bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergency esophagectomy for esophageal perforation following balloon dilation due to stenosis post-endoscopic submucosal dissection for esophageal cancer: a case report
Authors: Pham Binh Van , Nguyen Duy Duc , Tran Manh Dai , Nguyen Thanh Duy , Thai An Duc , Nguyen Hoa Thi Thanh 
Published: September 2024

Introduction and importance:
Esophageal perforation from endoscopic dilation is rare (0.53–0.6% incidence) but serious, with mortality rates of 12.5–20%. Optimal treatment is debated and depends on the medical facility’s capabilities, the patient’s symptoms, the extent of perforation, and the severity of associated lesions. Treatment options include medical management (fasting, antibiotics), esophageal stenting, surgical closure, or emergency esophagectomy. Early diagnosis and treatment are crucial to reduce mortality and hospital stay.

Case presentation:
A 49-year-old male with lower third esophageal cancer (stage cT1aN0M0) underwent endoscopic submucosal dissection (ESD) and developed esophageal stenosis. Dilation attempts led to esophageal perforation, necessitating emergency esophagectomy with gastric conduit reconstruction. The patient improved and was discharged on day 10 post-operation without complications.

Clinical discussion:
Managing esophageal perforation post-endoscopic dilation is complex. This case highlights the importance of rapid recognition and intervention. Esophageal dilation, while effective for stenosis, carries a perforation risk. Treatment decisions must be tailored to individual patients, considering perforation severity, patient’s health, and facility resources. Here, severe perforation and clinical condition warranted emergency esophagectomy. The successful outcome underscores the efficacy of this surgical intervention when performed timely at specialized centers.

Conclusion:
Emergency esophagectomy with gastric conduit reconstruction for treating esophageal perforation due to stenosis post-endoscopic submucosal dissection for esophageal cancer is considered a safe procedure and can be performed at an experienced esophageal surgery center.
Total Cranial Vault Remodelling Versus Minimally Invasive Suturectomy With Postoperative Helmet Therapy in Sagittal Craniosynostosis
Authors: Witters Leonie , Vercruysse Herman , De Praeter Mania 
Published: September 2024

Different surgical techniques have been explored over time to treat children with scaphocephaly. The objective of this study is to compare morbidity and cosmetic outcomes in total cranial vault remodelling (TCVR) and minimally invasive suturectomy with postoperative helmet therapy (MISPH) in patients with scaphocephaly. The authors performed a retrospective comparative cohort study, including 43 patients with isolated sagittal craniosynostosis who underwent TCVR (n=17) or MISPH (n=26) at the Antwerp University Hospital between April 2008 and December 2022. MISPH was associated with significantly shorter procedure duration (TCVR 199 ± 48 min, MISPH 69 ± 12 min, P<0.001), decreased blood loss (TCVR 610 ± 298 mL, MISPH 85 ± 73 mL, P<0.001) and lower transfusion rate (TCVR 100%, MISPH 54%, P<0.001). Mean length of stay at the intensive care unit and the hospital were significantly shorter after MISPH (TCVR 6 ± 1 d, MISPH 3 ± 0.5 d). The change in CI after TCVR was significantly larger than after MISPH during the first postoperative year. However, the CI in the MISPH group was significantly higher during the first year compared with the TCVR group. Mean CI of the MISPH group reached normal limits during the first year, while in the TCVR group, mean CI reached normal values 5 years after surgery. The authors could not find a statistically significant difference in cosmetic outcome between the 2 groups. The authors conclude that MISPH is associated with decreased morbidity and comparable cosmetic results when compared with TCVR in the treatment of scaphocephaly.
Extracorporeal Photopheresis Enhances the Frequency and Function of Highly Suppressive FoxP3+ Treg Subsets in Heart Transplanted Individuals
Authors: Mottola Maria , Bruzzaniti Sara , Piemonte Erica , Lepore Maria Teresa , Petraio Andrea , Romano Renata , Castiglione Antonella , Izzo Lavinia , Perna Francesco , De Falco Chiara , Brighel Federico , Formisano Luigi , Gravina Maria Teresa , Marino Marina , De Feo Marisa , Matarese Giuseppe , Galgani Mario 
Published: September 2024

Background.
Extracorporeal photopheresis (ECP) has emerged as a prophylactic and therapeutic immunomodulatory option for managing acute rejection in heart transplants (HTx). The underlying mechanisms through which ECP exerts its immunomodulatory effects remain under investigation. Regulatory T cells (Treg) are a heterogeneous subset of immune lymphocytes that ensure the maintenance of tissue homeostasis, avoiding graft rejection. The transcription factor forkhead box protein 3 (FoxP3) is an essential molecular marker of Treg, acting as a “master regulator” of their genesis, stability, and functions. No study has investigated whether ECP impacts FoxP3 expression and its highly suppressive variants containing the exon 2 (FoxP3-E2), particularly in HTx.

Methods.
In the current study, we recruited 14 HTx participants who had undergone ECP therapy. We explored the effect of in vivo ECP on CD4+FoxP3+ Treg frequency and in vitro suppressive function in 8 HTx participants before (T0) and after 3 (T1), 6 (T2), and 12 (T3) mo of treatment. As a control group, we included 4 HTx individuals who had not undergone ECP therapy.

Results.
We found that ECP increases the frequency of CD4+FoxP3+ Treg subset with highly suppressive phenotype, including CD4+FoxP3-E2+ Treg. At functional levels, we observed that ECP treatment in HTx individuals effectively improves Treg suppressive ability in controlling the proliferation of autologous conventional CD4+ T lymphocytes.

Conclusions.
Our findings collectively suggest that ECP exerts its immunomodulatory effects in HTx individuals by positively impacting the frequency and regulatory function of the FoxP3+ Treg compartment.
Single unit electrophysiology recordings and computational modeling can predict octopus arm movement
Authors: Gedela Nitish Satya Sai , Salim Sachin , Radawiec Ryan D. , Richie Julianna , Chestek Cynthia , Draelos Anne , Pelled Galit 
Published: September 2024

AbstractThe octopus simplified nervous system holds the potential to reveal principles of motor circuits and improve brain-machine interface devices through computational modeling with machine learning and statistical analysis. Here, an array of carbon electrodes providing single-unit electrophysiology recordings were implanted into the octopus anterior nerve cord. The number of spikes and arm movements in response to stimulation at different locations along the arm were recorded. We observed that the number of spikes occurring within the first 100ms after stimulation were predictive of the resultant movement response. Computational models showed that temporal electrophysiological features could be used to predict whether an arm movement occurred with 88.64% confidence, and if it was a lateral arm movement or a grasping motion with 75.45% confidence. Both supervised and unsupervised methods were applied to gain streaming measurements of octopus arm movements and how their motor circuitry produces rich movement types in real time. Deep learning models and unsupervised dimension reduction identified a consistent set of features that could be used to distinguish different types of arm movements. These models generated predictions for how to evoke a particular, complex movement in an orchestrated sequence for an individual motor circuit.
Genetic variation in the activity of a TREM2-p53 signaling axis determines oxygen-induced lung injury
Authors: Abe Yohei , Spann Nathaneal J. , Tang Wenxi , Zeng Fenghua , Richard John Lalith Charles , Seymour Cadence , Jansky Sean , Mooney Miguel , Huff Robert , Chanthavixay Kelly , Dhar Debanjan , Ganguly Souradipta , Guo Jason L. , Lopez David M. , Longaker Michael T. , Benner Christopher , Glass Christopher K. , Sajti Eniko 
Published: September 2024

AbstractBronchopulmonary dysplasia (BPD), a chronic lung disease, is the most common major complication of preterm birth. Supplemental oxygen administration, while lifesaving in the neonatal period, remains a key determinant of BPD pathophysiology. Exposure of the immature lung to increased levels of oxygen elicits an inflammatory response resulting in abnormal lung development. However, not every premature infant is equally sensitive to develop BPD. Using genetically diverse mouse strains, we show that the innate immune response activated in the lungs of mice sensitive to hyperoxia that develop BPD-like lung injury differs from mice resilient to disease. Specifically, we identified a selective upregulation of triggering receptor expressed on myeloid cells 2 (TREM2) on lung macrophages and monocytes in the hyperoxia-sensitive C57BL/6J mouse strain. We show that loss of function of TREM2 signaling in myeloid cells resulted in a dramatically improved phenotype after neonatal hyperoxia exposure characterized by a dampened immune response, preserved alveolar structure, and preserved cell proliferative potential supporting normal lung development. At the molecular level, inhibition of TREM2 signaling dampened the magnitude of p53 activation and resulted in cell cycle arrest instead of apoptosis. These findings show that TREM2 is a critical regulator of the pathogenic innate immune response to hyperoxia and highlight its importance as a potential therapeutic target for mitigating injury in the hyperoxia-exposed developing lung.
metagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads
Authors: Mainguy Jean , Vienne Maïna , Fourquet Joanna , Darbot Vincent , Noirot Céline , Castinel Adrien , Combes Sylvie , Gaspin Christine , Milan Denis , Donnadieu Cécile , Iampietro Carole , Bouchez Olivier , Pascal Géraldine , Hoede Claire 
Published: September 2024

AbstractBackgroundTo study communities of micro-organisms taxonomically and functionally, metagenomic analyses are now often used. If there is no reference gene catalogue, ade novoapproach is required. Because genomes are easier to interpret than contigs, the recovery of metagenome-assembled genomes (MAGs) by binning of contigs from metagenomic data has recently become a common task for microbial studies. However, during this process, there is a significant loss of information between the assembly and the binning of contigs. This is why it is important to produce taxonomic and functional matrices for all contigs and not just those included in correct bins. In addition, Pacbio HiFi reads (long and of good quality) are now a possible, albeit more expensive, alternative to short Illumina reads. We therefore developed a workflow that is easy to install with dependencies fixed using singularity images and easy to use on a computing cluster, that is capable of analyzing either short or long reads, and that should allow analysis at the contig and/or bin level, depending on the user’s choice.Following is a presentation of metagWGS, a fully automated workflow for metagenomic data analysis. It uses a new tool for refining bins (called Binette) that we will demonstrate is more efficient than competing tools.MethodsmetagWGS is a Nextflow workflow distributed with two singularity images and complete documentation to facilitate its installation and use.Because the main original features of metagWGS concern binning (short and long reads) and the analysis of HiFi reads, we compared metagWGS with the MAG construction workflow proposed by PacBio to a public dataset used by Pacbio to promote its workflow.ResultsmetagWGS differs from existing workflows by (i) offering flexible approaches for the assembly; (ii) supporting short reads (Illumina) or PacBio HiFi reads; (iii) combining multiple binning algorithms with a new bin refinement tool, referred to as “Binette”, to achieve high-quality genome bins; and (iv) providing taxonomic and functional annotation for all genes, all contigs built and bins.metagWGS produces more medium (708) and high-quality (255) bins on 11 public metagenomic samples from human gut data than the Pacbio HiFi dedicated workflow, referred to as the HiFi-MAGS-pipeline (659 medium quality bins and 231 high quality bins), primarily due to the better performance of Binette.
AvianLexiconAtlas: A database of descriptive categories of English-language bird names around the world
Authors: Morrison Erin S. , Pandolfi Guinevere P. , Aguillon Stepfanie M. , Ali Jarome R. , Archard Olivia , Baldassarre Daniel T. , Baquero Illeana , Bennett Kevin F.P. , Bonney Kevin M. , Bryant Riley , Catanach Rosanne M. , Catanach Therese A. , Chavoshan Ida , Davis Sarah N. , Goodman Brooke D. , Gulson-Castillo Eric R. , Hack Matthew , Hudon Jocelyn , Leighton Gavin M. , Long Kira M. , Ma Ziqi , McCoy Dakota E. , McLaughlin J.F. , Moreno Gaia Rueda , Mota Talia M. , Noguchi Lara , Nwigwe Ugo , Pegan Teresa , Provost Kaiya L. , Rasband Shauna A. , Salter Jessie Frances , Silvernail Lauren C. , Simard Jared A. , Skeen Heather R. , Soto-Patiño Juliana , Suh Young Ha , Wang Qingyue , Warshauer Matthew E. , Yan Sissy , Zalinski Betsy , Zhao Ziqi , Shultz Allison J. 
Published: September 2024

AbstractCommon names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a particular issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the common names of bird species and their frequency of use, we used a crowdsourcing approach and recruited 85 professional ornithologists and non-professional participants to classify unique descriptors in the English-language common names of all recognized bird species from around the world. Each species’ common name was assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contained specialized or historic terminology unknown to many of the data collectors, and this was documented in a glossary and gazetteer alongside the dataset. As the first comprehensive assessment of the state of terminology in English-language common names of birds, the AvianLexiconAtlas database sheds light on historical approaches to nomenclature and provides insight into how the general public currently engages with species through their names.
Manufacturing-Aware Generative Model Architectures Enable Biological Sequence Design and Synthesis at Petascale
Authors: Weinstein Eli N. , Gollub Mattia G. , Slabodkin Andrei , Gardner Cameron L. , Dobbs Kerry , Cui Xiao-Bing , Amin Alan N. , Church George M. , Wood Elizabeth B. 
Published: September 2024

AbstractWe introduce a method to reduce the cost of synthesizing proteins and other biological sequences designed by a generative model by as much as a trillion-fold. In particular, we make our generative models manufacturing-aware, such that model-designed sequences can be efficiently synthesized in the real world with extreme parallelism. We demonstrate by training and synthesizing samples from generative models of antibodies, T cell antigens and DNA polymerases. For example, we train a manufacturing-aware generative model on 300 million observed human antibodies and synthesize∼1017generated designs from the model, achieving a sample quality comparable to a state-of-the-art protein language model, at a cost of 103dollars. Using previous methods, synthesis of a library of the same accuracy and size would cost roughly a quadrillion (1015) dollars.
Population structure of the endangered Siberian flying squirrel (Pteromys volans) revealed by genomic and mitochondrial data
Authors: Ito dos Santos Fernanda , Lilley Thomas , Laine Veronika N. , Prost Stefan , Kurhinen Juri , Susi Hanna , Gashev Sergey , Saveljev Alexander , Bondarchuk Svetlana , Babina Svetlana , Shishikin Aleksander , Tirski Dmitry , Vasina Aleksandra , Karpin Vladimir , Kekkonen Jaana A 
Published: September 2024

ABSTRACTThe Siberian flying squirrel (Pteromys volans) is an arboreal rodent with a distribution range that covers large parts of the Eurasian taiga forest zone. However, extensive forestry has resulted in widespread local population declines and extinctions in recent decades. Even though it is widely distributed in Eurasia, almost nothing is known about its phylogeography. Here we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) to investigate population structure, connectivity and genetic diversity in different sites throughout its distribution. Overall, the species shows low nucleotide diversity and heterozygosity. Locations in Finland, on the western edge of the distribution, had the lowest diversities in genomic SNPs and mtDNA, while individuals in the Far East (Sikhote-Alin, Russia) show the highest diversity. These findings fit with a rapid range expansion from the Far East to the west. We found a strong genetic differentiation between Sikhote-Alin and all other populations investigated, which might warrant a revision of their taxonomic classification. The inferred low genetic diversities at the western edge of their distribution are especially worrisome as they are currently experiencing strong population declines and major habitat changes, which can be especially detrimental when standing variation is low. Thus, stressing the need for the revision of the species conservation status.
A Comprehensive UHPLC-MS/MS and Extraction Method for Spinach (Spinacia oleracea) Flavonoids
Authors: Dzakovich Michael P. , Le Elaine A. , Tak Alvin L. , Chacko Shaji K. 
Published: September 2024

ABSTRACTSpinach produces an array of unique flavonoids not commonly found in other fruits and vegetables. These molecules likely serve as defense agents against biotic and abiotic stress and may have health beneficial properties for humans. Current methods to analyze spinach flavonoids are incomplete and only capture a portion of this uncharacterized pathway. A comprehensive analysis method is needed to determine how genetics, environmental conditions, and other factors influence spinach flavonoid biosynthesis. We developed and validated a high-throughput extraction and ultra high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method to separate and quantify 39 spinach flavonoid species in 11.5 minutes. Spinach flavonoids without authentic standards were putatively identified using MS/MS fragmentation experiments, precursor scans, and matches to high-resolution MS literature reports. Our extraction method enables up to 48 samples to be extracted in 60 minutes with recovery estimates between 100.5 – 107.8%. To assess the suitability of our method and generate benchmark estimates for 39 spinach flavonoids, we grew a panel of 30 genetically diverse spinach accessions and compared quantification data generated with a traditional or our high-throughput approach. Data generated by either approach were comparable, estimating total flavonoid averages of 75.1 – 170.1 or 93.1 – 187.26 mg/100 g fresh weight for the high-throughput and traditional method, respectively. Many estimates generated by our analysis method represent the first quantitative literature reports of these compounds. These experiments indicate that our extraction and analysis method is efficient, robust, and an important tool needed to study the biosynthesis and biological role of spinach flavonoids.
LM-Merger: A workflow for merging logical models with an application to gene regulation
Authors: Li Luna Xingyu , Aguilar Boris , Gennari John H , Qin Guangrong 
Published: September 2024

SummaryMotivationGene regulatory network (GRN) models provide mechanistic understanding of genetic interactions that regulate gene expression and, consequently, influence cellular behavior. Dysregulated gene expression plays a critical role in disease progression and treatment response, making GRN models a promising tool for precision medicine. While researchers have built many models to describe specific subsets of gene interactions, more comprehensive models that cover a broader range of genes are challenging to build. This necessitates the development of automated approaches for merging existing models.ResultsWe present LM-Merger, a workflow for semi-automatically merging logical GRN models. The workflow consists of five main steps: (a) model identification, (b) model standardization and annotation, (c) model verification, (d) model merging, and (d) model evaluation. We demonstrate the feasibility and benefit of this workflow with two pairs of published models pertaining to acute myeloid leukemia (AML). The integrated models were able to retain the predictive accuracy of the original models, while expanding coverage of the biological system. Notably, when applied to a new dataset, the integrated models outperformed the individual models in predicting patient response. This study highlights the potential of logical model merging to advance systems biology research and our understanding of complex diseases.Availability and implementationThe workflow and accompanying tools, including modules for model standardization, automated logical model merging, and evaluation, are available athttps://github.com/IlyaLab/LogicModelMerger/.