bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sepsis Prognostic Scores Accuracy in Predicting Adverse Outcomes in Children With Sepsis Admitted to the Pediatric Intensive Care Unit From the Emergency Department
Authors: Marchetto Luca , Comoretto Rosanna , Gregori Dario , Da Dalt Liviana , Amigoni Angela , Daverio Marco 
Published: May 2023

Objective
To compare the performance of several prognostic scores calculated in the first 24 hours of admission (day 1) in predicting mortality and morbidity among critically ill children with sepsis presenting to the pediatric emergency department (PED) and then admitted to the pediatric intensive care unit (PICU).

Methods
Single-center, retrospective cohort study in children with a diagnosis of sepsis visiting the PED and then admitted to the PICU from January 1, 2010 to December 31, 2019. Sepsis organ dysfunction scores—pediatric Sequential Organ Failure Assessment (pSOFA) (Schlapbach, Matics, Shime), quickSOFA, quickSOFA-L, Pediatric Logistic Organ Dysfunction (PELOD)-2, quickPELOD-2, and Pediatric Multiple Organ Dysfunction score—were calculated during the first 24 hours of admission (day 1) and their performance compared with systemic inflammatory response syndrome (SIRS) and severe sepsis—International Consensus Conference on Pediatric Sepsis(ICCPS)-derived criteria—using the area under the receiver operating characteristic curve. Primary outcome was PICU mortality. Secondary outcomes were: a composite of death and new disability (ie, change from baseline Pediatric Overall Performance Category score ≥1); prolonged PICU length of stay (>5 d); prolonged invasive mechanical ventilation (MV) (>3 d).

Results
Among 60 patients with sepsis, 4 (6.7%) died, 7 (11.7%) developed new disability, 26 (43.3%) experienced prolonged length of stay, and 21 (35%) prolonged invasive MV. The prognostic ability in mortality discrimination was significantly higher for organ dysfunction scores, with PELOD-2 showing the best performance (area under the receiver operating characteristic curve, 0.924; 95% confidence interval, 0.837–1.000), significantly better than SIRS 3 criteria (0.924 vs 0.509, P = 0.009), SIRS 4 criteria (0.924 vs 0.509, P < 0.001), and severe sepsis (0.924 vs 0.527, P < 0.001). Among secondary outcomes, PELOD-2 performed significantly better than SIRS criteria and severe sepsis to predict prolonged duration of invasive MV, whereas better than severe sepsis to predict “poor outcome” (mortality or new disability).

Conclusions
Day 1 organ dysfunction scores performed better in predicting mortality and morbidity outcomes than ICCPS-derived criteria. The PELOD-2 was the organ dysfunction score with the best performance for all outcomes.
“Super-Microsurgical Anastomosis training using the chick embryos within the “Egg-in-Cube” system.”
Authors: Karakawa Ryo , Yoshimatsu Hidehiko , Nakatsuka Kengo , Fuse Yuma , Nishiyama Shohei , Kawahara Tomohiro , Yano Tomoyuki 
Published: May 2023

Summary:
Although the super-microsurgery technique is an essential skill for lymphatic surgery or perforator flap surgery, an ideal training model is yet to be found. Living animal models, such as rodents, are considered to be ideal microsurgical training models. However, the use of living animal models is costly and there are bioethical considerations. Hence, we aimed to develop a novel, cost-effective, highly reproducible, and easy-to-handle super-microsurgical anastomosis training system using the chicken embryo within the “Egg-in-Cube.” The chick embryos were fertilized in the artificial cubic eggshell, which was fabricated by integrating a polycarbonate frame structure and five polydimethylsiloxane (PDMS) membranes. Seven days later, the trainees underwent super-microsurgical training using the vitelline artery of the chick embryo. The trainees were able to perform super-microsurgical training using all eleven surviving chicken embryos. The average diameter of the vitelline artery was 0.43 mm. Patency and pulsation were observed after the anastomosis in four of the eleven cases. The super-microsurgical training system using the chicken embryo within the “Egg-in-cube” has several advantages. First, this system is ethically acceptable. Second, this system is less costly and easier to manage than other animal models. Third, this model is suitable as a super-microsurgical training model such as lymphovenular anastomosis (LVA) because the diameter of the vitelline artery was similar to that of the lymphatic vessels in lymphedema patients. Moreover, the trainee can confirm patency and leakage after the anastomosis because this model has a circulation system. The trainee can practice the super-microsurgical technique efficiently with simultaneous feedback on anastomosis results.
Impact of Two Urethral Stent Types on the Complications After One-Stage Hypospadias Repair Using the Duckett Procedure: A retrospective cohort study.
Authors: Zhou Shiying , Zhang Jian , Zhang Jiaqi , Xiao Xiaolian , Su Zheng , Liu Meng , Huang Zhaolun , Tian Dongjun , Liang Weiqiang , Jinming Zhang 
Published: May 2023

Purpose:
The purpose of this study was to evaluate whether the new nickel-titanium alloy stents are superior to traditional silicone stents in hypospadias repair surgery to prevent complications such as urinary fistula.

Methods:
This retrospective cohort study included 576 patients with hypospadias who underwent the placement either with nickel-titanium alloy stents or traditional silicone stents after hypospadias surgery between March 2002 and August 2019. The patients were assigned into the nickel-titanium alloy stent group (group NTAS) and the silicone stent group (group SS). The primary outcome was assessed with the rate of urinary fistula occurrence at four weeks (stent removal time), and the secondary outcomes were decided on the rate of other complications such as urethral stricture, and urethral diverticulum, infection, etc. The occurrence of complications in both groups was compared and the important contributing factors of urinary fistula and urethral stricture were determined.

Results:
Among 576 patients, 398 were assigned into group NTAS while 178 were into group SS. 35 patients in the group NTAS and 30 in the group SS developed urinary fistula with a ratio of 8.8% and 16.9%, respectively (p = 0.005). Subgroup analysis showed that the differences were mainly in preschool patients (≤ 6 years) (p = 0.004) and those with the penile type of hypospadias (p = 0.008). In addition, urethral stricture complicated five patients in the NTAS group and two in the SS group with a ratio of 1.3% and 1.1%, respectively (p = 1.000). Logistic regression showed that hypospadias type (p = 0.001) and stent type (p = 0.001) are the important risk factors for urethral fistula.

Conclusions:
Nickel-titanium alloy stents reduced the occurrence of urinary fistula complications after hypospadias repair in preschool patients, and can be optioned as a better choice for hypospadias surgery.
Soft Palate Dysplasia: Properties and Surgical Techniques
Authors: Qin Chuanqi , Li Jian , Yang Jiegang , Cheng Yibin , Fu Xiazhou 
Published: May 2023

Background:
The authors aimed to report a hitherto undescribed class of patients with the obvious phenotype of a novel soft palate dysplasia (SPD) combining unilateral soft palate hypoplasia with a fully developed uvula. The authors also aimed to investigate and evaluate the corresponding surgical approaches.

Methods:
Twelve patients were clinically diagnosed with SPD. Clinical examination, including radiographic tests, was performed to characterize the congenital deformity. The effectiveness of velopharyngeal closure and speech were tested preoperatively and postoperatively.

Results:
SPD was featured with velopharyngeal insufficiency, food regurgitation, and speech disorders. It was commonly manifested as structural deformities of the soft palate, tongue palatine arch, pharyngeal palatine arch, and pterygomandibular fold, but with complete uvula shape. According to radiographic analysis, in five patients, the lateral pterygoid processes were poorly developed, and other malformations were present. Velopharyngoplasty based on the unilateral posterior pharyngeal flap can well restore the velopharyngeal closure and speech intelligibility without respiration obstruction.

Conclusions:
SPD is characterized as congenital velopharyngeal insufficiency manifested as a primary soft palate defect. It is highly associated with other physical deformities but independent of conventionally known syndromes. The cause may be an abnormal development of the pterygoid process. Unilateral velopharyngoplasty based on the posterior pharyngeal flap is a great technique to repair SPD.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Bivalent mRNA COVID-19 Vaccine–Related Pericarditis on 18F-FDG PET/CT
Authors: Wu Yu-Chin , Kao Chia-Hung , Liao Chiung-Wei , Sun Shung Shung , Hsieh Te-Chun 
Published: May 2023

Abstract
A 13-year-old boy was suspected with pericarditis after a second booster dose of bivalent mRNA COVID-19 vaccine. After specific preparation for cardiac inflammation with carbohydrate-free, high-fat diet, the 18F-FDG PET/CT successfully demonstrated simultaneous presentation of vaccination-related axillary lymphadenopathy and pericarditis without the interference of physiological myocardial uptake.
Operative management and outcomes of colorectal injuries after gunshot wounds in the deployed military setting versus civilian trauma centers
Authors: Dilday Joshua , Owattanapanich Natthida , Benjamin Elizabeth R. , Biswas Subarna , Shackelford Stacy , Demetriades Demetrios 
Published: May 2023

INTRODUCTION
Colon and rectal injuries have been diverted at higher rates in military trauma compared with civilian injuries. However, in the last few years, there has been a shift to more liberal primary anastomosis in wartime injuries. The purpose of this study was to compare the management and outcomes in colorectal gunshot wounds (GSWs) between military and civilian settings.

METHODS
The study included Department of Defense Trauma Registry and Trauma Quality Improvement Program database patients who sustained colorectal GSWs, during the period 2013 to 2016. Department of Defense Trauma Registry patients were propensity score matched 1:3 based on age, sex, grade of colorectal injury, and extra-abdominal Abbreviated Injury Scale. Patients without signs of life, transfers from an outside hospital, and nonspecific colorectal Organ Injury Scale were excluded. Operative management and outcomes were compared between the two groups. Subanalysis was performed on the military cohort to identify any differences in the use primary repair, colectomy, or fecal diversion based upon military affiliation or North Atlantic Treaty Organization status.

RESULTS
Overall, there were 2,693 patients with colorectal GSWs; 60 patients in the military group were propensity score matched with 180 patients in the civilian group. Overall, colectomy was the most common procedure performed (72.1%) and was used more frequently in the military group (83.3% vs. 68.3%; p < 0.05). However, the rate of fecal diversion was similar in the two groups (23.3% vs. 27.8%; p = 0.500). Among those in the military group, no difference was seen in primary repair, colectomy, or fecal diversion based upon military affiliation or North Atlantic Treaty Organization status. The rates of in-hospital compilations and mortality were similar between the military and civilian groups.

CONCLUSION
The severity of GSW colorectal injuries in military and civilian trauma was comparable. There was no significant difference in terms of fecal diversion, mortality, and complications between groups. Military personnel are treated similarly regardless of affiliation.

LEVEL OF EVIDENCE
Therapeutic/Care Management; Level III.
Meltwater generation in ice stream shear margins: case study in Antarctic ice streams
Authors: Ranganathan Meghana , Barotta Jack-William , Meyer Colin R. , Minchew Brent 
Published: May 2023

Liquid water within glacier ice and at the glacier beds exerts a significant control on ice flow and glacier stability through a number of processes, including altering the rheology of the ice and lubricating the bed. Some of this water is generated as melt from regions of rapid deformation, including shear margins, due to heating by viscous dissipation. However, how much meltwater is generated and drained from shear margins remains unclear. Here, we apply a model that describes the evolution of ice temperature, melting, and water transport within deforming ice to estimate the flux of meltwater from shear margins in glaciers. We estimate the flux of meltwater from temperate ice zones in three Antarctic regions: Bindschadler and MacAyeal Ice Streams, Pine Island Glacier, and Byrd Glacier. We show that the flux of meltwater from shear margins in these regions may be as significant as the meltwater produced by frictional heating at the bed, with average fluxes of

∼
0.005
–
0.1

m

yr

−
1

. This contribution of shear heating to meltwater flux at the bed may thus affect both the rheology of the ice as well as sliding at the bed, both key controls on fast ice flow.
A Roadmap to Artificial Intelligence (AI): Methods for Designing and Building AI ready Data for Women’s Health Studies
Authors: Kidwai-Khan Farah , Wang Rixin , Skanderson Melissa , Brandt Cynthia A. , Fodeh Samah , Womack Julie A. 
Published: May 2023

AbstractObjectivesEvaluating methods for building data frameworks for application of AI in large scale datasets for women’s health studies.MethodsWe created methods for transforming raw data to a data framework for applying machine learning (ML) and natural language processing (NLP) techniques for predicting falls and fractures.ResultsPrediction of falls was higher in women compared to men. Information extracted from radiology reports was converted to a matrix for applying machine learning. For fractures, by applying specialized algorithms, we extracted snippets from dual x-ray absorptiometry (DXA) scans for meaningful terms usable for predicting fracture risk.DiscussionLife cycle of data from raw to analytic form includes data governance, cleaning, management, and analysis. For applying AI, data must be prepared optimally to reduce algorithmic bias.ConclusionAlgorithmic bias is harmful for research using AI methods. Building AI ready data frameworks that improve efficiency can be especially valuable for women’s health.Lay SummaryWomen’s health studies are rare in large cohorts of women. The department of Veterans affairs (VA) has data for a large number of women in care. Prediction of falls and fractures are important areas of study related to women’s health. Artificial Intelligence (AI) methods have been developed at the VA for predicting falls and fractures. In this paper we discuss data preparation for applying these AI methods. We discuss how data preparation can affect bias and reproducibility in AI outcomes.
TGIRT-seq of Inflammatory Breast Cancer Tumor and Blood Samples Reveals Widespread Enhanced Transcription Impacting RNA Splicing and Intronic RNAs in Plasma
Authors: Wylie Dennis , Wang Xiaoping , Yao Jun , Xu Hengyi , Ferrick-Kiddie Elizabeth A. , Iwase Toshiaki , Krishnamurthy Savitri , Ueno Naoto T. , Lambowitz Alan M. 
Published: May 2023

ABSTRACTInflammatory breast cancer (IBC) is the most aggressive and lethal breast cancer subtype but lacks unequivocal genomic differences or robust biomarkers that differentiate it from non-IBC. Here, Thermostable Group II intron Reverse Transcriptase RNA-sequencing (TGIRT-seq) revealed myriad differences in tumor samples, Peripheral Blood Mononuclear Cells (PBMCs), and plasma that distinguished IBC from non-IBC patients and healthy donors across all tested receptor-based subtypes. These included numerous differentially expressed protein-coding gene and non-coding RNAs in all three sample types, a granulocytic immune response in IBC PBMCs, and over- expression of antisense RNAs, suggesting wide-spread enhanced transcription in both IBC tumors and PBMCs. By using TGIRT-seq to quantitate Intron-exon Depth Ratios (IDRs) and mapping reads to both genome and transcriptome reference sequences, we developed methods for parallel analysis of transcriptional and post-transcriptional gene regulation. This analysis identified numerous differentially and non-differentially expressed protein-coding genes in IBC tumors and PBMCs with high IDRs, the latter reflecting rate-limiting RNA splicing that negatively impacts mRNA production. Mirroring gene expression differences in tumors and PBMCs, over-represented protein-coding gene RNAs in IBC patient plasma were largely intronic RNAs, while those in non- IBC patients and healthy donor plasma were largely mRNA fragments. Potential IBC biomarkers in plasma included T-cell receptor pre-mRNAs and intronic, LINE-1, and antisense RNAs. Our findings provide new insights into IBC and set the stage for monitoring disease progression and response to treatment by liquid biopsy. The methods developed for parallel transcriptional and post- transcriptional gene regulation analysis have potentially broad RNA-seq and clinical applications.
Four classic “de novo” genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences
Authors: Hannon Joseph 
Published: May 2023

AbstractDespite being previously regarded as extremely unlikely, the idea that entirely novel protein-coding genes can emerge from non-coding sequences has gradually become accepted over the past two decades. Examples of “de novo origination”, resulting in lineage-specific “orphan” genes, lacking orthologs, are now produced every year. However, many are likely cases of duplicates that are difficult to recognize. Here, I re-examine the claims and show that four very well-known examples of genes alleged to have emerged de novo “from scratch” - namelyFLJ33706in humans,Goddardin fruit flies,BSC4in baker’s yeast andAFGP2in codfish - all have plausible evolutionary ancestors in pre-existing genes. In the case of the first two, highly diverged retrogenes that code for regulatory proteins may have been misidentified as being orphans. The antifreeze glycoproteins in cod, moreover, are shown to have likely not evolved from repetitive non-genic sequences but, as in other related cases, from an apolipoprotein that may well have been pseudogenized before later being reactivated. These findings detract from various claims made about de novo gene birth and show there has been a tendency not to invest the necessary effort in searching for homologs outside of a very limited syntenic or phylostratigraphic methodology. An approach used here for improving homology detection draws upon similarities, not just in terms of statistical sequence analysis, but also with biochemistry and function, in order to obviate failure.
Transformer with Convolution and Graph-Node co-embedding: An accurate and interpretable vision backbone for predicting gene expressions from local histopathological image
Authors: Xiao Xiao , Kong Yan , Wang Zuoheng , Lu Hui 
Published: May 2023

AbstractInferring gene expressions from histopathological images has always been a fascinating but challenging task due to the huge differences between the two modal data. Previous works have used modified DenseNet121 to encode the local images and make gene expression predictions. And later works improved the prediction accuracy of gene expression by incorporating the coordinate information from images and using all spots in the tissue region as input. While these methods were limited in use due to model complexity, large demand on GPU memory, and insufficient encoding of local images, thus the results had low interpretability, relatively low accuracy, and over-smooth prediction of gene expression among neighbor spots. In this paper, we propose TCGN, (Transformer with Convolution and Graph-Node co-embedding method) for gene expression prediction from H&E stained pathological slide images. TCGN consists of convolutional layers, transformer encoders, and graph neural networks, and is the first to integrate these blocks in a general and interpretable computer vision backbone for histopathological image analysis. We trained TCGN and compared its performance with three existing methods on a publicly available spatial transcriptomic dataset. Even in the absence of the coordinates information and neighbor spots, TCGN still outperformed the existing methods by 5% and achieved 10 times higher prediction accuracy than the counterpart model. Besides its higher accuracy, our model is also small enough to be run on a personal computer and does not need complex building graph preprocessing compared to the existing methods. Moreover, TCGN is interpretable in recognizing special cell morphology and cell-cell interactions compared to models using all spots as input that are not interpretable. A more accurate omics information prediction from pathological images not only links genotypes to phenotypes so that we can predict more biomarkers that are expensive to test from histopathological images that are low-cost to obtain, but also provides a theoretical basis for future modeling of multi-modal data. Our results support that TCGN is a useful tool for inferring gene expressions from histopathological images and other potential histopathological image analysis studies.HighlightsFirst deep learning model to integrate CNN, GNN, and transformer for image analysisAn interpretable model that uses cell morphology and organizations to predict genesHigher gene expression prediction accuracy without global informationAccurately predicted genes are related to immune escape and abnormal metabolismPredict important biomarkers for breast cancer accurately from cheaper imagesGraphical abstract
Epigenetics Insights from Perceived Facial Aging
Authors: Vladimir Klemo , Perišić Marija Majda , Štorga Mario , Mostashari Ali , Khanin Raya 
Published: May 2023

AbstractFacial aging is the most visible manifestation of aging. People desire to look younger than others of the same chronological age. Hence, perceived age is often used as a visible marker of aging, while biological age, often estimated by methylation markers, is used as an objective measure of age. Multiple epigenetics-based clocks have been developed for accurate estimation of general biological age and the age of specific organs, including the skin. However, it is not clear whether the epigenetic biomarkers (CpGs) used in these clocks are drivers of aging processes or consequences of aging.In this proof-of-concept study, we integrate data from GWAS on perceived facial aging, and EWAS on CpGs measured in blood. By running EW Mendelian randomization, we identify hundreds of putative CpGs that are potentially causal to perceived facial aging with similar numbers of damaging markers that causally drive or accelerate facial aging and protective methylation markers that causally slow down or protect from aging. We further demonstrate that while candidate causal CpGs have little overlap with known epigenetics-based clocks, they affect genes or proteins with known functions in skin aging such as skin pigmentation, elastin, and collagen levels. Overall, our results suggest that blood methylation markers reflect facial aging processes, and thus can be used to quantify skin aging and develop anti-aging solutions that target the root causes of aging.