bluuebunny/crossref_metadata_2025_split huggingface dataset:
Key research questions for implementation of artificial intelligence in capsule endoscopy
Authors: Leenhardt Romain , Koulaouzidis Anastasios , Histace Aymeric , Baatrup Gunnar , Beg Sabina , Bourreille Arnaud , de Lange Thomas , Eliakim Rami , Iakovidis Dimitris , Dam Jensen Michael , Keuchel Martin , Margalit Yehuda Reuma , McNamara Deirdre , Mascarenhas Miguel , Spada Cristiano , Segui Santi , Smedsrud Pia , Toth Ervin , Tontini Gian Eugenio , Klang Eyal , Dray Xavier , Kopylov Uri 
Published: October 2022

Background: Artificial intelligence (AI) is rapidly infiltrating multiple areas in medicine, with gastrointestinal endoscopy paving the way in both research and clinical applications. Multiple challenges associated with the incorporation of AI in endoscopy are being addressed in recent consensus documents. Objectives: In the current paper, we aimed to map future challenges and areas of research for the incorporation of AI in capsule endoscopy (CE) practice. Design: Modified three-round Delphi consensus online survey. Methods: The study design was based on a modified three-round Delphi consensus online survey distributed to a group of CE and AI experts. Round one aimed to map out key research statements and challenges for the implementation of AI in CE. All queries addressing the same questions were merged into a single issue. The second round aimed to rank all generated questions during round one and to identify the top-ranked statements with the highest total score. Finally, the third round aimed to redistribute and rescore the top-ranked statements. Results: Twenty-one (16 gastroenterologists and 5 data scientists) experts participated in the survey. In the first round, 48 statements divided into seven themes were generated. After scoring all statements and rescoring the top 12, the question of AI use for identification and grading of small bowel pathologies was scored the highest (mean score 9.15), correlation of AI and human expert reading-second (9.05), and real-life feasibility-third (9.0). Conclusion: In summary, our current study points out a roadmap for future challenges and research areas on our way to fully incorporating AI in CE reading.
Predictors of reoperation after transurethral resection of the prostate in a diverse, urban academic centre
Authors: Loloi Justin , Wang Sarah , Labagnara Kevin , Plummer Melissa , Douglass Laura , Watts Kara , Abraham Nitya , Ohmann Erin 
Published: October 2022

Objective: To evaluate predictors of reoperation after transurethral resection of the prostate (TURP) for benign prostatic hyperplasia (BPH) in a diverse patient population. Materials and methods: A retrospective chart review was performed on men who underwent TURP between 2013 and 2016 at our institution with follow-up data post-operatively. Variables collected included patient demographics and clinical characteristics. Primary outcomes included whether the patient underwent repeat TURP and months elapsed since initial TURP. Results: A total of 304 men underwent TURP during the study period. Thirty men (10%) underwent repeat TURP at a mean interval of 26 months. Reoperation after TURP was not associated with race, body mass index (BMI), 5-alpha-reductase inhibitor (5-ARI) use, or pre-operative prostate volume. An elevated pre-operative haemoglobin A1c (HbA1c) was associated with both reoperation (odds ratio (OR) = 1.32, 95% confidence interval (CI): 1.03–1.69), 30 day readmission (OR = 1.96, 95% CI: 1.17–3.28) and 30-day hematuria (OR: 2.37, 95% CI: 1.29–4.38). Pre-operative prostate specific antigen (PSA) levels > 4 and hydronephrosis on imaging were also associated with a higher risk of reoperation. Conclusions: Reoperation after TURP occurred in 10% of our study cohort at a median of 26 months after surgery. Elevated HbA1c prior to surgery was associated with reoperation, 30-day readmission and 30-day hematuria. Higher risk of post-operative complications in patients with poorly controlled diabetes should be communicated at the time of decision for surgery. Future studies should evaluate whether optimising diabetes control prior to TURP reduces risk of reoperation or whether this risk is non-modifiable due to permanent changes in the lower urinary tract due to chronic hyperglycaemia. Level of evidence: III
Transient myocardial thickening associated with acute myocardial injury and congestive heart failure in two Toxoplasma gondii-positive cats
Authors: Romito Giovanni , Fracassi Federico , Cipone Mario 
Published: October 2022

Case series summary In this report, we provide detailed clinical, laboratory, electrocardiographic and echocardiographic descriptions of two Toxoplasma gondii-positive cats diagnosed with transient myocardial thickening (TMT) and acute myocardial injury (MI). In both cases, aetiological diagnosis was based on the antibody screening test (all cats had IgM titres ⩾1:64) and MI was demonstrated by a concomitant severe increase of the serum concentration of cardiac troponin I (5.1–23.6 ng/ml; upper hospital limit <0.2 ng/ml). In both cats, TMT and MI were aggravated by left atrial dilation and dysfunction, as well as congestive heart failure. In one cat, atrial standstill was also documented, while the other cat showed an intracardiac thrombus. Both cats underwent an extensive diagnostic work-up aimed at excluding additional comorbidities that could contribute to able to contribute to TMT and MI, and received appropriate antiprotozoal (ie, clindamycin) and cardiovascular therapy (eg, furosemide, pimobendan and clopidogrel). This was followed by a simultaneous decline in T gondii serology titres, normalisation of troponin level and the resolution of clinical, electrocardiographic, radiographic and echocardiographic abnormalities. In the light of these results, therapies were interrupted and subsequent controls ruled out any disease relapse. Relevance and novel information Although T gondii represents an often-cited cause of myocarditis in feline medicine, the existing literature on the demonstration of T gondii-associated cardiac compromise in cats is extremely limited. Accordingly, this report provides a useful contribution to pertinent scientific literature since it describes TMT and acute MI in two T gondii-positive cats.
Liberal use of local anaesthetic and the risk of toxicity in elective arthroplasties at a tertiary teaching hospital
Authors: McConnell Luke , Bulman James 
Published: October 2022

Background Local anaesthetic systemic toxicity (LAST) is a life-threatening potential complication that may follow the administration of local anaesthetic (LA) drugs, and is cumulative across the drug class. Local anaesthetics are commonly administered via different routes for elective orthopaedic procedures – both by anaesthetists and surgeons. We hypothesized that total doses of LA may be routinely encroaching upon toxicity. Methods All total hip or knee arthroplasties (THAs and TKAs) performed within a 3 month period at the John Hunter Hospital (tertiary referral centre and teaching hospital) were audited to assess total administration of LA. Demographics, surgical characteristics, use of general anaesthesia or sedation, and use of local anaesthetic via any route of administration was recorded. For each patient, a weight-based theoretical maximum safe dose was calculated and compared against the dose they received. Data is presented as mean ± SD, percentages. Statistical significance was determined at p < 0.05. Results 130 THAs and TKAs were identified within the audit period. 52 patients exceeded their drug-class theoretical maximum safe dose. 49 patients exceeded their weight-based maximum dose for a single LA agent, in all cases ropivacaine. Non-obese individuals receive significantly higher mean dose than obese individuals (119.4% [98.6–140.3] vs 78.82% [65.95–91.69], p = 0.001). No LAST events were identified. Conclusions Patients who received elective total hip or knee arthroplasties were exposed to concerningly high total doses of local anaesthetic, suggesting that greater awareness of the additive toxicity of drugs within this class is required.
Dietary iron restriction protects against vaso-occlusion and organ damage in murine sickle cell disease
Authors: Li Huihui , Kazmi Jacob S. , Lee Sungkyun , Zhang Dachuan , Gao Xin , Maryanovich Maria , Torres Lidiane , Verma Divij , Kelly Libusha , Ginzburg Yelena Z. , Frenette Paul S. , Manwani Deepa 
Published: October 2022

Abstract
Sickle cell disease (SCD) is an inherited disorder resulting from a β-globin gene mutation, and SCD patients experience erythrocyte sickling, vaso-occlusive episodes (VOE), and progressive organ damage. Chronic hemolysis, inflammation, and repeated red blood cell transfusions in SCD can disrupt iron homeostasis. Patients who receive multiple blood transfusions develop iron overload, and another subpopulation of SCD patients manifest iron deficiency. To elucidate connections between dietary iron, the microbiome, and SCD pathogenesis, we treated SCD mice with an iron-restricted diet (IRD). IRD treatment reduced iron availability and hemolysis, decreased acute VOE, and ameliorated chronic organ damage in SCD mice. Our results extend previous studies indicating that the gut microbiota regulate disease in SCD mice. IRD alters microbiota load and improves gut integrity, together preventing crosstalk between the gut microbiome and inflammatory factors such as aged neutrophils, dampening VOE, and organ damage. These findings provide strong evidence for the therapeutic potential of manipulating iron homeostasis and the gut microbiome to ameliorate SCD pathophysiology. Many treatments, which are under development, focus on lowering the systemic iron concentration to relieve disease complications, and our data suggest that iron-induced changes in microbiota load and gut integrity are related- and novel-therapeutic targets.
How I treat anemia with red blood cell transfusion and iron
Authors: Carson Jeffrey L. , Brittenham Gary M. 
Published: October 2022

Abstract
Severe anemia is commonly treated with red blood cell transfusion. Clinical trials have demonstrated that a restrictive transfusion strategy of 7 to 8 g/dL is as safe as a liberal transfusion strategy of 9 to 10 g/dL in many clinical settings. Evidence is lacking for subgroups of patients, including those with preexisting coronary artery disease, acute myocardial infarction, congestive heart failure, and myelodysplastic neoplasms. We present 3 clinical vignettes that highlight the clinical challenges in caring for patients with coronary artery disease with gastrointestinal bleeding, congestive heart failure, or myelodysplastic neoplasms. We emphasize that transfusion practice should be guided by patient symptoms and preferences in conjunction with the patient’s hemoglobin concentration. Along with the transfusion decision, evaluation and management of the etiology of the anemia is essential. Iron-restricted erythropoiesis is a common cause of anemia severe enough to be considered for red blood cell transfusion but diagnosis and management of absolute iron deficiency anemia, the anemia of inflammation with functional iron deficiency, or their combination may be problematic. Intravenous iron therapy is generally the treatment of choice for absolute iron deficiency in patients with complex medical disorders, with or without coexisting functional iron deficiency.
Infant lung function and maternal physical activity in the first half of pregnancy
Authors: Gudmundsdóttir Hrefna Katrín , Carlsen Oda C.L. , Bains Karen Eline Stensby , Färdig Martin , Haugen Guttorm , Jonassen Christine M. , LeBlanc Marissa , Nordlund Björn , Rehbinder Eva Maria , Skjerven Håvard O. , Staff Anne Cathrine , Vettukattil Riyas , Lødrup Carlsen Karin C. 
Published: October 2022

Background and aimPhysical activity (PA) in pregnancy is important for maternal and possibly offspring health. To study the early origins of lung function we aimed to determine whether PA in the first half of pregnancy is associated with lung function in healthy 3-month-old infants.MethodsFrom the general population-based Preventing Atopic Dermatitis and Allergies in Children birth cohort recruiting infants antenatally in Norway and Sweden, all 812 infants (48.8% girls) with available tidal flow–volume measures in the awake state at 3 months of age and mid-pregnancy data on PA were included. PA was self-reported by the mothers and, based on intensity, we categorised them as active or inactive during pregnancy. Furthermore, we defined active mothers as fairly or highly active. The main outcome was a ratio of time to peak tidal expiratory flow to expiratory time (tPTEF/tE) <0.25. Associations were analysed by logistic regression, adjusting for maternal age, education, parity, pre-pregnancy body mass index,in uteronicotine exposure and parental atopy.ResultsThe mean±sdtPTEF/tEwas 0.391±0.08 and did not differ significantly according to maternal PA level in pregnancy. The 290 infants of inactive mothers had higher odds of havingtPTEF/tE<0.25 compared to infants of all active mothers (OR 2.07, 95% CI 1.13–3.82; p=0.019) and compared to infants (n=224) of fairly active (OR 2.83, 95% CI 1.26–7.24; p=0.018) but not highly active mothers (n=298).ConclusionBased on self-reported maternal PA in the first half of pregnancy, 3-month-old infants of inactive compared to active mothers had higher odds of a lowtPTEF/tE.
Joint reconstruction of neuron and ultrastructure via connectivity consensus in electron microscope volumes
Authors: Hong Bei , Liu Jing , Zhai Hao , Liu Jiazheng , Shen Lijun , Chen Xi , Xie Qiwei , Han Hua 
Published: October 2022

Abstract
Background
Nanoscale connectomics, which aims to map the fine connections between neurons with synaptic-level detail, has attracted increasing attention in recent years. Currently, the automated reconstruction algorithms in electron microscope volumes are in great demand. Most existing reconstruction methodologies for cellular and subcellular structures are independent, and exploring the inter-relationships between structures will contribute to image analysis. The primary goal of this research is to construct a joint optimization framework to improve the accuracy and efficiency of neural structure reconstruction algorithms.

Results
In this investigation, we introduce the concept of connectivity consensus between cellular and subcellular structures based on biological domain knowledge for neural structure agglomeration problems. We propose a joint graph partitioning model for solving ultrastructural and neuronal connections to overcome the limitations of connectivity cues at different levels. The advantage of the optimization model is the simultaneous reconstruction of multiple structures in one optimization step. The experimental results on several public datasets demonstrate that the joint optimization model outperforms existing hierarchical agglomeration algorithms.

Conclusions
We present a joint optimization model by connectivity consensus to solve the neural structure agglomeration problem and demonstrate its superiority to existing methods. The intention of introducing connectivity consensus between different structures is to build a suitable optimization model that makes the reconstruction goals more consistent with biological plausible and domain knowledge. This idea can inspire other researchers to optimize existing reconstruction algorithms and other areas of biological data analysis.
pSuc-EDBAM: Predicting lysine succinylation sites in proteins based on ensemble dense blocks and an attention module
Authors: Jia Jianhua , Wu Genqiang , Li Meifang , Qiu Wangren 
Published: October 2022

Abstract
Background
Lysine succinylation is a newly discovered protein post-translational modifications. Predicting succinylation sites helps investigate the metabolic disease treatments. However, the biological experimental approaches are costly and inefficient, it is necessary to develop efficient computational approaches.

Results
In this paper, we proposed a novel predictor based on ensemble dense blocks and an attention module, called as pSuc-EDBAM, which adopted one hot encoding to derive the feature maps of protein sequences, and generated the low-level feature maps through 1-D CNN. Afterward, the ensemble dense blocks were used to capture feature information at different levels in the process of feature learning. We also introduced an attention module to evaluate the importance degrees of different features. The experimental results show that Acc reaches 74.25%, and MCC reaches 0.2927 on the testing dataset, which suggest that the pSuc-EDBAM outperforms the existing predictors.

Conclusions
The experimental results of ten-fold cross-validation on the training dataset and independent test on the testing dataset showed that pSuc-EDBAM outperforms the existing succinylation site predictors and can predict potential succinylation sites effectively. The pSuc-EDBAM is feasible and obtains the credible predictive results, which may also provide valuable references for other related research. To make the convenience of the experimental scientists, a user-friendly web server has been established (http://bioinfo.wugenqiang.top/pSuc-EDBAM/), by which the desired results can be easily obtained.
Sex differences exist in adult heart group 2 innate lymphoid cells
Authors: Peng Hongyan , Wu Shuting , Wang Shanshan , Yang Qinglan , Wang Lili , Zhang Shuju , Huang Minghui , Li Yana , Xiong Peiwen , Zhang Zhaohui , Cai Yue , Li Liping , Deng Youcai , Deng Yafei 
Published: October 2022

Abstract
Background
Group 2 innate lymphoid cells (ILC2s) are the most dominant ILCs in heart tissue, and sex-related differences exist in mouse lung ILC2 phenotypes and functions; however, it is still unclear whether there are sex differences in heart ILC2s.

Results
Compared with age-matched wild-type (WT) male mice, 8-week-old but not 3-week-old WT female mice harbored an obviously greater percentage and number of heart ILC2s in homeostasis. However, the percentage of killer-cell lectin-like receptor G1 (Klrg1)− ILC2s was higher, but the Klrg1+ ILC2s were lower in female mice than in male mice in both heart tissues of 3- and 8-week-old mice. Eight-week-old Rag2−/− mice also showed sex differences similar to those of age-matched WT mice. Regarding surface marker expression, compared to age-matched male mice, WT female mice showed higher expression of CD90.2 and Ki67 and lower expression of Klrg1 and Sca-1 in heart total ILC2s. There was no sex difference in IL-4 and IL-5 secretion by male and female mouse heart ILC2s. Increased IL-33 mRNA levels within the heart tissues were also found in female mice compared with male mice. By reanalyzing published single-cell RNA sequencing data, we found 2 differentially expressed genes between female and male mouse heart ILC2s. Gene set variation analysis revealed that the glycine, serine and threonine metabolism pathway was upregulated in female heart ILC2s. Subcluster analysis revealed that one cluster of heart ILC2s with relatively lower expression of Semaphorin 4a and thioredoxin interacting protein but higher expression of hypoxia-inducible lipid droplet-associated.

Conclusions
These results revealed greater numbers of ILC2s, higher expression of CD90.2, reduced Klrg1 and Sca-1 expression in the hearts of female mice than in male mice and no sex difference in IL-4 and IL-5 production in male and female mouse heart ILC2s. These sex differences in heart ILC2s might be due to the heterogeneity of IL-33 within the heart tissue.
Current state and practice variation in the use of Meningitis/Encephalitis (ME) FilmArray panel in children
Authors: Rajbhandari Prabi , Goodrich Nathaniel , Nabower Aleisha M. , Brown Miraides F. , Ekambaram Maheswari , Eisenberg Jaclyn , Forbes Michael L. , Gollehon Nathan , Martin Kimberly C. , McCulloh Russell , Stone Bryan , Tandy Matt , Snowden Jessica 
Published: October 2022

Abstract
Background
The Meningitis/Encephalitis FilmArray® Panel (ME panel) was approved by the U.S. Food and Drug Administration in 2015 and provides rapid results when assessing patients with suspected meningitis or encephalitis. These patients are evaluated by various subspecialties including pediatric hospital medicine (PHM), pediatric emergency medicine (PEM), pediatric infectious diseases, and pediatric intensive care unit (PICU) physicians. The objective of this study was to evaluate the current use of the ME panel and describe the provider and subspecialty practice variation.

Methods
We conducted an online cross-sectional survey via the American Academy of Pediatrics Section of Hospital Medicine (AAP-SOHM) ListServe, Brown University PEM ListServe, and PICU Virtual pediatric system (VPS) Listserve.

Results
A total of 335 participants out of an estimated 6998 ListServe subscribers responded to the survey. 68% reported currently using the ME panel at their institutions. Among test users, most reported not having institutional guidelines on test indications (75%) or interpretation (76%). 58% of providers self-reported lack of knowledge of the test’s performance characteristics. Providers from institutions that have established guidelines reported higher knowledge compared to those that did not (51% vs. 38%; p = 0.01). More PHM providers reported awareness of ME panel performance characteristics compared to PEM physicians (48% vs. 27%; p = 0.004); confidence in test interpretation was similar between both groups (72 vs. 69%; p = 0.80).

Conclusion
Despite the widespread use of the ME panel, few providers report having institutional guidelines on test indications or interpretation. There is an opportunity to provide knowledge and guidance about the ME panel among various pediatric subspecialties.