bluuebunny/crossref_metadata_2025_split huggingface dataset:
Free Flap Failure and Complications in Acute Burns: A Systematic Review and Meta-analysis
Authors: Kasmirski Julia A. , Alessandri-Bonetti Mario , Liu Hilary , Corcos Alain C. , Ziembicki Jenny A. , Stofman Guy M. , Egro Francesco M. 
Published: October 2023

Background:
Severe acute burn injuries represent a challenge to the reconstructive surgeon. Free flap reconstruction might be required in cases of significant critical structure exposure and soft tissue deficits, when local options are unavailable. This study aimed to determine the free flap complication rate in acute burn patients.

Methods:
A systematic review and meta-analysis were conducted and reported according to Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines and registered on the International Prospective Register of Systematic Reviews database (CRD42023404478). The following databases were accessed: Embase, PubMed, Web of Science, and Cochrane Library. The primary outcome was the free flap failure rate.

Results:
The study identified 31 articles for inclusion. A total of 427 patients (83.3% men, 16.7% women) accounting for 454 free flaps were included. The mean patient age was 36.21 [95% confidence interval (CI), 31.25–41.16]. Total free flap loss rate was 9.91% [95% CI, 7.48%–13.02%], and partial flap loss was 4.76% [95% CI, 2.66%–8.39%]. The rate of venous thrombosis was 6.41% [95% CI, 3.90%–10.36%] and arterial thrombosis was 5.08% [95% CI, 3.09%–8.26%]. Acute return to the operating room occurred in 20.63% [16.33%–25.71%] of cases. Stratified by body region, free flaps in the lower extremity had a failure rate of 8.33% [95% CI, 4.39%–15.24%], whereas in the upper extremity, the failure rate was 6.74% [95% CI, 3.95%–11.25%].

Conclusion:
This study highlights the high risk of free flap complications and failure in acute burn patients.
Angiotensin-converting enzyme 2: virus accomplice or host defender?
Authors: Wang Jiyan , Chang Hongkai , Qiao Yaya , Sun Huanran , Li Xichuan , Yuan Shuofeng , Zhang Shuai , Shan Changliang 
Published: October 2023

Objective:
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to social disruptions, mainly because we know too little about SARS-CoV-2.

Methods and Results:
In this study, we integrated RNA sequencing results and found that SARS-CoV-2 infection alters aerobic glycolysis, the oxidative pentose phosphate pathway (oxiPPP), and DNA replication in lung tissues and cells. However, the direction of metabolic flux and DNA replication are dominated by angiotensin-converting enzyme 2 (ACE2), a host cell-expressed viral receptor protein. More interestingly, although hosts with a high expression of ACE2 are more likely to be infected with SARS-CoV-2, the invading virus cannot perform nucleic acid replication well due to the restriction of glucose metabolism, eventually resulting in a prolonged infection cycle or infection failure.

Conclusion:
Our findings preliminarily explain the reasons for the emergence of asymptomatic infections at an early stage, which will provide assistance for the development of detection methods for diagnosing COVID-19.
Suicide and Self-Harm in Adolescents During the COVID-19 Pandemic: A U.S. Virtual Pediatric Systems, LLC, Database Study of PICU Admissions, 2016–2021
Authors: McCluskey Casey K. , Black Tyler R. , Zee-Cheng Janine , Klein Margaret J. , Lin Anna , Rogerson Colin M. , Carroll Christopher L. , Remy Kenneth E. , Scanlon Matthew C. , Shein Steven L. , Wright Melvin , Rotta Alexandre T. 
Published: October 2023

OBJECTIVES:To characterize the epidemiology of suicide and self-harm among adolescents admitted to PICUs during the first 2 years of the COVID-19 pandemic in the United States.DESIGN:Descriptive analysis of a large, multicenter, quality-controlled database (Virtual Pediatric Systems [VPS]), and of a national public health dataset (U.S. Centers for Disease Control and Prevention web-based Wide-ranging ONline Data for Epidemiology Research [CDC WONDER]).SETTING:The 69 PICUs participating in the VPS database that contributed data for the entire the study period, January 1, 2016, to December 31, 2021.PATIENTS:Adolescents older than 12 years to younger than 18 years old admitted to a participating PICU during the study period with a diagnosis involving self-harm or a suicide attempt (VPS sample), or adolescent suicide deaths over the same period (CDC WONDER sample).INTERVENTIONS:None.MEASUREMENTS AND MAIN RESULTS:We identified 10,239 suicide deaths and 7,692 PICU admissions for self-harm, including 5,414 admissions in the pre-pandemic period (Q1-2016 to Q1-2020) and 2,278 in the pandemic period (Q2-2020 to Q4-2021). Compared with the pre-pandemic period, there was no increase in the median (interquartile range) number of suicide deaths per quarter (429 [399–453] vs. 416 [390–482]) or PICU admissions for self-harm per quarter (315 [289–353] vs. 310 [286–387]) during the pandemic period, respectively. There was an increase in the ratio of self-harm PICU admissions to all-cause PICU admissions per quarter during the pandemic (1.98 [1.43–2.12]) compared with the pre-pandemic period per quarter (1.59 [1.46–1.74]). We also observed a significant decrease in all-cause PICU admissions per quarter early in the pandemic compared with the pre-pandemic period (16,026 [13,721–16,297] vs. 19,607 [18,371–20,581]).CONCLUSIONS:The number of suicide deaths and PICU admissions per quarter for self-harm remained relatively constant during the pandemic, while the number of all-cause PICU admissions per quarter decreased compared with the pre-pandemic period. The resultant higher ratio of self-harm admissions to all-cause PICU admissions may have contributed to the perception that more adolescents required critical care for mental health-related conditions early in the pandemic.
68Ga-PSMA PET/CT Images of Multiple Cutaneous Metastases in a Patient With Prostate Carcinoma
Authors: Sivrikoz Ilknur Ak , Deveci Hakan , Ak Ali Murat , Acer Ersoy 
Published: October 2023

AbstractAlthough distant cutaneous metastasis is an uncommon presentation of prostate cancer, it remains an important diagnostic consideration as an advanced disease and a poor prognosis. Herein we present a rare case of prostate cancer patient whose multiple cutaneous metastases were treated with177Lu-PSMA-617 radioligand treatment. To our knowledge, it is the first report in which a complete response was seen with68Ga-PSMA PET/CT scan after177Lu-PSMA-617 radioligand treatment.
Comparison of 68Ga-PSMA-HBED-CC and 18F-FDG PET/CT in the Evaluation of Adenoid Cystic Carcinoma—A Prospective Study
Authors: Shamim Shamim Ahmed , Kumar Naresh , Arora Geetanjali , Kumar Deepak , Pathak Anshika , Thakkar Alok , Sikka Kapil , Singh Chirom Amit , Kakkar Aanchal , Bhalla Ashu Seith 
Published: October 2023

Purpose of Study

18F-FDG PET/CT plays a major role in diagnosis and staging of head and neck cancer; however, FDG has lower uptake in adenoid cystic carcinoma (AdCC). Prostate-specific membrane antigen (PSMA) expression is found to be associated with endothelial cells or tumor neovasculature in malignant AdCC and salivary duct carcinoma. Thus, present study is aimed to compare the role of 68Ga-PSMA and 18F-FDG PET/CT in patients with primary and/or metastatic AdCC.

Materials and Methods
Histopathologically proven AdCC patients were intravenously injected with 370 MBq (10 mCi) of 18F-FDG and 111–185 MBq (3–5 mCi) of 68Ga-PSMA. Images were acquired at 60 and 45 minutes postinjection for 18F-FDG and 68Ga-PSMA, respectively, on dedicated PET/CT scanners. Visual and semiquantitative analyses of PSMA expression in regional and metastatic sites were performed by 2 experienced nuclear medicine physicians.

Results
Seventeen patients (7 men, 10 women) having mean age of 44 ± 14.19 years were prospectively included in the study. Of 17 patients, FDG PET/CT was performed in only 14 (82%) patients. PSMA and FDG uptakes were seen at the primary site in 16 (94%) and 13 (93%) patients, respectively, whereas 1 patient was postradical tumor excision. Lung lesions (n = 7) and lymph nodes (n = 5) were detected on both FDG and PSMA PET scans. However, cerebellar and meningeal metastasis (n = 1, 6%) and bony lesions (n = 2, 12%) were detected only on PSMA PET/CT but not visualized on FDG PET/CT scan.

Conclusions
PSMA may have theranostic importance in unresectable or metastatic AdCC, besides having a role in staging/restaging.
Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species
Authors: Fischer Daniel , Tapio Miika , Bitz Oliver , Iso-Touru Terhi , Kause Antti , Tapio Ilma 
Published: October 2023

AbstractBackgroundDiversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The application of the optimization was demonstrated on non-model European whitefish data.ResultsDdRAD data generation was designed for a reliable estimation of relatedness and is scalable to up to 384 samples. The GBS sequencing yielded approximately one million reads for each of the around 100 assessed samples. Optimizing various strategies to create a de-novo reference genome for variant calling (mock reference) showed that using three samples outperformed other building strategies with single or very large number of samples. Adjustments to most pipeline tuning parameters had limited impact on high-quality data, except for the identity criterion for merging mock reference genome clusters. For each species, over 15k GBS variants based on the mock reference were obtained and showed comparable results with the ones called using an existing reference genome. Repeatability analysis showed high concordance over replicates, particularly in bovine while in European whitefish data repeatability did not exceed earlier observations.ConclusionsThe proposed cost-effective ddRAD strategy, coupled with an efficient bioinformatics workflow, enables broad adoption of ddRAD GBS across diverse farmed species. While beneficial, a reference genome is not obligatory. The integration of Snakemake streamlines the pipeline usage on computer clusters and supports customization. This user-friendly solution facilitates genotyping for both model and non-model species.
Criticality and partial synchronization analysis in Wilson-Cowan and Jansen-Rit neural mass models
Authors: Kazemi Sheida , Farokhniaee AmirAli , Jamali Yousef 
Published: October 2023

AbstractSynchronization is a phenomenon observed in neuronal networks involved in diverse brain activities. Neural mass models such as Wilson-Cowan (WC) and Jansen-Rit (JR) manifest synchronized states. Although they have been studied for decades, their ability to demonstrate second-order phase transition (SOPT) and criticality has not received enough attention, which serves as candidates for the development of healthy brain networks. In this study, two networks of coupled WC and JR nodes with small-world topologies were constructed and Kuramoto order parameter (KOP) was used to quantify the amount of synchronization. In addition, we investigated the presence of SOPT using the synchronization coefficient of variation. Both networks reached high synchrony by changing the coupling weight between their nodes. Moreover, they exhibited abrupt changes in the synchronization at certain values of the control parameter not necessarily related to a phase transition. While SOPT was observed only in JR model, neither WC nor JR model showed power-law behavior. Our study further investigated the global synchronization phenomenon that is known to exist in pathological brain states, such as seizure. JR model showed global synchronization, while WC model seemed to be more suitable in producing partially synchronized patterns.Corresponding author summaryYousef Jamali received his M.Sc. degree in physics from Sharif University, Tehran, Iran, in 2004, and his Ph.D. degree in physics from Sharif University, Tehran, Iran, in 2009. After finishing his Ph.D. thesis, in 2009, he got two years postdoctoral research associate position at the University of California at Berkeley, Department of Bioengineering. He is currently an Associate Professor in the Applied Mathematics Department (Biomathematics division), at Tarbiat Modares University, Tehran, Iran. His current research interests include the interdisciplinary area of the complex system especially on the modeling of brain. In fact, his interests are how the brain works at the critical state and how this complex system synchronized under different conditions.
eNODAL: an experimentally guided nutriomics data clustering method to unravel complex drug-diet interactions
Authors: Xu Xiangnan , Senior Alistair M. , Le Couteur David G. , Cogger Victoria C. , Raubenheimer David , James David E. , Parker Benjamin , Simpson Stephen J. , Muller Samuel , Yang Jean Y.H. 
Published: October 2023

AbstractUnraveling the complex interplay between nutrients and drugs via their effects on ‘omics’ features could revolutionize our fundamental understanding of nutritional physiology, personalized nutrition and ultimately human health-span. Experimental studies in nutrition are starting to use large-scale ‘omics’ experiments to pick apart the effects of such interacting factors. However, the high dimensionality of the omics features, coupled with complex fully-factorial experimental designs together pose a challenge to the analysis. Current strategies for analyzing such types of data are based on between-feature correlations. However, these techniques risk overlooking important signals that arise from the experimental design and produce clusters that are hard to interpret. We present a novel approach for analyzing high-dimensional outcomes in nutriomics experiments, termedexperiment-guidedNutriOmicsDatAcLustering (eNODAL). This three-step hybrid framework takes advantage of both ANOVA-type analyses and unsupervised learning methods to extract maximum information from experimental nutriomics studies. First, eNODAL categorizes the omics features into interpretable groups based on the significance of response to the different experimental variables using an ANOVA-like test. Such groups may include the main effects of a nutritional intervention, and drug exposure, or their interaction. Second, consensus clustering is performed within each interpretable group to further identify subclusters of features with similar response profiles to these experimental factors. Third, eNODAL annotates these subclusters based on their experimental responses and biological pathways enriched within the subcluster. We validate eNODAL using data from a mouse experiment to test for the interaction effects of macronutrient intake and drugs that target aging mechanisms in mice.
EMDB - the Electron Microscopy Data Bank
Authors: Turner Jack ,   The wwPDB Consortium
Published: October 2023

AbstractThe Electron Microscopy Data Bank (EMDB) is the archive of three-dimensional electron microscopy (3DEM) maps of biological specimens. As of 2021, EMDB has been managed by the Worldwide Protein Data Bank (wwPDB) as a wwPDB Core Archive. Today, the EMDB houses over 29,000 entries with maps containing cells, organelles, viruses, complexes and macromolecules. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.
Eliminating steam pops and improving lesion safety in atrial ablation with conductive hydrogels
Authors: Post Allison , Jaworski Lukas , Bernard Drew , Gao Shang , Nkansah Abbey , Zhang Haichong , Cosgriff-Hernandez Elizabeth , Razavi Mehdi 
Published: October 2023

ABSTRACTBackgroundAtrial fibrillation (AF) is a significant burden worldwide, and the existing treatments leave much to be desired. There are, however, opportunities to improve the safety and efficacy of the most popular treatment, radiofrequency (RF) cardiac ablation, using conductive hydrogels as an ablation mediator.MethodsLesions were created in ex vivo ventricular tissues using bare metal traditional RF catheters and three different hydrogels with varying conductivities to assess the effect of conductivity on lesion formation. Similar procedures were performed in atrial/esophageal tissue stacks to mimic physiological AF ablation and demonstrate the initial safety profile of conductive hydrogel-mediated ablation.ResultsThe hydrogel mediated lesions were overall shallower and narrower than bare metal, and also exhibited less char and improved lesion homogeneity. The hydrogel also eliminated steam pops. Finally, the hydrogel appeared to be more thermally protective of the esophagus in the atrial/esophageal tissue stack, greatly reducing the lesion formation on the esophagus while still achieving transmural lesions in the atrial tissue.ConclusionsHydrogel-mediated RF ablation holds promise as a novel method to improve ablation outcomes for AF patients. Future work will confirm this in vivo and establish the chemistry required to create a conductive hydrogel coating for RF ablation catheters.
ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction
Authors: Faria José P. , Liu Filipe , Edirisinghe Janaka N. , Gupta Nidhi , Seaver Samuel M.D. , Freiburger Andrew P. , Zhang Qizhi , Weisenhorn Pamela , Conrad Neal , Zarecki Raphy , Song Hyun-Seob , DeJongh Matthew , Best Aaron A. , Cottingham Robert W. , Arkin Adam P. , Henry Christopher S. 
Published: October 2023

AbstractSince the release of ModelSEED in 2010, the systems biology research community has used the ModelSEED genome-scale metabolic model reconstruction pipeline to build over 200,000 draft metabolic reconstructions that support hundreds of publications. Here we describe the first comprehensive update to this reconstruction tool, with new features such as (i) a dramatically improved representation of energy metabolism, which ensures that models produce accurate amounts of ATP per mol of nutrient consumed; (ii) a new template for Archaea model reconstruction; and (iii) a significantly improved curation of all metabolic pathways with mappings to RAST subsystems annotations. We applied the improved pipeline to build and analyze core and genome-scale models for Archaea and Bacteria genomes in KEGG. The new ModelSEED pipeline generates larger models that possess more reactions and genes and require fewer gap-filled reactions. In addition, we see conserved patterns in the ATP biosynthesis mechanism across phylogeny, and identify clades where our understanding of energy biosynthesis is still poor. The ModelSEED v2 pipeline is currently available only as new reconstruction and gap-filling Apps in the KBase platform.
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors
Authors: Psatha Nikoletta , Sova Pavel , Georgolopoulos Grigorios , Paschoudi Kiriaki , Iwata Mineo , Bloom Jordan , Ulyanova Tatyana , Wang Hao , Kirtsou Alexandra , Vasiloudis Ninos-Ioannis , Wilken Matthew S. , Stamatoyannopoulos John A. , Yannaki Evangelia , Papayanopoulou Thalia , Stamatoyannopoulos George , Vierstra Jeff 
Published: October 2023

AbstractRegulation of gene expression during cell development and differentiation is chiefly orchestrated by distal noncoding regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors rely on the cellular and context specificity of regulatory DNA elements to express therapeutic transgenes in the correct location and time. Here, we develop a straight-forward, one-shot approach to screen putative regulatory sequences identified in large-scale epigenomics profiling experiments for precise and programmable control of transgenes encoded within gene therapy viral vectors. We designed a library of 15,000 short sequences (∼200bp) derived from a set of developmentally active DHS elements during humanex vivoerythropoiesis and cloned them into a GFP reporter lentiviral vector. In an erythroid progenitor cell line, these elements display a gradient of transcriptional enhancer activity, with some demonstrating equivalent activity to the canonical β-globin μLCR despite a 9-fold smaller size. We show that these elements are both highly cell type restricted and developmental stage specific bothin vitroandin vivo. Finally, we replace the μLCR element with one of the novel short enhancers in a β-thalassemia lentiviral therapeutic vector and efficiently correct the thalassemic phenotype in patient-derived HSPCs. More broadly, our approach provides further insights into enhancer biology with wider implications into the development of highly cell type specific and efficacious viral vectors for human gene therapy.
The socio-spatial ecology of giant anteaters in the Brazilian Cerrado
Authors: Chhen Aimee , Bertassoni Alessandra , Desbiez Arnaud LJ , Noonan Michael J 
Published: October 2023

AbstractMovement is a key component of an animal’s life history. While there are numerous factors that influence movement, there is an inherent link between a species’ social ecology and its movement ecology. Despite this inherent relationship, the socio-spatial ecology of many species remains unknown, hampering ecological theory and conservation alike. Here, we use fine-scale GPS location data and continuous-time stochastic processes to study the socio-spatial ecology of 23 giant anteaters (Myrmecophaga tridactyla) in the Brazilian Cerrado. We found that individuals occupied stable home ranges with a mean area of 5.45 km2with males having significantly larger home ranges than females. The average amount of home-range overlap was low (0.20, n = 121 dyads), with no evidence that giant anteater home ranges were structured based on territorial, mate guarding, nor other social behaviour. We also identified a total of 2774 encounter events. Interestingly, both female-male and male-male dyads had significantly more encounters than female-female dyads, with two pronounced seasonal peaks in female-male encounters. Though encounters occurred frequently, associations between dyads were generally weak and there was little evidence of any correlated movement (mean amount of total correlation = 0.01). Collectively, these findings suggest giant anteaters are a solitary and largely asocial species that readily share space with conspecifics. Despite their present capacity to share space, the combined pressures of being condensed into smaller areas and decreased food availability due to increased pesticide use may see behavioural changes radiating throughout the population. Our study provides insight into heretofore unknown aspects of the socio-spatial ecology of this iconic, but understudied species, as well as crucial information for proactive area-based management. Ultimately, these findings contribute towards sustainable development while potentially maintaining the ecological integrity of giant anteaters and their habitats.