bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cervical Lymph Node Metastasis as the Initial Presentation of Femoral Epithelioid Hemangioendothelioma Revealed by 18F-FDG PET/CT
Authors: Hu Xianwen 
Published: December 2023

Abstract
Femoral epithelioid hemangioendothelioma with cervical lymph node metastasis is rare. We report the FDG PET/CT findings of cervical lymph node metastasis from left femoral epithelioid hemangioendothelioma in a 50-year-old woman with painless enlargement of the left cervical lymph nodes as the initial presentation. Ultrasound and MRI revealed multiple enlarged lymph nodes in the left cervical sheath area. PET/CT showed strong radioactive uptake in the left cervical lymph nodes, and there was additional lesion with increased FDG uptake in the left femur, which was later confirmed as cervical lymph nodes metastasis from left femoral epithelioid hemangioendothelioma by pathological examination.
C-X-C Motif Chemokine Receptor 4–Targeted Radioligand Therapy in Hematological Malignancies—Myeloablative Effects, Antilymphoma Activity, and Safety Profile
Authors: Dreher Niklas , Dörrler Anna-Lena , Kraus Sabrina , Higuchi Takahiro , Serfling Sebastian E. , Samnick Samuel , Einsele Hermann , Grigoleit Götz Ulrich , Buck Andreas K. , Werner Rudolf A. 
Published: December 2023

Background
After C-X-C motif chemokine receptor 4 (CXCR4)–directed radioligand therapy (RLT), lymphoma patients are scheduled for conditioning therapy (CON) followed by hematopoietic stem cell transplantation (HSCT). We aimed to determine whether CXCR4-RLT can achieve bone marrow ablation and direct antilymphoma activity independent from CON/HSCT and also evaluated the safety profile of this theranostic approach in an acute setting.

Patients and Methods
After CXCR4-directed 68Ga-pentixafor PET/CT, 21 heavily pretreated patients with hematological malignancies underwent CXCR4-directed RLT using 90Y-pentixather. The extent of myeloablative efficacy was determined by investigating hematologic laboratory parameters before RLT (day −1), at the day of RLT (day 0), 2 days after RLT (day 2), and before CON (median day 10). Serving as surrogate marker of antilymphoma activity, lactate dehydrogenase (LDH) levels were also assessed until CON. We also screened for laboratory-defined tumor lysis syndrome after the Cairo-Bishop definition and recorded acute laboratory adverse events using the Common Terminology Criteria for Adverse Events version 5.0.

Results
After RLT, we observed a significant decline of leukocyte levels by 79.4% ± 18.7% till CON (granulocytes, drop by 70.3% ± 21%; platelets, reduction by 43.1% ± 36%; P ≤ 0.0005 vs day 0, respectively). After RLT, LDH levels already reached a peak at day 2, which was followed by a rapid decline thereafter (peak vs day of CON, P = 0.0006), indicating that 90Y-pentixather exhibits direct antilymphoma activity. At day of CON, LDH levels were also significantly lower when compared with day −1 (P = 0.04), suggestive for durable response mediated by RLT. No patient fulfilled the criteria of tumor lysis syndrome, whereas 25 laboratory adverse events attributable to CXCR4-directed treatment were identified (≥grade 3 in 2/25 [8%]). During further treatment course, all patients (100%) received HSCT.

Conclusions
CXCR4-directed RLT causes effective myeloablation, which allows for HSCT. In addition, it also exerts direct antilymphoma activity independent of subsequent therapeutic steps, whereas safety profile was acceptable.
Airborne eDNA captures three decades of ecosystem biodiversity
Authors: Sullivan Alexis R. , Karlsson Edvin , Svensson Daniel , Brindefalk Björn , Villegas Jose Antonio , Mikko Amanda , Bellieny Daniel , Siddique Abu Bakar , Johansson Anna-Mia , Grahn Håkan , Sundell David , Norman Anita , Esseen Per-Anders , Sjödin Andreas , Singh Navinder J , Brodin Tomas , Forsman Mats , Stenberg Per 
Published: December 2023

AbstractConserving biodiversity is a global imperative, yet our capacity to quantify and understand species occurrences has been limited. To help address this challenge, we develop a novel monitoring approach based on deep sequencing of airborne eDNA. When applied to a 34-year archive of weekly filters from an aerosol sampling station in northern Sweden, our methods enabled robust detection of over 2,700 genera across all domains of life and estimates of eDNA catchment areas. Reconstructed time series revealed regional biodiversity declines consistent with contemporary, large-scale transformations of forest composition and structure. Our results show airborne eDNA can reliably monitor biodiversity and underscore the immense latent potential in the thousands of aerosol monitoring stations deployed worldwide.One-Sentence SummaryDNA captured from air reveals organisms from all domains of life and their long-term trends.
Assessing the potential of BirdNET to infer European bird communities from large-scale ecoacoustic data
Authors: Funosas David , Barbaro Luc , Schillé Laura , Elger Arnaud , Castagneyrol Bastien , Cauchoix Maxime 
Published: December 2023

AbstractPassive acoustic monitoring has become increasingly popular as a practical and cost-effective way of obtaining highly reliable acoustic data in ecological research projects. Increased ease of collecting these data means that, currently, the main bottleneck in ecoacoustic monitoring projects is often the time required for the manual analysis of passively collected recordings. In this study we evaluate the potential and current limitations of BirdNET-Analyzer v2.4, the most advanced and generic deep learning algorithm for bird recognition to date, as a tool to assess bird community composition through the automated analysis of large-scale ecoacoustic data.To this end, we study 3 acoustic datasets comprising a total of 629 environmental soundscapes collected in 194 different sites spread across a 19° latitude span in Europe. We analyze these recordings both with BirdNET and by manual listening by local expert birders, and we then compare the results obtained through the two methods to evaluate the performance of the algorithm both at the level of each single vocalization and for entire recording sequences (1, 5 or 10 min).Our analyses reveal that BirdNET identifications can be highly reliable if a sufficiently high minimum confidence threshold is used. However, the current recall of the algorithm is markedly low when the minimum confidence threshold is adjusted to ensure high levels of precision. Thus, we found that F1-scores remain moderate (<0.5) for all datasets and confidence thresholds studied. We therefore estimate that acoustic datasets of extended duration are currently necessary for BirdNET to provide a reliable and minimally comprehensive picture of the target bird community. Our results also suggest that BirdNET performance is not significantly influenced by the type of recorder used or the habitat recorded but is modulated by the volume of species-specific acoustic data available online.We conclude that a judicious use of AI-based IDs provided by BirdNET can represent a novel and powerful method to assist in the assessment of bird community composition through the automated analysis of large-scale ecoacoustic data. Finally, we provide best use recommendations to ensure optimal results from the algorithm for the ecological study of bird communities.
3D Nuclei Segmentation by Combining GAN Based Image Synthesis and Existing 3D Manual Annotations
Authors: Galindo Xareni , Barry Thierno , Guyot Pauline , Rivière Charlotte , Galland Rémi , Levet Florian 
Published: December 2023

AbstractNuclei segmentation is an important task in cell biology analysis that requires accurate and reliable methods, especially within complex low signal to noise ratio images with crowded cells populations. In this context, deep learning-based methods such as Stardist have emerged as the best performing solutions for segmenting nucleus. Unfortunately, the performances of such methods rely on the availability of vast libraries of ground truth hand-annotated data-sets, which become especially tedious to create for 3D cell cultures in which nuclei tend to overlap. In this work, we present a workflow to segment nuclei in 3D in such conditions when no specific ground truth exists. It combines the use of a robust 2D segmentation method, Stardist 2D, which have been trained on thousands of already available ground truth datasets, with the generation of pair of 3D masks and synthetic fluorescence volumes through a conditional GAN. It allows to train a Stardist 3D model with 3D ground truth masks and synthetic volumes that mimic our fluorescence ones. This strategy allows to segment 3D data that have no available ground truth, alleviating the need to perform manual annotations, and improving the results obtained by training Stardist with the original ground truth data.
Addressing Overlapping Sample Challenges in Genome-Wide Association Studies: Meta-Reductive Approach
Authors: Rajabli Farid 
Published: December 2023

AbstractPolygenic risk scores (PRS) are instrumental in genetics, offering insights into an individual level genetic risk to a range of diseases based on accumulated genetic variations. These scores rely on Genome-Wide Association Studies (GWAS). However, precision in PRS is often challenged by the requirement of extensive sample sizes and the potential for overlapping datasets that can inflate PRS calculations. In this study, we present a novel methodology, Meta-Reductive Approach (MRA), that was derived algebraically to adjust GWAS results, aiming to neutralize the influence of select cohorts. Our approach recalibrates summary statistics using algebraic derivations. Validating our technique with datasets from Alzheimer’s disease studies, we showed perfect correlation between summary statistics of proposed approach and “leave-one-out” strategy. This innovative method offers a promising avenue for enhancing the accuracy of PRS, especially when derived from meta-analyzed GWAS data.Availability and implementationMRA script is freely available athttps://github.com/hihg-um/MRAas an R function.
Decoding Prognostic Markers: Bioinformatics Insights into PIH1D1 and p53 in Children’s Brain Cancer
Authors: Kumar Dhiraj , Ranjan Prashant , Verma Amit Kumar , Mir Riyaz Ahmad 
Published: December 2023

AbstractGenetic alterations in normal brain cells lead to the development of brain tumors (BT). The incidence of newly diagnosed cases is on the rise over time. Understanding the molecular biology of pediatric brain tumors is crucial for advancing novel therapeutic approaches to prevent or effectively manage this disease. The R2TP complex, a conserved co-chaperone from yeast to mammals, including RUVBL1, RUVBL2, PIH1D1, and RPAP3 in humans, plays a crucial role in the assembly and maturation of various multi-subunit complexes. This study evaluates the expression of PIH1D1 and p53 in pediatric brain cancers using The Cancer Genome Atlas (TCGA) data through the UALCAN platform—a novel, user-friendly resource for cancer OMICS data analysis.Our analysis revealed elevated expression levels of PIH1D1 in pediatric brain tumors across all age groups compared to normal tissues, suggesting its potential as an early detection marker and a prognostic indicator. Additionally, P53 emerged as a promising target for brain tumor treatment, warranting exploration for age-specific applications. The Venn Diagram analysis further delineated key genes within the PIH1D1 and P53 networks, providing insights into the genetic landscape of childhood brain cancer.Despite these findings, the study has limitations, primarily relying on bioinformatics databases. Future research will incorporate clinical tissues and cell lines in in vivo and in vitro experiments to unravel the mechanistic roles of PIH1D1 and p53 in brain tumors. This comprehensive approach bridges bioinformatics and clinical exploration, contributing to a holistic understanding of pediatric brain cancer molecular biology and paving the way for targeted therapeutic interventions.
Cost-effectiveness of vector control strategies for supplementing mass drug administration for eliminating lymphatic filariasis in India
Authors: Shepard Donald S. , Lwin Aung K. , Pulikkottil Sunish I. , Kalimuthu Mariapillai , Arunachalam Natarajan , Tyagi Brij K. , White Graham B. 
Published: December 2023

AbstractBackground/MethodologyDespite progress using mass drug administration (MDA), lymphatic filariasis (LF) remains a major public health issue in India. Vector control (VC) is hypothesized as a potentially useful addition to MDA towards LF elimination. We conducted cost-effectiveness analysis of MDA alone and augmented by VC single (VCS) or integrated VC approaches (VCI). Data came from historical controls and a 3-arm cluster randomized trial of 36 villages at risk of LF transmission in Tamil Nadu, India. The arms were: MDA alone (the standard of care); VCS (MDA plus expanded polystyrene beads for covering the water surface in wells and cesspits to suppress the filariasis vector mosquitoCulex quinquefasciatus), and VCI (VCS plus insecticidal pyrethroid impregnated curtains over windows, doors, and eaves). Economic costs in 2010 US$ combined government and community inputs from household to state levels. Outcomes were controlled microfilaria prevalence (MfP) and antigen prevalence (AgP) to conventional elimination targets (MfP<1% and AgP<2%) from 2010 to 2013, and disability adjusted life years (DALYs) averted.Principal FindingsThe estimated annual economic cost per resident was US$0.53 for MDA alone, US$1.02 for VCS, and US$1.83 for VCI. With MDA offered in all arms, all reduced LF prevalence substantially and significantly from 2010 to 2013. MDA proved highly cost effective at $112 per DALY, a very small (8%) share of India’s then per capita GDP. Progress towards elimination was comparable across all three study arms.ConclusionsThe well-functioning MDA was effective and very cost-effective for eliminating LF, leaving little scope for further improvement. Supplementary VC demonstrated no statistically significant additional benefit in this trial.Authors’ SummaryLymphatic filariasis (LF) is one of the twenty neglected tropical diseases (NTDs) that affect more than one billion people worldwide. As part of the effort toward global elimination of LF, the Indian State of Tamil Nadu government has implemented mass drug administration (MDA) repeatedly since 1996. Despite their efforts, LF had not yet been eliminated. Although vector control (VC) is proposed to augment regular MDA to help eliminate LF, little is known about the increased impact or costs. Our study compares the costs of MDA alone to the combination of MDA with alternative VC interventions. We calculated both program operating costs and costs to communities. We found MDA to be very cost-effective for eliminating LF. Against low levels of LF endemicity (≤10%), the study had limited ability to detect further improvements and found no significant incremental improvements from VC.
Brain activations during execution and observation of visually guided sequential manual movements in autism and in typical development: A study protocol
Authors: Domellöf Erik , Hjärtström Hanna , Johansson Anna-Maria , Rudolfsson Thomas , Stillesjö Sara , Säfström Daniel 
Published: December 2023

AbstractMotor issues are frequently observed accompanying core deficits in autism spectrum disorder (ASD). Impaired motor behavior has also been linked to cognitive and social abnormalities, and problems with predictive ability have been suggested to play an important, possibly shared, part across all these domains. Brain imaging of sensory-motor behavior is a promising method for characterizing the neurobiological foundation for this proposed key trait. The present functional magnetic resonance imaging (fMRI) developmental study, involving children/youth with ASD, typically developing (TD) children/youth, and neurotypical adults, will investigate brain activations during execution and observation of a visually guided, goal-directed sequential (two-step) manual task. Neural processing related to both execution and observation of the task, as well as activation patterns during the preparation stage before execution/observation will be investigated. Main regions of interest include frontoparietal and occipitotemporal cortical areas, the human mirror neuron system (MNS), and the cerebellum.
Complete genomic assembly of Mauritian cynomolgus macaque killer immunoglobulin-like receptor and natural killer group 2 haplotypes
Authors: Prall Trent M. , Karl Julie A. , Varghese Joshua M. , Baker David A. , Minor Nicholas R. , Raveendran Muthuswamy , Alan Harris R. , Rogers Jeffery , Wiseman Roger W. , O’Connor David H. 
Published: December 2023

AbstractMauritian-origin cynomolgus macaques (MCM) serve as a powerful nonhuman primate model in biomedical research due to their unique genetic homogeneity, which simplifies experimental designs. Despite their extensive use, a comprehensive understanding of crucial immune-regulating gene families, particularly killer immunoglobulin-like receptors (KIR) and natural killer group 2 (NKG2), has been hindered by the lack of detailed genomic reference assemblies. In this study, we employ advanced long-read sequencing techniques to completely assemble eight KIR and seven NKG2 genomic haplotypes, providing an extensive insight into the structural and allelic diversity of these immunoregulatory gene clusters. Leveraging these genomic resources, we prototype a strategy for genotyping KIR and NKG2 using short-read, whole exome capture data, illustrating the potential for cost-effective multi-locus genotyping at colony scale. These results mark a significant enhancement for biomedical research in MCMs and underscores the feasibility of broad-scale genetic investigations.
Tuning of cortical color mechanism revealed using steady-state visually evoked potentials
Authors: Watts Dylan J. , Rozman Ana , Somers Lucy P. , Gunel Bora , Racey Chris , Barnes Katie , Bosten Jenny M. 
Published: December 2023

AbstractColor information is thought to be received by the primary visual cortex via two dominant retinogeniculate pathways, one signals color variation between teal and red, and the other signals color variation between violet and lime. This representation is thought to be transformed in the cortex so that there are a number of different cell populations representing a greater variety of hues. However, the properties of cortical color mechanisms are not well understood. In four experiments, we characterized the tuning functions of cortical color mechanisms by measuring the intermodulation of steady-state visually evoked potentials (SSVEPs). Stimuli were isoluminant chromatic checkerboards where odd and even checks flickered at different frequencies. As hue dissimilarity between the odd and even checks increased, the amplitude of an intermodulation component (I1) at the sum of the two stimulus frequencies decreased, revealing cortical color tuning functions. In Experiment 1 we found similar broad tuning functions for ‘cardinal’ and intermediate color axes, implying that the cortex has intermediately tuned color mechanisms. In Experiment 2 we found similar broad tuning functions for ‘checkerboards’ with no perceptible edges because the checks were formed from single pixels (∼0.096°), implying that the underlying neural populations do not rely on spatial chromatic edges. In Experiment 3 we manipulated check size and found that color tuning functions were consistent across check sizes used. In Experiment 4 we measured full 360° tuning functions for a ‘cardinal’ cortical color mechanism and found evidence for opponent color responses. The observed cortical color tuning functions were consistent with those measured using psychophysics and electrophysiology, implying that tracking intermodulation using SSVEPs provides a useful method for measuring them.
Astrocyte CB1 receptors are required for inhibitory maturation and ocular dominance plasticity in the mouse visual cortex
Authors: Min Rogier , Qin Yi , Kerst Sven , Saiepour M. Hadi , van Lier Mariska , Levelt Christiaan N. 
Published: December 2023

Summary and IntroductionNeuronal circuits are shaped by experience. This happens much more readily in the young compared to the adult brain. The unique learning capacity of the young brain is regulated through postnatal critical periods, during which the ability of neuronal networks to re-wire is greatly enhanced1. Endocannabinoids, which signal through the cannabinoid CB1 receptor (CB1R), regulate several forms of neuronal plasticity2. In the developing neocortex, CB1Rs play a key role in the maturation of inhibitory circuits. For example, interfering with CB1R signaling during development disrupts inhibitory maturation in the prefrontal cortex3. In developing primary visual cortex (V1), endocannabinoid-mediated plasticity at inhibitory synapses regulates the maturation of inhibitory synaptic transmission, shifting synapses from an immature state characterized by strong short-term depression to a mature state with reduced short-term depression4,5. This maturation step correlates with the timing of the critical period. While CB1Rs were originally thought to reside mainly on presynaptic axon terminals, recent studies have highlighted an unexpected role for astrocytic CB1Rs in endocannabinoid mediated plasticity6-8. Here, we investigate the impact of cell-type specific removal of CB1Rs from interneurons or astrocytes on development of inhibitory synapses and network plasticity of V1. We show that removing CB1Rs from astrocytes interferes with maturation of inhibitory synaptic transmission in V1. In addition, it strongly reduces ocular dominance (OD) plasticity during the critical period. In contrast, removing interneuron CB1Rs leaves these processes intact. Our results reveal an unexpected role of astrocytic CB1Rs in critical period plasticity in V1, and highlight the involvement of glial cells in the plasticity and synaptic maturation of sensory circuits.
STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature
Authors: Mehryary Farrokh , Nastou Katerina , Ohta Tomoko , Jensen Lars Juhl , Pyysalo Sampo 
Published: December 2023

AbstractUnderstanding biological processes relies heavily on curated knowledge of physical interactions between proteins. Yet, a notable gap remains between the information stored in databases of curated knowledge and the plethora of interactions documented in the scientific literature. To bridge this gap, we introduce ComplexTome, a manually annotated corpus designed to facilitate the development of text-mining methods for the extraction of complex formation relationships among biomedical entities. This corpus comprises 1,287 documents with ∼3, 500 relationships. We train a novel relation extraction model on this corpus and find that it can highly reliably identify physical protein interactions (F1-score=82.8%). We additionally enhance the model’s capabilities through unsupervised trigger word detection and apply it to extract relations and trigger words for these relations from all open publications in the domain literature. This information has been fully integrated into the latest version of the STRING database, and all introduced resources are openly accessible via Zenodo and GitHub.