organic compounds that are harmful to the environment and human health. One promising approach for eliminating toluene is catalytic combustion. Although precious metal-based catalysts are known to show high activity for toluene combustion, the high price of precious metals has restricted their widespread applications. In this study, precious metal-free catalysts of Co3O4/ZrSn1−xFexO4−δ were synthesized for toluene combustion. Here, scrutinyite-type ZrSnO4 was focused as a promoter, which can supply active oxygen species from inside the lattice toward the Co3O4 activator. In addition, Fe2+/3+ ions were introduced into the ZrSnO4 lattice to enhance the oxygen supply ability considering the improvement of redox properties and the formation of oxygen vacancies for a smooth oxide ion migration. The oxygen supply from the ZrSn1−xFexO4−δ lattice facilitated toluene oxidation on Co3O4, and the highest catalytic activity was obtained for the 19 wt.% Co3O4/ZrSn0.93Fe0.07O4−δ (Co3O4/ZSF0.07) catalyst, wherein the complete combustion was realized at a temperature as low as 250 °C. The toluene combustion reaction over Co3O4/ZSF0.07 was considered to proceed along a typical route of the rapid transformation of toluene into the intermediates (benzyl alcohol, benzaldehyde, benzoate, and maleic anhydride) and, finally, to the formation of carbon dioxide and water.
Healthy dietary choices involve prefrontal mechanisms associated with long-term reward maximization but not working memory
Authors: Takehana Ai , Tanaka Daiki , Arai Mariko , Hattori Yoshiki , Yoshimoto Takaaki , Matsui Teppei , Sadato Norihiro , Chikazoe Junichi , Jimura Koji 
Published: July 2024

Abstract
Taste and health are critical factors to be considered when choosing foods. Prioritizing healthiness over tastiness requires self-control. It has also been suggested that self-control is guided by cognitive control. We then hypothesized that neural mechanisms underlying healthy food choice are associated with both self-control and cognitive control. Human participants performed a food choice task and a working memory task during functional MRI scanning. Their degree of self-control was assessed behaviorally by the value discount of delayed monetary rewards in intertemporal choice. Prioritizing healthiness in food choice was associated with greater activity in the superior, dorsolateral, and medial prefrontal cortices. Importantly, the prefrontal activity was greater in individuals with smaller delay discounting (i.e. high self-control) who preferred a delayed larger reward to an immediate smaller reward in intertemporal choice. On the other hand, working memory activity did not show a correlation with delay discounting or food choice activity, which was further supported by supplementary results that analyzed data from the Human Connectome Project. Our results suggest that the prefrontal cortex plays a critical role in healthy food choice, which requires self-control, but not working memory, for maximization of reward attainments in a remote future.
Trans-selective carboxylative cyclization of 1,6-dienes using the CO2 radical anion
Authors: Song Yan , Hayashi Hiroki , Mangaonkar Saeesh R , Mita Tsuyoshi 
Published: July 2024

Abstract
The reactivity of the carbon dioxide radical anion (CO2•−) toward alkenes has garnered remarkable attention owing to its potential to synthesize valuable organic compounds. Herein, we report the reactions between CO2•− and 1,6-dienes, yielding 5-membered lactam derivatives via highly trans-selective 5-exo-trig cyclization. Both carboxylative cyclization and hydrocyclization occur with up to 74% combined yield. Computational studies show that the transition state during cyclization favors the trans-configuration over the cis-configuration. This work offers new insights into the synthesis of N-heterocycles.
Using cone-beam CT for appropriate nostril selection in nasotracheal intubation
Authors: Arun Funda , Icoz Derya , Akti Ahmet , Gurses Gokhan 
Published: July 2024

Abstract

Objectives
Nasotracheal intubation is a standard blind procedure associated with various complications. The selection of the appropriate nostril is crucial to preventing most of these complications. The present study aimed to evaluate the predictive ability of cone-beam CT (CBCT) images to select the correct nostril for nasotracheal intubation.

Methods
The study encompassed 60 patients who underwent maxillofacial surgery with nasotracheal intubation under general anaesthesia. While the anaesthetist made the appropriate nostril selection clinically according to a simple occlusion test and spatula test, the radiologist made the selection after analysing various CBCT findings such as the angle and direction of nasal septum deviation (NSD), minimum bone distance along the intubation path, and the presence of inferior turbinate hypertrophy. The appropriateness of these choices made blindly at different times was evaluated using descriptive statistics, chi-squared test, and independent samples t-test.

Results
The study found that 83.3% of the suggested nostril intubations were successful. We also observed that intubation duration was longer when inferior turbinate hypertrophy was present (P = .031). However, there was no statistical relationship between the presence of epistaxis and septal deviation (P = .395). Nonetheless, in 64.3% of cases with epistaxis, the intubated nostril and the septum deviation direction were the same.

Conclusions
Pre-operative evaluations using CBCT can aid anaesthetists for septum deviation and turbinate hypertrophy, as both can impact intubation success rates and duration.
Analysis of CenKR essentiality in Sinorhizobium meliloti and its activity at a target gene promoter in vivo
Authors: Freire Isabela R , Bensig Eukene O , Kuang ZiYu , MacLellan Shawn R 
Published: July 2024

Abstract
The two-component regulatory system CenK–CenR has recently emerged as a regulator of cell envelope and cell division processes in the alpha-proteobacteria. In Sinorhizobium meliloti, CenK–CenR regulates the expression of SrlA, a thioredoxin-domain protein of unknown function. Deletion of srlA causes sensitivity to salt and oxidizing agents on solid growth medium. In this work, we report that the response regulator CenR, but not the histidine kinase CenK, is essential for cell viability in S. meliloti. We also demonstrate that phosphorylation of the target residue D55 is not required for viability, suggesting that the unphosphorylated transcription factor sufficiently regulates expression of one or more essential genes in the genome. Using transcription assays and phenotype testing we examine CenK–CenR-dependent activation of the srlA promoter and demonstrate its absolute dependence on phosphoryl-CenR for activity and that the CenR substitution D55E acts as a phosphomimetic that partially restores activity at the srlA promoter in the absence of phosphorylation by CenK. Finally, we report a mutational analysis of the CenR binding site in the srlA promoter required for transcriptional activation.
Enterococcal quorum-controlled protease alters phage infection
Authors: Sheriff Emma K , Salvato Fernanda , Andersen Shelby E , Chatterjee Anushila , Kleiner Manuel , Duerkop Breck A 
Published: July 2024

Abstract
Increased prevalence of multidrug-resistant bacterial infections has sparked interest in alternative antimicrobials, including bacteriophages (phages). Limited understanding of the phage infection process hampers our ability to utilize phages to their full therapeutic potential. To understand phage infection dynamics, we performed proteomics on Enterococcus faecalis infected with the phage VPE25. We discovered that numerous uncharacterized phage proteins are produced during phage infection of E. faecalis. Additionally, we identified hundreds of changes in bacterial protein abundances during infection. One such protein, enterococcal gelatinase (GelE), an fsr quorum-sensing-regulated protease involved in biofilm formation and virulence, was reduced during VPE25 infection. Plaque assays showed that mutation of either the quorum-sensing regulator fsrA or gelE resulted in plaques with a “halo” morphology and significantly larger diameters, suggesting decreased protection from phage infection. GelE-associated protection during phage infection is dependent on the putative murein hydrolase regulator LrgA and antiholin-like protein LrgB, whose expression have been shown to be regulated by GelE. Our work may be leveraged in the development of phage therapies that can modulate the production of GelE thereby altering biofilm formation and decreasing E. faecalis virulence.
Community case management to accelerate access to healthcare in Mali: a realist process evaluation nested within a cluster randomized trial
Authors: Whidden Caroline , Cissé Amadou Beydi , Cole Faith , Doumbia Saibou , Guindo Abdoulaye , Karambé Youssouf , Treleaven Emily , Liu Jenny , Tolo Oumar , Guindo Lamine , Togola Bréhima , Chiu Calvin , Tembely Aly , Keita Youssouf , Greenwood Brian , Chandramohan Daniel , Johnson Ari , Kayentao Kassoum , Webster Jayne 
Published: July 2024

Abstract
The Proactive Community Case Management (ProCCM) trial in Mali reinforced the health system across both arms with user fee removal, professional community health workers (CHWs) and upgraded primary health centres (PHCs)—and randomized village-clusters to receive proactive home visits by CHWs (intervention) or fixed site-based services by passive CHWs (control). Across both arms, sick children’s 24-hour treatment and pregnant women’s four or more antenatal visits doubled, and under-5 mortality halved, over 3 years compared with baseline. In the intervention arm, proactive CHW home visits had modest effects on children’s curative and women’s antenatal care utilization, but no effect on under-5 mortality, compared with the control arm. We aimed to explain these results by examining implementation, mechanisms and context in both arms We conducted a process evaluation with a mixed method convergent design that included 79 in-depth interviews with providers and participants over two time-points, surveys with 195 providers and secondary analyses of clinical data. We embedded realist approaches in novel ways to test, refine and consolidate theories about how ProCCM worked, generating three context-intervention-actor-mechanism-outcome nodes that unfolded in a cascade. First, removing user fees and deploying professional CHWs in every cluster enabled participants to seek health sector care promptly and created a context of facilitated access. Second, health systems support to all CHWs and PHCs enabled equitable, respectful, quality healthcare, which motivated increased, rapid utilization. Third, proactive CHW home visits facilitated CHWs and participants to deliver and seek care, and build relationships, trust and expectations, but these mechanisms were also activated in both arms. Addressing multiple structural barriers to care, user fee removal, professional CHWs and upgraded clinics interacted with providers’ and patients’ agency to achieve rapid care and child survival in both arms. Proactive home visits expedited or compounded mechanisms that were activated and changed the context across arms.
Improvement and application of vacuum-infiltration system in tomato
Authors: Yao Xinghao , Taheri Ayat , Liu Hang , Zhang Yaojie , Li Ling , Shao Jin , Wu Ke , Miao Qing , He Weizhi , Hu Xinyi , Tang Kexuan 
Published: July 2024

Abstract
The Agrobacterium-mediated transient expression system has been developed and applied to various plants as an alternative to stable transformation. However, its application in tomatoes is still limited due to low expression efficiency. In this study, we describe an improved vacuum-infiltration system that can be used in both tomato fruits and leaves. Notably, this study is the first report of vacuum infiltration in attached tomato fruits. The feasibility of the improved vacuum-infiltration system in Micro-Tom tomato was confirmed by various assays, including multiple fluorescent protein expression analysis, β-glucuronidase activity analysis, and RUBY reporter visualization. Subsequently, the improved vacuum-infiltration system was successfully applied to tomato biotechnology research. Herein, a trichome-specific promoter in tomato was identified that can drive the directional synthesis of specific plant natural products (PNPs). Additionally, based on the assessment results of the improved vacuum-infiltration system, we obtained a flavonoid-rich tomato variety through the stable transformation of AmRosea and AmDelila. In a significant practical application, we successfully synthesized the high-value scutellarin in tomato, which provides an alternative route for the production of PNPs from plants. In addition, the improved vacuum-infiltration system has been demonstrated to be suitable for commercial tomato varieties (‘Emerald’ and ‘Provence’) as well. The improved vacuum-infiltration system not only speeds up fundamental and applied research in tomato but also offers an additional powerful tool for advancing tomato synthetic biology research.
Agar and agarose used forStaphylococcus aureusbiofilm cultivation impact fluoroquinolone tolerance
Authors: Power Angela D , Mok Wendy W K 
Published: July 2024

AbstractAimsStaphylococcus aureus is an opportunistic pathogen whose treatment is further complicated by its ability to form biofilms. In this study, we examine the impact of growing S. aureus biofilms on different polymerizing surfaces, specifically agar and agarose, on the pathogen’s tolerance to fluoroquinolones.Methods and resultsBiofilms of two methicillin-resistant strains of S. aureus were grown on agar or agarose in the presence of the same added nutrients, and their antibiotic susceptibility to two fluoroquinolones, moxifloxacin (MXF) and delafloxacin (DLX), were measured. We also compared the metabolism and extracellular polymeric substances (EPS) production of biofilms that were grown on agar and agarose.ConclusionsBiofilms that were grown on agarose were consistently more susceptible to antibiotics than those grown on agar. We found that in biofilms that were grown on agar, extracellular protein composition was higher, and adding EPS to agarose-grown biofilms increased their tolerance to DLX to levels that were comparable to agar-grown biofilms.
An evaluation of the All of Us Research Program database to examine cumulative stress
Authors: Beese Shawna , Abshire Demetrius A , DeJong Trey L , Carbone Jason T 
Published: July 2024

Abstract

Objectives
To evaluate the NIH All of Us Research Program database as a potential data source for studying allostatic load and stress among adults in the United States (US).

Materials and Methods
We evaluated the All of Us database to determine sample size significance for original-10 allostatic load biomarkers, Allostatic Load Index-5 (ALI-5), Allostatic Load Five, and Cohen’s Perceived Stress Scale (PSS). We conducted a priori, post hoc, and sensitivity power analyses to determine sample sizes for conducting null hypothesis significance tests.

Results
The maximum number of responses available for each measure is 21 participants for the original-10 allostatic load biomarkers, 150 for the ALI-5, 22 476 for Allostatic Load Five, and n = 90 583 for the PSS.

Discussion
The NIH All of Us Research Program is well-suited for studying allostatic load using the Allostatic Load Five and psychological stress using PSS.

Conclusion
Improving biomarker data collection in All of Us will facilitate more nuanced examinations of allostatic load among US adults.
Development and application of Breadth-Depth-Context (BDC), a conceptual framework for measuring technology engagement with a qualified clinical data registry
Authors: Kersey Emma , Li Jing , Kay Julia , Adler-Milstein Julia , Yazdany Jinoos , Schmajuk Gabriela 
Published: July 2024

Abstract

Objectives
Despite the proliferation of dashboards that display performance data derived from Qualified Clinical Data Registries (QCDR), the degree to which clinicians and practices engage with such dashboards has not been well described. We aimed to develop a conceptual framework for assessing user engagement with dashboard technology and to demonstrate its application to a rheumatology QCDR.

Materials and Methods
We developed the BDC (Breadth-Depth-Context) framework, which included concepts of breadth (derived from dashboard sessions), depth (derived from dashboard actions), and context (derived from practice characteristics). We demonstrated its application via user log data from the American College of Rheumatology’s Rheumatology Informatics System for Effectiveness (RISE) registry to define engagement profiles and characterize practice-level factors associated with different profiles.

Results
We applied the BDC framework to 213 ambulatory practices from the RISE registry in 2020-2021, and classified practices into 4 engagement profiles: not engaged (8%), minimally engaged (39%), moderately engaged (34%), and most engaged (19%). Practices with more patients and with specific electronic health record vendors (eClinicalWorks and eMDs) had a higher likelihood of being in the most engaged group, even after adjusting for other factors.

Discussion
We developed the BDC framework to characterize user engagement with a registry dashboard and demonstrated its use in a specialty QCDR. The application of the BDC framework revealed a wide range of breadth and depth of use and that specific contextual factors were associated with nature of engagement.

Conclusion
Going forward, the BDC framework can be used to study engagement with similar dashboards.
Biofertilizer and biostimulant potentials of phosphate-solubilizing Bacillus subtilis subsp. subtilis M1 strain and silicon in improving low phosphorus availability tolerance in rosemary
Authors: Msaad Hamid , Lamsaadi Nadia , Farssi Omar , Oubenali Aziz , Lahmaoui Soukaina , Boulli Abdelali , Ghoulam Cherki , El Moukhtari Ahmed , Farissi Mohamed 
Published: July 2024

Abstract
The present study aimed to evaluate the single and combined effects of Si exogenous treatment and Bacillus subtilis subsp. subtilis M1 strain inoculation on rosemary tolerance to low phosphorus (P) availability. Hence, rosemary plants were fertilized with 250 µmol Ca3HPO4 (stressed plants) or 250 µmol KH2PO4 (control plants) under Si treatment and B. subtilis M1 strain inoculation. P starvation negatively affected rosemary growth and its P nutrition. However, exogenous Si supply or B. subtilis M1 strain inoculation significantly (P &lt; 0.001) alleviated the deficiency-induced effects and significantly improved rhizogenesis, acid phosphatase activity, P uptake, and eventually dry weight of shoot and root. Moreover, Si-treatment and/or B. subtilis M1 strain inoculation significantly (P &lt; 0.001) reduced the oxidative damage, in terms of malondialdehyde and hydrogen peroxide accumulation. This was found positively correlated with the higher superoxide dismutase activity, and the elevated non-enzymatic antioxidant molecules accumulation, including total polyphenols in Si-treated and inoculated P-deficient plants. Taken together, Si supplementation and/or B. subtilis M1 strain inoculation could be a good strategy to sustain rosemary plant growth under P starvation conditions.