bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of multi-criteria decision analysis techniques and decision support framework for informing plant select agent designation and decision making
Authors: Pillai Segaran P. , Fruetel Julia , West Todd , Anderson Kevin , Hernandez Patricia , Ball Cameron , McNeil Carrie , Beck Nataly , Morse Stephen A. 
Published: September 2023

The United States Department of Agriculture (USDA) Division of Agricultural Select Agents and Toxins (DASAT) established a list of biological agents (Select Agents List) that threaten crops of economic importance to the United States and regulates the procedures governing containment, incident response, and the security of entities working with them. Every 2 years the USDA DASAT reviews their select agent list, utilizing assessments by subject matter experts (SMEs) to rank the agents. We explored the applicability of multi-criteria decision analysis (MCDA) techniques and a decision support framework (DSF) to support the USDA DASAT biennial review process. The evaluation includes both current and non-select agents to provide a robust assessment. We initially conducted a literature review of 16 pathogens against 9 criteria for assessing plant health and bioterrorism risk and documented the findings to support this analysis. Technical review of published data and associated scoring recommendations by pathogen-specific SMEs was found to be critical for ensuring accuracy. Scoring criteria were adopted to ensure consistency. The MCDA supported the expectation that select agents would rank high on the relative risk scale when considering the agricultural consequences of a bioterrorism attack; however, application of analytical thresholds as a basis for designating select agents led to some exceptions to current designations. A second analytical approach used agent-specific data to designate key criteria in a DSF logic tree format to identify pathogens of low concern that can be ruled out for further consideration as select agents. Both the MCDA and DSF approaches arrived at similar conclusions, suggesting the value of employing the two analytical approaches to add robustness for decision making.
A deep learning method for foot-type classification using plantar pressure images
Authors: Zhao Yangyang , Zhou Jiali , Qiu Fei , Liao Xuying , Jiang Jianhua , Chen Heqing , Lin Xiaomei , Hu Yiqun , He Jianquan , Chen Jian 
Published: September 2023

Background: Flat foot deformity is a prevalent and challenging condition often leading to various clinical complications. Accurate identification of abnormal foot types is essential for appropriate interventions.Method: A dataset consisting of 1573 plantar pressure images from 125 individuals was collected. The performance of the You Only Look Once v5 (YOLO-v5) model, improved YOLO-v5 model, and multi-label classification model was evaluated for foot type identification using the collected images. A new dataset was also collected to verify and compare the models.Results: The multi-label classification algorithm based on ResNet-50 outperformed other algorithms. The improved YOLO-v5 model with Squeeze-and-Excitation (SE), the improved YOLO-v5 model with Convolutional Block Attention Module (CBAM), and the multilabel classification model based on ResNet-50 achieved an accuracy of 0.652, 0.717, and 0.826, respectively, which is significantly higher than those obtained using the ordinary plantar-pressure system and the standard YOLO-v5 model.Conclusion: These results indicate that the proposed DL-based multilabel classification model based on ResNet-50 is superior in flat foot type detection and can be used to evaluate the clinical rehabilitation status of patients with abnormal foot types and various foot pathologies when more data on patients with various diseases are available for training.
Association between cardiovascular risk factors and atrial fibrillation
Authors: Wu Guohao , Wu Jingguo , Lu Qin , Cheng Yunjiu , Mei Weiyi 
Published: September 2023

BackgroundThe most prevalent sustained arrhythmia in medical practice, atrial fibrillation (AF) is closely associated with a high risk of cardiovascular disease. Nevertheless, the risk of AF associated with cardiovascular risk factors has not been well elucidated. We pooled all published studies to provide a better depiction of the relationship among cardiovascular risk factors with AF.MethodsStudies were searched in the MEDLINE, Web of Science, and EMBASE databases since initiation until January 15, 2022. Prospective cohort studies assessing the relationship a minimum of single cardiovascular risk factors to AF incidence were included if they contained adequate data for obtaining relative risks (RR) and 95% confidence intervals (CI). Random-effects models were utilized to perform independent meta-analyses on each cardiovascular risk factor. PROSPERO registry number: CRD42022310882.ResultsA total of 17,098,955 individuals and 738,843 incident cases were reported for data from 101 studies included in the analysis. In all, the risk of AF was 1.39 (95% CI, 1.30–1.49) for obesity, 1.27 (95% CI, 1.22–1.32) per 5 kg/m2 for increase in body mass index, 1.19 (95% CI, 1.10–1.28) for former smokers, 1.23 (95% CI, 1.09–1.38) for current smokers, 1.31 (95% CI, 1.23–1.39) for diabetes mellitus, 1.68 (95% CI, 1.51–1.87) for hypertension, and 1.12 (95% CI, 0.95–1.32) for dyslipidemia.InterpretationAdverse cardiovascular risk factors correlate with an increased risk of AF, yet dyslipidemia does not increase the risk of AF in the general population, potentially providing new insights for AF screening strategies among patients with these risk factors.Systematic Review Registrationhttps://www.crd.york.ac.uk/PROSPERO/, PROSPERO identifier (CRD42022310882).
Quality control-driven deep ensemble for accountable automated segmentation of cardiac magnetic resonance LGE and VNE images
Authors: Gonzales Ricardo A. , Ibáñez Daniel H. , Hann Evan , Popescu Iulia A. , Burrage Matthew K. , Lee Yung P. , Altun İbrahim , Weintraub William S. , Kwong Raymond Y. , Kramer Christopher M. , Neubauer Stefan ,   Hypertrophic Cardiomyopathy Registry (HCMR) Investigators,   Oxford Acute Myocardial Infarction (OxAMI) Study, Ferreira Vanessa M. , Zhang Qiang , Piechnik Stefan K. 
Published: September 2023

BackgroundLate gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) imaging is the gold standard for non-invasive myocardial tissue characterisation. However, accurate segmentation of the left ventricular (LV) myocardium remains a challenge due to limited training data and lack of quality control. This study addresses these issues by leveraging generative adversarial networks (GAN)-generated virtual native enhancement (VNE) images to expand the training set and incorporating an automated quality control-driven (QCD) framework to improve segmentation reliability.MethodsA dataset comprising 4,716 LGE images (from 1,363 patients with hypertrophic cardiomyopathy and myocardial infarction) was used for development. To generate additional clinically validated data, LGE data were augmented with a GAN-based generator to produce VNE images. LV was contoured on these images manually by clinical observers. To create diverse candidate segmentations, the QCD framework involved multiple U-Nets, which were combined using statistical rank filters. The framework predicted the Dice Similarity Coefficient (DSC) for each candidate segmentation, with the highest predicted DSC indicating the most accurate and reliable result. The performance of the QCD ensemble framework was evaluated on both LGE and VNE test datasets (309 LGE/VNE images from 103 patients), assessing segmentation accuracy (DSC) and quality prediction (mean absolute error (MAE) and binary classification accuracy).ResultsThe QCD framework effectively and rapidly segmented the LV myocardium (&lt;1 s per image) on both LGE and VNE images, demonstrating robust performance on both test datasets with similar mean DSC (LGE: 0.845±0.075; VNE: 0.845±0.071; p=ns). Incorporating GAN-generated VNE data into the training process consistently led to enhanced performance for both individual models and the overall framework. The quality control mechanism yielded a high performance (MAE=0.043, accuracy=0.951) emphasising the accuracy of the quality control-driven strategy in predicting segmentation quality in clinical settings. Overall, no statistical difference (p=ns) was found when comparing the LGE and VNE test sets across all experiments.ConclusionsThe QCD ensemble framework, leveraging GAN-generated VNE data and an automated quality control mechanism, significantly improved the accuracy and reliability of LGE segmentation, paving the way for enhanced and accountable diagnostic imaging in routine clinical use.
Comparative effectiveness of endoscopic and microscopic adenoma removal in acromegaly
Authors: Vassilyeva Natalya , Mena Natmir , Kirov Kiril , Diatlova Ekaterina 
Published: September 2023

IntroductionSomatotropinomas are the main cause of acromegaly. Surgery is the primary and most efficient method of treatment. The study aimed to compare the radicality of small-sized and medium (&lt;30 mm) somatotropinoma removal and the incidence of postoperative complications in patients with acromegaly when using microscopic and endoscopic techniques.MethodsIn this randomized controlled trial, a total of 83 patients with acromegaly underwent transspheroidal endoscopy or microscopic surgery. Somatotropinoma was the cause of acromegaly in all cases. Patients were randomly divided into two comparison groups depending on the applied surgical technique. Group 1 (n = 40) consisted of patients who underwent adenomectomy with transnasal transsphenoidal access by a microscope. Group 2 (n = 43) included patients who underwent the same surgical procedure with an endoscope. The following indicators were assessed: radicality of tumor removal, treatment effectiveness, postoperative complications, and remission rate.ResultsThe study has shown that removal of somatotropinoma in patients with acromegaly using endoscopic technique increases the radicality of tumor removal in comparison with microscopic technique. Total removal of somatotropinoma was successful in 88.4% of cases when using the endoscopic technique. Secondly, the segmentation of patients according to their tumor characteristics poses challenges, primarily owing to the rarity of acromegaly as a disease. The difference between groups was not statistically significant (p=1.02). There were no statistically significant differences in basal GH level and IGF-1 level between groups (p=0.546 and p=0.784, respectively).DiscussionEndonasal transsphenoidal endoscopic adenomectomy is proven efficacy, a less traumatic degree, and higher somatotropinoma removal radicality. Both surgical methods lead to disease remission.
Association between sex steroid hormones and subsequent hyperglycemia during pregnancy
Authors: Meng Ying , Thornburg Loralei L. , Hoeger Kathleen M. , Núñez Zorimar Rivera- , Kautz Amber , Evans Adam T. , Wang Christina , Miller Richard K. , Groth Susan W. , O’Connor Thomas G. , Barrett Emily S. 
Published: September 2023

ObjectiveSex steroid hormones may play a role in insulin resistance and glucose dysregulation. However, evidence regarding associations between early-pregnancy sex steroid hormones and hyperglycemia during pregnancy is limited. The primary objective of this study was to assess the relationships between first trimester sex steroid hormones and the subsequent development of hyperglycemia during pregnancy; with secondary evaluation of sex steroid hormones levels in mid-late pregnancy, concurrent with and subsequent to diagnosis of gestational diabetes.MethodsRetrospective analysis of a prospective pregnancy cohort study was conducted. Medically low-risk participants with no known major endocrine disorders were recruited in the first trimester of pregnancy (n=319). Sex steroid hormones in each trimester, including total testosterone, free testosterone, estrone, estradiol, and estriol, were assessed using high-performance liquid chromatography and tandem mass spectrometry. Glucose levels of the 1-hour oral glucose tolerance test and gestational diabetes diagnosis were abstracted from medical records. Multivariable linear regression models were fitted to assess the associations of individual first trimester sex steroids and glucose levels.ResultsIn adjusted models, first trimester total testosterone (β=5.24, 95% CI: 0.01, 10.46, p=0.05) and free testosterone (β=5.98, 95% CI: 0.97, 10.98, p=0.02) were positively associated with subsequent glucose concentrations and gestational diabetes diagnosis (total testosterone: OR=3.63, 95% CI: 1.50, 8.78; free testosterone: OR=3.69; 95% CI: 1.56, 8.73). First trimester estrone was also positively associated with gestational diabetes (OR=3.66, 95% CI: 1.56, 8.55). In mid-late pregnancy, pregnant people with gestational diabetes had lower total testosterone levels (β=-0.19, 95% CI: -0.36, -0.02) after adjustment for first trimester total testosterone.ConclusionEarly-pregnancy sex steroid hormones, including total testosterone, free testosterone, and estrone, were positively associated with glucose levels and gestational diabetes in mid-late pregnancy. These hormones may serve as early predictors of gestational diabetes in combination with other risk factors.
Dried urine spot method for detection of Schistosoma mansoni circulating cathodic antigen in resource-limited settings: a proof of concept study
Authors: Zacharia Abdallah , Makene Twilumba , Kinabo Clemence , Ogweno George , Lyamuya Faraja , Ngasala Billy 
Published: September 2023

BackgroundAmong the challenges in schistosomiasis surveillance and mapping surveys is the lack of a sensitive diagnostic method especially in low transmission setting. Currently, the WHO recommends the use point-of-care circulating cathodic antigen (Schisto POC-CCA) tests for surveillance and mapping of intestinal schistosomiasis. However, Schisto POC-CCA test has its drawbacks, one of which is the timely availability of test kits. One approach to overcoming this challenge is to develop a low-cost sampling method that allows for the collection and transport of urine specimens even in resource-limited settings.ObjectiveTo develop a simple and efficient method for the collection and detection of Schistosoma mansoni (S. mansoni) CCA using urine spotted onto filter paper.MethodologyTo develop a dried urine spot (DUS) method, various dried matrix extraction parameters were tested and optimized using predesigned steps. The parameters include the size of filter paper (determined by the number of punches), volume of solvents, and type of solvent. Moreover, we optimized the incubation conditions (time and temperature). Urine and stool specimens to conduct the experiments were collected from volunteer fishermen in Mwanza and this project staff. Data were entered into the Microsoft Excel spreadsheet and IBM Statistical Package for the Social Sciences, version 20 for analysis.ResultsThe optimal results were obtained when the procedure was run under the following conditions: Five punches of filter paper containing DUS were dissolved in 150 µl of distilled water and incubated at room temperature for 24 hours in an Eppendorf tube. More than 93% of the assays performed under these conditions produced results that were either comparable to or significantly better than the standard method.ConclusionThis study demonstrates the feasibility of collecting urine specimen (DUS) using filter paper and detecting Schistosoma CCA from DUS specimen using the Schisto POC-CCA cassette test.
Causal relationships between circulating inflammatory factors and IgA vasculitis: a bidirectional Mendelian randomization study
Authors: Qin Jiading , Zhang Ling , Ke Bo , Liu Tingting , Kong Chunfang , Jin Chenghao 
Published: September 2023

BackgroundIgA vasculitis (IgAV) is an immune-associated vasculitis, yet its exact etiology remains unclear. Here, we explore the interaction between IgAV and inflammatory factors using bidirectional Mendelian randomization (MR).MethodsWe conducted a bidirectional summary-level MR analysis to delineate the causality of C-reactive protein (CRP), procalcitonin (PCT), and 41 circulating inflammatory regulators with IgAV. Data on genetic variants related to inflammation were obtained from three genome-wide association studies (GWASs) on CRP, PCT, and human cytokines, whereas data on IgAV was from large meta-analyses of GWAS among 216 569 FinnGen Biobank participants. The primary MR analysis was performed using the inverse-variance weighted (IVW) approach, and the sensitivity analyses were carried out using MR-Egger, weighted median, weighted mode, and MR-pleiotropy residual sum and outlier.ResultsThis study revealed the association of CRP higher levels with increased risk of IgAV through IVW method (Estimate odds ratio [OR] = 1.41, 95% confidence interval [CI]: 1.01-1.98, P = 0.04), MR-Egger (OR = 1.87, CI: 1.15-3.02, P = 0.01), weighted median (OR = 2.00, CI: 1.21-3.30, P = 0.01) and weighted mode (OR = 1.74, CI: 1.13-2.68, P = 0.02). Furthermore, elevated IL-8 was strongly implicated with a higher risk of IgAV (IVW OR = 1.42, CI: 1.05-1.92; P = 0.02). Conversely, genetically predicted IgAV was associated with decreased levels of TNF-β (IVW estimate β = -0.093, CI: -0.178 - -0.007; P = 0.033). Additionally, no such significant statistical differences for other inflammatory factors were found.ConclusionOur current study using bidirectional MR analysis provides compelling evidence for a causal effect of CRP, PCT, and circulating inflammatory regulators on IgAV. These findings contribute to a better understanding of the pathogenesis of IgAV and emphasize the potential of targeting inflammatory factors for therapeutic interventions.
Clinical outcomes of COVID-19 and influenza in hospitalized children <5 years in the US
Authors: McGrath Leah J. , Moran Mary M. , Alfred Tamuno , Reimbaeva Maya , Di Fusco Manuela , Khan Farid , Welch Verna L. , Malhotra Deepa , Cane Alejandro , Lopez Santiago M. C. 
Published: September 2023

IntroductionWe compared hospitalization outcomes of young children hospitalized with COVID-19 to those hospitalized with influenza in the United States.MethodsPatients aged 0-&lt;5 years hospitalized with an admission diagnosis of acute COVID-19 (April 2021-March 2022) or influenza (April 2019-March 2020) were selected from the PINC AI Healthcare Database Special Release. Hospitalization outcomes included length of stay (LOS), intensive care unit (ICU) admission, oxygen supplementation, and mechanical ventilation (MV). Inverse probability of treatment weighting was used to adjust for confounders in logistic regression analyses.ResultsAmong children hospitalized with COVID-19 (n = 4,839; median age: 0 years), 21.3% had an ICU admission, 19.6% received oxygen supplementation, 7.9% received MV support, and 0.5% died. Among children hospitalized with influenza (n = 4,349; median age: 1 year), 17.4% were admitted to the ICU, 26.7% received oxygen supplementation, 7.6% received MV support, and 0.3% died. Compared to children hospitalized with influenza, those with COVID-19 were more likely to have an ICU admission (adjusted odds ratio [aOR]: 1.34; 95% confidence interval [CI]: 1.21–1.48). However, children with COVID-19 were less likely to receive oxygen supplementation (aOR: 0.71; 95% CI: 0.64–0.78), have a prolonged LOS (aOR: 0.81; 95% CI: 0.75–0.88), or a prolonged ICU stay (aOR: 0.56; 95% CI: 0.46–0.68). The likelihood of receiving MV was similar (aOR: 0.94; 95% CI: 0.81, 1.1).ConclusionsHospitalized children with either SARS-CoV-2 or influenza had severe complications including ICU admission and oxygen supplementation. Nearly 10% received MV support. Both SARS-CoV-2 and influenza have the potential to cause severe illness in young children.
Differences in rhizosphere soil fungal communities of wild and cultivated Paeonia ludlowii species
Authors: Qiao Hongyong , Gao Danlei , Yuan Tao 
Published: September 2023

IntroductionPaeonia ludlowii is a rare and endangered plant species with a high application value. However, its low cultivation success rate in China has severely limited its protection, development, and utilization. In addition to natural factors, microorganisms in the rhizosphere play an important role in determining its cultivation success.MethodsIn this study, growth indexes and soil physicochemical properties of both wild (origin: Nyingchi) and cultivated (introduction: Luanchuan) species of P. ludlowii were measured during the flowering, fruiting, and autumn foliage stages. ITS high-throughput sequencing technology was employed to detect rhizosphere soil fungi, and the diversity, community structure, functional prediction, molecular network, and ecological processes of the microbial community assembly were examined by multidirectional analysis.Results and discussionThe results indicated that: both wild and cultivated P. ludlowii species were able to flower and fruit normally, although the wild species had a higher number of flowers and fruits and higher soil available phosphorus and available potassium contents than those of the cultivated species. Ascomycota and Basidiomycota were the dominant rhizosphere soil fungal phyla in both P. ludlowii species. However, our network analysis showed that Ascomycota as the key fungal phylum of the wild species, whereas the cultivated species lacked key fungi. The community assembly mechanisms of rhizosphere soil fungi in both wild and cultivated species were primarily stochasticity, with no significant differences between them. Based on the results of FUNGuild and molecular network analyses, cultivated species had a higher proportion of fungi, such as Soil Saprotroph, that can easily cause diseases. Additionally, the network connections among fungi were weaker in the cultivated species than those in the wild species, which increased the cultivated species susceptibility to external environmental interferences. Therefore, from a soil microorganism perspective, this study suggests that, after the introduction and cultivation of P. ludlowii, if rhizosphere soil fungi fail to gradually form a close network relationship and instead promote the growth of pathogenic fungi, the fungal ecosystem would become vulnerable.