bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza
Authors: Perlas Albert , Reska Tim , Croville Guillaume , Tarrés-Freixas Ferran , Guérin Jean-Luc , Majó Natàlia , Urban Lara 
Published: February 2025

Abstract
Avian influenza virus (AIV) currently causes a panzootic with extensive mortality in wild birds, poultry, and wild mammals, thus posing a major threat to global health and underscoring the need for efficient monitoring of its distribution and evolution. We here utilized a well-defined AIV strain to systematically investigate AIV genetic characterization through rapid, portable nanopore sequencing by comparing the latest DNA and RNA nanopore sequencing approaches and various computational pipelines for viral consensus sequence generation and phylogenetic analysis. We show that the latest direct RNA nanopore sequencing updates improve consensus sequence generation, but that the application of the latest DNA nanopore chemistry after reverse transcription and amplification outperforms such native viral RNA sequencing by achieving higher sequencing accuracy and throughput. We additionally leveraged the direct RNA nanopore sequencing data for the detection of RNA modifications, such as N6-methyladenosine and pseudouridine, which play a role in viral immune evasion. Finally, we applied these sequencing approaches together with portable AIV diagnosis and quantification tools to environmental samples from a poultry farm, demonstrating the feasibility of nanopore sequencing for on-site non-invasive AIV monitoring in real-world outbreak scenarios.
“Blessed Be the Fruit”—The Contemporary Rise of Pronatalism
Authors: Forati R , Bartz D 
Published: February 2025

(N Engl J Med. 2024;391(17):1569–1571. doi:10.1056/NEJMp2410208)
Margaret Atwood’s novel The Handmaid’s Tale, published in 1985, was influenced by the political changes during the Reagan administration. These changes involved shifts in voter demographics and alliances with religious traditionalists, leading to increased polarization on issues such as abortion and LGBTQIA+ rights. While not as severe as the dystopia in Atwood’s fiction, current policies regarding abortion, contraception, and in vitro fertilization have deviated from the beliefs of the majority of Americans. Present-day politicians still support laws that limit the choices of women who do not have children on purpose or due to circumstances, often using rhetoric associated with White supremacy and eugenics.
Likelihood of Primary Cesarean Section Following Induction of Labor in Singleton Cephalic Pregnancies at Term, Compared With Expectant Management: An Australian Population-Based, Historical Cohort Study
Authors: Hu Y , Homer CSE , Ellwood D , Slavin V , Vogel JP , Enticott J , Callander EJ 
Published: February 2025

(Acta Obstet Gynecol Scand. 2024;103:946–954. doi:10.1111/aogs.14785)
In high-income countries, there has been a clear trend toward earlier deliveries and a rise in the use of labor induction (IOL) and cesarean deliveries (CD) for women with term pregnancies. From 1990 to 2018, the average CD rate in high-income settings increased from 12% to 27% and is expected to reach 37% by 2030. Likewise, the rate of IOL rose from 20% in 1990 to 30% in 2019. Subsequently, the average length of pregnancy at delivery has dropped in the United States and Australia from 40 to 39 weeks. Australia has seen greater IOL and CD rates than other affluent nations. From 2010 to 2020, there was a rise in IOL rates from 25% to 37%, and CD rates increased from 31% to 36% for pregnancies at full term. There is concern that Australia’s CD rate may hit 45% by 2030. Cesarean delivery imparts increased risk for maternal and neonatal morbidity as well as substantial financial challenges for individuals and health care systems. This study investigated the probability of needing a CD after IOL in women with single, head-first pregnancies at 37 to 40 weeks, compared to women with spontaneous labor.
Routine Use of Cell Salvage During Cesarean Section: A Practice Evaluation
Authors: Leeson C , Jones M , Odendaal J , Choksey F , Quenby S 
Published: February 2025

(Acta Obstet Gynecol Scand. 2024;103:498–504. doi:10.1111/aogs.14753)
A leading global cause of maternal death is obstetric peripartum hemorrhage (PPH). When PPH occurs during cesarean delivery (CD), there are increased risks of requiring a hysterectomy, developing disseminated intravascular coagulation, or needing intensive care unit admission. Some of these can be taken into account before a CD, but unexpected bleeding can always occur. A common treatment for PPH is blood transfusion, but donor blood is scarce and there are risks associated with it such as ABO mismatch and blood borne infection. An alternative to this treatment is intraoperative cell salvage (IOCS) with autologous blood transfusion, which involves collecting, washing, and reinfusing blood during the procedure. Potential risks of this procedure include fetal cell alloimmunization and amniotic fluid embolism. This study was designed to assess routine use of IOCS in a tertiary obstetric center over 4 years, analyzing rates of isoimmunization in subsequent pregnancies and maternal and fetal complications over 8 years of follow-up.
Facilitating Positive Birth Experience When Preferences Are Not Met: A Qualitative Analysis
Authors: Lawal T , Dodge LE , Toffey D , Zera C , Wu M , Larson E 
Published: February 2025

(Birth. 2024;51:275–283. doi:10.1111/birt.12783)
Effective health care systems prioritize patient-focused care that incorporates personal preferences and needs, ultimately boosting patient contentment and wellness. Loss of fulfillment of preferences during childbirth can detrimentally effect childbirth experiences and patient well-being. Meeting the desires of patients is essential in providing top-notch birthing care; studies show that satisfying a birth plan is associated with increased contentment. When discrepancies arise between preferences and actual experiences, even when medically indicated, they can result in a negative birth experience. A frequent source of disagreement is labor induction. In 2020, induction was used for 31% of births, even though many patients would rather experience spontaneous labor. Research indicates that many women were coerced into induction by health care providers and did not fully comprehend the rationale behind it, impacting their capacity to provide informed consent.
Allogenic Umbilical Cord-Derived Mesenchymal Stromal Cells Improve Motor Function in Prenatal Surgical Repair of Myelomeningocele: An Ovine Model Study
Authors: Athiel Y , Jouannic J-M , Mauffré  , Dehan C , Adam C , Blot S , Lallemant P , De Saint Denis T , Larghero J , Nasone J , Guilbaud L 
Published: February 2025

(BJOG. 2024;131(6):759–767. https://doi.org/10.1111/1471-0528.17624)
Myelomeningocele (MMC), also referred to as open spina bifida, is the most severe type of spina bifida and a significant abnormality in the neural tube. It consists of a sac filled with fluid found on the back of infants and is linked to dysfunction with the lower limbs, digestion, and urinary systems, as well as possible cognitive impacts. Research conducted by MOMS revealed the advantages of prenatal repair for MMC compared with surgery after birth, resulting in the widespread acceptance of prenatal surgical methods. Even with these improvements, 71% of patients are still unable to walk without assistance by the time they turn 8, and 75% must use a urinary catheter every day by the age of 10. Therefore, further tactics are needed to improve results. Umbilical cord mesenchymal stem cells (UC-MSCs) may be beneficial in MMC due to their protective and repair mechanisms. Preliminary research showed only slight, insignificant enhancements in motor function from UC-MSCs in a sheep MMC model, leading to the need for more study.
The Association Between Epidural Labor Analgesia and Postpartum Depression: A Randomized Controlled Trial
Authors: Tan HS , Tan CW , Sultana R , Chen HY , Chua T , Rahman N , Gandhi M , Sia ATH , Sng BL 
Published: February 2025

(Anaesthesia. 2024;79(4):357–367. doi:10.1111/anae.16178. PMID: 37990597)
Postpartum depression (PPD) has many adverse effects, including the objective rates of increased maternal and infant morbidity and increased health care expenses, as well as the more subjective effects on breastfeeding, infant and maternal bonding, maternal responsiveness to infant needs, social emotional, behavioral, and cognitive development of the child. A significant challenge in PPD care lies in the fact that some symptoms require treatments that are not safe for pregnant women. Severe peripartum pain has also been associated with PPD, leading to a consideration that a method for clinical improvement may be preventing such pain through epidural analgesia. Recent meta-analyses provide conflicting data and results on whether epidural use reduces risk of PPD. Thus, the authors sought to elucidate this using a randomized controlled trial.
Examining the Relationship Between Autism Spectrum Disorder in Children Whose Mother Had Labour Epidural Analgesia for Their Birth: A Retrospective Cohort Study
Authors: Zamstein O , Sheiner E , Binyamin Y , Pariente G , Wainstock T 
Published: February 2025

(Eur J Anaesthesiol. 2024;41(4):282–287. doi:10.1097/EJA.0000000000001932. PMID: 38084085)
Many mothers choose to use labor epidural analgesia (LEA); however, new concerns have been raised as to whether this inadvertently contributes to the neurodevelopmental disorder, autism spectrum disorder (ASD). The developmental field incompletely understands the pathogenesis of ASD, however, it is generally believed to be a result of environmental influences that affect the epigenetic expression of genes of already susceptible individuals. Recent hypotheses about the influence of LEA on the epigenetics related to autism have been investigated, without consensus. This group sought to investigate and provide further evidence to the field of childhood autism.
Mechanism of Chronic Iatrogenic CSF Leak Following Dural Puncture-Ventral Dural Leak: Case Report
Authors: Caroll IR , Lansinger O , Do HM , Dodd R , Mahaney K , Li D 
Published: February 2025

(Reg Anesth Pain Med. 2024;49:293–297. doi:10.1136/rapm-2023-105197)
Unintended dural puncture (UDP) is a possible complication of epidural catheter placement, which can cause acute postdural puncture headache (PDPH). The resulting cerebrospinal fluid (CSF) leak can heal without treatment, but the third most common cause of lawsuits against anesthesiologists by obstetric patients was headache (HA), showing that the impact of these symptoms is not benign and can be long-term. This article is a case report focused on a patient with UDP that reported persistent severe symptoms despite treatment with epidural blood patch (EBP) triggering further investigation and the confirmation of a persistent ventral dural puncture.
Combination Use of 1440-nm and 1927-nm Nonablative Fractional Laser With Monopolar Radiofrequency for the Treatment of Facial Skin Laxity, Skin Texture, and Pigmentation
Authors: Peters John D. , Salame Nicole , Eber Ariel , Labadie Jessica G. , Kandula Prasanthi , Dover Jeffrey S. 
Published: February 2025

BACKGROUND
Facial aging, marked by skin laxity, wrinkling, and dyspigmentation, remains a common aesthetic concern. Few studies have investigated combination approaches to treat these concomitant components of aging.

OBJECTIVE
To investigate the effect of combining monopolar radiofrequency with fractional nonablative diode laser treatments to improve skin laxity, wrinkling, and dyspigmentation.

METHODS AND MATERIALS
A prospective, single-arm study enrolled 20 females with mild to moderate facial skin laxity and photoaging. Subjects underwent a sequence of one monopolar radiofrequency treatment (Thermage FLX, Solta, Bausch Medica, Bothell, WA) followed by 4 fractional 1440-/1927-nm nonablative diode laser treatments (Clear + Brilliant Touch, Solta, Bausch Medica). Assessments included clinical evaluations, blinded photographic assessments, and patient satisfaction scores.

RESULTS
At the 6-month follow-up, a significant improvement was observed in Skin Laxity Grading Scale and Glogau Classification of Photoaging scale scores (1.65 ± 0.49–1.30 ± 0.47, p = .039, and 1.85 ± 0.36–1.35 ± 0.49, p = .00082, respectively). Blinded reviewers correctly identified 67% of post-treatment photographs, and 77% of participants were considered responders. No serious adverse events occurred.

CONCLUSION
Monopolar radiofrequency combined with fractional diode led to significant efficacy, suggesting a safe and promising strategy for addressing facial skin laxity, wrinkles, and dyspigmentation.
Corneal Myofibromatous and Pterygium-Like Changes in a Family With a PDGFRB Variant
Authors: Raber Irving M. , Khalili Ashley , Khang Rin , Buch Preema M. , Eagle Ralph C. , Seo Go Hun , Lee Hane , Milman Tatyana 
Published: February 2025

Purpose:
To report the clinical, pathologic, and genetic findings in a family with early-onset pterygia, corneal vascularization, and corneal myofibromatous lesions.

Methods:
We performed clinical, pathologic, and genetic analysis of 12 members of a family originating in Puebla Mexico, who manifested with pterygia/pseudopterygia and corneal opacification transmitted in an autosomal-dominant inheritance pattern. Three unaffected family members also were evaluated.

Results:
Clinical findings included isolated pterygia, isolated corneal subepithelial and anterior stromal opacities associated with varying degree of corneal vascularization, and a combination of pterygia and corneal opacities. Nine patients (17 eyes) underwent surgical procedures, including penetrating keratoplasty (9/17), superficial keratectomy (7/17), and pterygium excision (7/17). Five patients (eight eyes) had more than one surgery for recurrence of pterygia (2/8), recurrent corneal opacities obscuring the visual axis (3/8), penetrating keratoplasty failure (1/8), and indication not known (2/8). Documented recurrences occurred early, within 1 to 2 years of surgery. Histopathology of 21 specimens available for evaluation (nine penetrating keratoplasty corneas, seven superficial keratectomies, and five conjunctival-corneal tissues from pterygium/pseudopterygium excision) from seven patients showed varying degrees of myofibroblastic proliferation. Exome sequencing identified a heterozygous c.1610C>A (p.Ala537Asp) variant in the platelet-derived growth factor receptor beta (PDGFRB) gene in all 11 affected family members tested and in one of three unaffected family members.

Conclusions:
The combined clinical presentation, histopathologic features, and genetic findings suggest an autosomal dominantly inherited predisposition to exuberant corneal myofibroblastic proliferation, driven by the platelet-derived growth factor receptor activation.
Interpretation of basal nuclei in brain dopamine transporter scans using a deep convolutional neural network
Authors: Chen Hsin-Yung , Tsai Ya-Ju , Peng Syu-Jyun 
Published: February 2025

Objective
Functional imaging using the dopamine transporter (DAT) as a biomarker has proven effective in assessing dopaminergic neuron degeneration in the striatum. In assessing the neuron degeneration, visual and semiquantitative methods are used to interpret DAT single-photon emission tomography (SPECT) scans based on striatal to background activity, striatal shape, and symmetry. Visual analysis, however, is subjective and reviewer dependent, whereas semiquantitative methods are operator dependent. Our goal in the current study was to derive results via deep learning to facilitate the clinical diagnosis of Parkinson’s disease (PD).

Methods
This retrospective study collected data from 416 patients with clinically uncertain Parkinsonian syndrome who underwent DAT SPECT via 99mTc-TRODAT-1 ([2-[[2-[[[3-(4-chlorophenyl)-8-methyl-8-azabicyclo[3,2,1]oct-2-yl]methyl](2-mercaptoethyl)amino]ethyl]amino]ethanethiolato (3-)-N2,N2’,S2,S2’]oxo-[1R-(exo-exo)]). Transfer learning was used to estimate the degree of dopaminergic neuron degeneration in the caudate and putamen for use in classifying images according to stage. Three pretrained models – Xception, InceptionV3, and ResNet101 – were retrained and tested after undergoing transfer learning for the classification of striatum dopaminergic neuron degeneration.

Results
Overall, the performance of Xception exceeded that of InceptionV3 and ResNet101. The accuracy, macro F1 score, and kappa value of the proposed caudate classification model were 81.93%, 0.70, and 0.64, respectively. The accuracy, macro F1 score, and kappa value of the proposed putamen classification model were 88.75%, 0.64, and 0.61, respectively.

Conclusion
The proposed deep convolutional neural network provided a good model by which to interpret DAT SPECT of basal nuclei. We believe that the model could be used as an auxiliary tool to facilitate image interpretation and enhance accuracy in the diagnosis of PD.
Individualizing the choice of surgical therapy for gastroesophageal reflux disease
Authors: Bonavina Luigi 
Published: February 2025

Purpose of review
Proton-pump inhibitor therapy does not provide complete relief of symptoms in up to 40% of patients with gastroesophageal reflux disease (GERD). Antireflux surgery (ARS) aims to reconstruct the natural antireflux barrier consisting of the diaphragmatic crura, the lower esophageal sphincter, and the gastroesophageal flap valve.

Recent findings
Although the 360° Nissen fundoplication combined with crural repair remains the gold-standard ARS treatment for GERD, the Toupet and Dor partial fundoplications and the magnetic sphincter augmentation (LINX) procedure have emerged as suitable alternative options with fewer side-effects. Randomized and observational clinical studies show that reflux control with partial fundoplications and LINX is acceptable and the risk of side-effects is minimal. Early results with the novel Refluxstop procedure show that restoration of distal esophageal length and the gastroesophageal flap valve, combined with anterior fundoplication and a silicon prosthesis to stabilize the esophagogastric junction below the diaphragm, can also provide excellent reflux control with minimal side-effects.

Summary
Laparoscopic ARS should be performed in centers offering a comprehensive diagnostic pathway and a spectrum of techniques tailored to the individual GERD patient's phenotype and expectations. Further research is needed to provide more personalized and durable ARS.
Optimal marker genes forc-separated cell types
Authors: Borozan Bartol , Borozan Luka , Ševerdija Domagoj , Matijević Domagoj , Canzar Stefan 
Published: February 2025

AbstractThe identification of cell types in single-cell RNA-seq studies relies on the distinct expression signature of marker genes. A small set of target genes is also needed to design probes for targeted spatial transcriptomics experiments and to target proteins in single-cell spatial proteomics or for cell sorting. While traditional approaches have relied on testing one gene at a time for differential expression between a given cell type and the rest, more recent methods have highlighted the benefits of a joint selection of markers that together distinguish all pairs of cell types simultaneously. These combinatorial methods differ mostly in the notion of discrimination between cell types, using Euclidean or Manhattan distance in the dimensions of the selected marker genes, or the difference in the fraction of cells expressing a given marker gene. The resulting combinatorial optimization problems then seeks to identify a small set of genes that yield discrimination above a given threshold between all pairs of cell types. However, existing methods either consider all pairs of individual cells which becomes intractable even for medium-sized datasets, or ignore intra-cell type expression variation entirely by collapsing all cells of a given type to a single representative. Here we address these limitations and propose to find a small set of genes such that cell types arec-separated in the selected dimensions, a notion introduced previously in learning a mixture of Gaussians. To this end, we formulate a linear program that naturally takes into account expression variation within cell types without including each pair of individual cells in the model, leading to a highly stable set of marker genes that allow to accurately discriminate between cell types and that can be computed to optimality efficiently.
TabVI: Leveraging Lightweight Transformer Architectures to Learn Biologically Meaningful Cellular Representations
Authors: Chandrashekar Aditi , Gala Rohan , Tjärnberg Andreas , Khullar Saniya , Huynh Grace , Gabitto Mariano 
Published: February 2025

AbstractTransformer-based foundation models are changing the landscape of natural language processing (NLP), computer vision, and audio, achieving human-level performance across a variety of tasks. Extending these models to single-cell genomics holds significant potential for revealing the cellular and molecular perturbations associated with disease. However, unlike the sequential structure of language, the functional organization of genes is hierarchical and modular. This fundamental difference necessitates the development of meaningful feature selection strategies to adapt NLP transformer architectures effectively. In contrast to many large-scale foundation models, probabilistic models have shown success in learning complex cellular representations from single-cell datasets. In this work, we present TabVI, a probabilistic deep generative model that leverages tabular transformer architectures to improve latent embedding learning. We validate TabVI’s performance in cell type annotation and integration benchmarks. We demonstrate that TabVI improves performance across down-stream tasks and is robust to scaling dataset sizes, producing interpretable, sample-specific feature attention masks. TabVI is a lightweight, scientifically-meaningful, transformer architecture for single-cell analysis that excels where large scale foundation models are less effective.
Revisiting synthetic lethality of Gcn5-related N-acetyltransferase (GNAT) family mutations inHaloferax volcanii
Authors: Weber Katherine R. , Novillo Brianna , Maupin-Furlow Julie A. 
Published: February 2025

ABSTRACTLysine acetylation is a post-translational modification that occurs in all domains of life, highlighting its evolutionary significance. Previous genome comparison identified three Gcn5-related N-acetyltransferase (GNAT) family members as lysine acetyltransferase homologs (Pat1, Pat2, and Elp3) and two deacetylase homologs (Sir2 and HdaI) in the halophilic archaeonHaloferax volcanii, withelp3andpat2proposed as a synthetic lethal gene pair. Here we advance these findings by performing single and double mutagenesis ofelp3with thepat1andpat2lysine acetyltransferase gene homologs. Genome sequencing and PCR screens of these strains reveal successful generation ofΔelp3, Δpat1Δelp3, andΔpat2Δelp3mutant strains. Although these mutant strains exhibited a reduced growth rate compared to the parent, they remained viable. Overall, this study provides genetic evidence thatelp3andpat2, while impacting cell growth, are not a synthetic lethal gene pair as previously reported.IMPORTANCEHere we reveal by whole genome sequencing that the GNAT family gene homologselp3andpat2can be deleted in the sameH. volcaniistrain. Beyond the targeted deletions, minimal differences between the parent andΔelp3 Δpat2mutant were observed suggesting that suppressor mutations are not responsible for our ability to generate this double mutant strain. Elp3 and Pat2, thus, may not share as close a functional relationship as implied by earlier study. Our finding is significant as Elp3 is thought to function in acetylation in tRNA modification, while Pat2 likely functions in the lysine acetylation of proteins.