bluuebunny/crossref_metadata_2025_split huggingface dataset:
A guide to mycetisms: A toxicological and preventive overview
Authors: Benvenuti Mirko , Zotti Mirca , La Maestra Sebastiano 
Published: April 2024

Abstract
Fungi are often considered a delicacy and are primarily cultivated and harvested, although numerous species are responsible for intoxication due to toxin content. Foodborne diseases are a significant public health concern, causing approximately 420 000 deaths and 600 million morbidities yearly, of which mushroom poisoning is one of the leading causes. Epidemiological data on non-cultivated mushroom poisoning in individual countries are often unrepresentative, as intoxication rarely requires emergency intervention. On the other hand, the lack of specialist knowledge among medical personnel about the toxicological manifestations of mushroom consumption may result in ineffective therapeutic interventions. This work aims to provide an easy-to-consult and wide-ranging tool useful for better understanding the variability of mushroom intoxications, the associated symptoms, and the main treatments for the most severe cases, given the absence of a complete species mapping tool toxic. Moreover, we establish an effective collection network that describes the incidence of mushroom poisonings by reporting the species and associated toxicological manifestations for each case. In conclusion, we highlight the need to establish appropriate primary prevention interventions, such as training the affected population and increasing consultancy relationships between mycological experts and specialised healthcare personnel.
WTP 10aaauow: discovery of a new FU Ori outburst towards the RCW 49 star-forming region in NEOWISE data
Authors: Tran Vinh , De Kishalay , Hillenbrand Lynne 
Published: April 2024

ABSTRACT
Large-amplitude accretion outbursts in young stars are expected to play a central role in protostellar assembly. Outburst identification historically has taken place using optical techniques, but recent, systematic infrared searches are enabling their discovery in heavily dust-obscured regions of the Galactic plane. Here, we present the discovery of Wide-field Infrared Survey Explorer transient pipeline (WTP) 10aaauow, a large-amplitude mid-infrared (MIR) outburst identified in a systematic search of NEOWISE data using new image subtraction techniques. The source is located towards the RCW 49 star-forming region, and estimated to be at a distance of ≈4 kpc via Gaia parallax measurement. Concurrent with the MIR brightening, the source underwent a ≳5 mag outburst in the optical and near-infrared (NIR) bands, reaching a peak luminosity of ≈260 L⊙ in 2014–2015, followed by a slow decline over the next 7 yr. Analysis of the pre- and post-outburst spectral energy distributions reveals a pre-outburst stellar photosphere at a temperature of 3600–4000 K, surrounded by a likely two-component dust structure similar to a flat-spectrum or Class I type young stellar object. We present optical and NIR spectroscopy that shows a GK-type spectrum in the optical bands exhibiting complex line profiles in strong absorption features, and evidence for a wind reaching a terminal velocity of ≈400 km s−1. The NIR bands are characterized by a cooler M-type spectrum exhibiting a forest of atomic and molecular features. Alltogether, the spectra demonstrate that WTP 10aaauow is an FU Ori type outburst. Ongoing systematic infrared searches will continue to reveal the extent of this population in the Galactic disc.
On the tension between the radial acceleration relation and Solar system quadrupole in modified gravity MOND
Authors: Desmond Harry , Hees Aurélien , Famaey Benoit 
Published: April 2024

ABSTRACT
Modified Newtonian dynamics (MOND), postulating a breakdown of Newtonian mechanics at low accelerations, has considerable success at explaining galaxy kinematics. However, the quadrupole of the gravitational field of the Solar system (SS) provides a strong constraint on the way in which Newtonian gravity can be modified. In this paper, we assess the extent to which the AQUAdratic Lagrangian (AQUAL) and QUasilinear MOND (QUMOND) modified gravity formulations of MOND are capable of accounting simultaneously for the radial acceleration relation (RAR), the Cassini measurement of the SS quadrupole and the kinematics of wide binaries in the Solar neighbourhood. We achieve this by inferring the location and sharpness of the MOND transition from the Spitzer Photometry and Accurate Rotation Curves (SPARC) RAR under broad assumptions for the behaviour of the interpolating function and external field effect. We constrain the same quantities from the SS quadrupole, finding that this requires a significantly sharper transition between the deep-MOND and Newtonian regimes than is allowed by the RAR (an 8.7σ tension under fiducial model assumptions). This may be relieved somewhat by allowing additional freedom in galaxies’ mass-to-light ratios – which also improves the RAR fit – and more significantly (to 1.9σ) by removing galaxies with bulges. For the first time, we also apply to the SPARC RAR fit an AQUAL correction for flattened systems, obtaining similar results. Finally, we show that the SS quadrupole constraint implies, to high precision, no deviation from Newtonian gravity in nearby wide binaries, and speculate on possible resolutions of this tension between SS and galaxy data within the MOND paradigm.
Diverse features of dust particles and their aggregates inferred from experimental nanoparticles
Authors: Nakano Yuki , Kimura Yuki , Hashimoto Akihiko 
Published: April 2024

ABSTRACT
Nanometre- to micrometre-sized solid dust particles play a vital role in star and planet formations. Despite of their importance, however, our understanding of physical and chemical properties of dust particles is still provisional. We have conducted a condensation experiment of the vapour generated from a solid starting material having nearly cosmic proportions in elements. A laser flash heating and subsequent cooling has produced a diverse type of nanoparticles simultaneously. Here we introduce four types of nanoparticles as potential dust particles in space: amorphous silicate nanoparticles (type S); core/mantle nanoparticles with iron or hydrogenized iron core and amorphous silicate mantle (type IS); silicon oxycarbide nanoparticles and hydrogenized silicon oxycarbide nanoparticles (type SiOC); and carbon nanoparticles (type C), all produced in a single heating–cooling event. Type IS and SiOC nanoparticles are new for potential astrophysical dust. The nanoparticles are aggregated to a wide variety of structures: compact, fluffy, and networked. A simultaneous formation of these nanoparticles, which are diverse in chemistry, shape, and structure, prompts a re-evaluation of astrophysical dust particles.
Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation
Authors: Sahoo Bikash R , Kocman Vojč , Clark Nathan , Myers Nikhil , Deng Xiexiong , Wong Ee L , Yang Harry J , Kotar Anita , Guzman Bryan B , Dominguez Daniel , Plavec Janez , Bardwell James C A 
Published: April 2024

Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706’s ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge
Authors: Wei Chih-Hsuan , Allot Alexis , Lai Po-Ting , Leaman Robert , Tian Shubo , Luo Ling , Jin Qiao , Wang Zhizheng , Chen Qingyu , Lu Zhiyong 
Published: April 2024

Abstract
PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly. PubTator 3.0's online interface and API utilize these precomputed entity relations and synonyms to provide advanced search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results. We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive set of features and tools that allow researchers to navigate the ever-expanding wealth of biomedical literature, expediting research and unlocking valuable insights for scientific discovery.
The determinants of the rarity of nucleic and peptide short sequences in nature
Authors: Chantzi Nikol , Mareboina Manvita , Konnaris Maxwell A , Montgomery Austin , Patsakis Michail , Mouratidis Ioannis , Georgakopoulos-Soares Ilias 
Published: April 2024

Abstract
The prevalence of nucleic and peptide short sequences across organismal genomes and proteomes has not been thoroughly investigated. We examined 45 785 reference genomes and 21 871 reference proteomes, spanning archaea, bacteria, eukaryotes and viruses to calculate the rarity of short sequences in them. To capture this, we developed a metric of the rarity of each sequence in nature, the rarity index. We find that the frequency of certain dipeptides in rare oligopeptide sequences is hundreds of times lower than expected, which is not the case for any dinucleotides. We also generate predictive regression models that infer the rarity of nucleic and proteomic sequences across nature or within each domain of life and viruses separately. When examining each of the three domains of life and viruses separately, the R² performance of the model predicting rarity for 5-mer peptides from mono- and dipeptides ranged between 0.814 and 0.932. A separate model predicting rarity for 10-mer oligonucleotides from mono- and dinucleotides achieved R² performance between 0.408 and 0.606. Our results indicate that the mono- and dinucleotide composition of nucleic sequences and the mono- and dipeptide composition of peptide sequences can explain a significant proportion of the variance in their frequencies in nature.
Treatment response as surrogate to predict risk for disease progression in pediatric medulloblastoma with persistent magnetic resonance imaging lesions after first-line treatment
Authors: Obrecht-Sturm Denise , Schömig Lena , Mynarek Martin , Bison Brigitte , Schwarz Rudolf , Pietsch Torsten , Pfister Stefan M , Sill Martin , Sturm Dominik , Sahm Felix , Kortmann Rolf-Dieter , Gerber Nicolas U , von Bueren André O , Fleischhack Gudrun , Schüller Ulrich , Nussbaumer Gunther , Benesch Martin , Rutkowski Stefan 
Published: April 2024

Abstract

Background
This study aims at clarifying the impact of persistent residual lesions following first-line treatment for pediatric medulloblastoma.

Methods
Data on 84 pediatric patients with medulloblastoma and persistent residual lesions on centrally reviewed magnetic resonance imaging (MRI) at the end of first-line therapy were analyzed.

Results
Twenty patients (23.8%) had residual lesions in the tumor bed (R+/M0), 51 (60.7%) had distant lesions (R0/M+) and 13 (15.5%) had both (R+/M+). Overall response to first-line therapy was minor or partial (≥ 25% reduction, minor response [MR]/PR) for 64 (76.2%) and stable disease (SD) for 20 patients (23.8%). Five-year post-primary-treatment progression-free (pptPFS) and overall survival (pptOS) were superior after MR/PR (pptPFS: 62.5 ± 7.0%[MR/PR] vs. 35.9 ± 12.8%[SD], P = .03; pptOS: 79.7 ± 5.9[MR/PR] vs. 55.5 ± 13.9[SD], P = .04). Furthermore, R+/M + was associated with a higher risk for progression (5-year pptPFS: 22.9 ± 17.9%[R+, M+] vs. 72.4 ± 12.0%[R+, M0]; P = .03). Watch-and-wait was pursued in 58 patients, while n = 26 received additional treatments (chemotherapy only, n = 19; surgery only, n = 2; combined, n = 3; valproic acid, n = 2), and their outcomes were not superior to watch-and-wait (5-year pptPFS: 58.5 ± 7.7% vs. 51.6 ± 10.7% P = .71; 5-year pptOS: 76.3 ± 6.9% vs. 69.8 ± 9.7%, P = .74). For the whole cohort, 5-year pptPFS by molecular subgroup (58 cases) were WNT: 100%, SHH: 50.0 ± 35.4%, group-4, 52.5 ± 10.5, group-3 54.2 ± 13.8%; (P = .08).

Conclusions
Overall response and extent of lesions can function as surrogate parameters to predict outcomes in pediatric MB patients with persistent lesions after first-line therapy. Especially in the case of solitary persistent medulloblastoma MRI lesions, additional therapy was not beneficial. Therefore, treatment response, extent/kind of residual lesions and further diagnostic information need consideration for indication of additional treatments for persisting lesions.
Fear and Loathing: How Demographic Change Affects Support for Christian Nationalism
Authors: Walker Brooklyn , Haider-Markel Donald P 
Published: April 2024

Abstract
Christian nationalism, the fusion of religious and national identities, has emerged as an important factor shaping public opinion on a range of issues. However, debates in the existing literature on the motivations behind support for Christian nationalism remain unresolved: Is Christian nationalism a response to secularization and/or a cover for discomfort with racial diversity and equality? Is Christian nationalism rooted in fear of social change, disgust about social change, or something else? We use an experiment embedded in a national survey of adults to isolate the effects of knowledge of both religious and racial demographic change among White Christians. Our analysis suggests that exposure to religious demographic change shifts support for Christian nationalism and perceptions of discrimination against Whites and Christians, but exposure to racial demographic change has limited impact. This effect is mediated by emotion—religious demographic change increases fear and disgust, which then influence support for Christian nationalism and perceptions of discrimination against Whites and Christians. Although our treatment suggesting exposure to racial demographic change had null effects, we note that racial attitudes do independently influence support for Christian nationalism and perceptions of discrimination against Whites and Christians.
Responsiveness and sensitivity of PROMs to change in disease activity status in early and established rheumatoid arthritis
Authors: Looijen Agnes E M , van Mulligen Elise , Vonkeman Harald E , van der Helm-van Mil Annette H M , de Jong Pascal H P 
Published: April 2024

Abstract

Objectives
To determine whether patient-reported outcome measures (PROMs) capturing activity limitations, health impact, pain, fatigue and work ability are responsive and sensitive to changes in disease activity status in patients with early and established RA.

Methods
All early RA patients (n = 557) from the tREACH trial and established RA patients (n = 188) from the TARA trial were included. Both studies were multicentre, single-blinded trials with a treat-to-target management approach. The following PROMs were studied: HAQ Disability Index (HAQ-DI), morning stiffness severity, EQ-5D, general health, 36-item short form (SF-36), joint pain, fatigue and productivity loss. Mean changes in PROMs between two consecutive visits were compared with changes in disease activity status (remission, low disease activity and active disease) using linear mixed models and standardized response means. Additionally, the proportion of individual observations that showed an expected PROM response to disease activity status alterations was calculated.

Results
HAQ-DI, morning stiffness severity, general health, EQ-5D and joint pain demonstrated responsiveness to improvement or worsening of disease activity status in both early and established RA. SF-36 physical and mental component scale, fatigue and productivity loss did not show this effect in both groups. Across nearly all PROMs, the magnitude of change and the proportion of individual observations that reflect a shift from and to active disease remained low.

Conclusion
HAQ-DI, morning stiffness severity, EQ-5D, general health and joint pain are responsive to disease activity status alterations on a group level in both early and established RA. For the individual patient the responsiveness of these PROMs is poor.

Clinical trial registration
tREACH trial (www.isrctn.com, ISRCTN26791028) and TARA trial (www.onderzoekmetmensen.nl, NTR2754)
Online feeding behavior monitoring of individual group-housed grow-finish pigs using a low-frequency RFID electronic feeding system
Authors: Funk Taran H , Rohrer Gary A , Brown-Brandl Tami M , Keel Brittney N 
Published: April 2024

Abstract
Early identification of animals in need of management intervention is critical to maximize animal health and welfare and minimize issues with productivity. Feeding behavior, captured by automated feeding systems, can be used to monitor the health and welfare status of individual pigs. Here, we present a framework for monitoring feeding behavior of grow-finish pigs in real time, using a low-frequency radio frequency identification (RFID) system. Using historical data, an autoregressive linear model for predicting daily time at the feeder was developed and utilized to detect anomalous decreases in feeding behavior associated with health status of the pig. A total of 2,826 pigs were individually monitored with our warning system over the entire grow-finish period, and health warnings were compared to caretaker diagnoses. The system detected 55.7% of the caretaker diagnoses, and on average these events were detected 2.8 d earlier than diagnosis by the caretaker. High numbers of potentially spurious health warnings, generated by the system, can be partly explained by the lack of a reliable and repeatable gold standard reference data set. Results from this work provide a solid basis for monitoring individual animals, but further improvements to the system are necessary for practical implementation.
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies
Authors: Westfall Dylan H , Deng Wenjie , Pankow Alec , Murrell Hugh , Chen Lennie , Zhao Hong , Williamson Carolyn , Rolland Morgane , Murrell Ben , Mullins James I 
Published: April 2024

Abstract
Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing, which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence polymerase-chain reaction (PCR) amplicons derived from cDNA templates tagged with unique molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR. The use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Production of highly accurate sequences from the large datasets produced from SMRT-UMI sequencing is facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline). PORPIDpipeline automatically filters and parses circular consensus reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination, heteroduplex formation, or early cycle PCR errors. The optimized SMRT-UMI sequencing and PORPIDpipeline methods presented here represent a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus quasispecies in a virus transmitter-recipient pair of individuals.
Point-of-care ultrasound in pediatric anesthesiology: considerations for training and credentialing
Authors: Lockhart Thomas J. , Lin Elaina E. , Adler Adam C. 
Published: April 2024

Purpose of review
To discuss considerations surrounding the use of point-of-care ultrasound (POCUS) in pediatric anesthesiology.

Recent findings
POCUS is an indispensable tool in various medical specialties, including pediatric anesthesiology. Credentialing for POCUS should be considered to ensure that practitioners are able to acquire images, interpret them correctly, and use ultrasound to guide procedures safely and effectively. In the absence of formal guidelines for anesthesiology, current practice and oversight varies by institution. In this review, we will explore the significance of POCUS in pediatric anesthesiology, discuss credentialing, and compare the specific requirements and challenges currently associated with using POCUS in pediatric anesthesia.

Summary
Point-of-care ultrasound is being utilized by the pediatric anesthesiologist and has the potential to improve patient assessment, procedure guidance, and decision-making. Guidelines increase standardization and quality assurance procedures help maintain high-quality data. Credentialing standards for POCUS in pediatric anesthesiology are essential to ensure that practitioners have the necessary skills and knowledge to use this technology effectively and safely. Currently, there are no national pediatric POCUS guidelines to base credentialing processes on for pediatric anesthesia practices. Further work directed at establishing pediatric-specific curriculum goals and competency standards are needed to train current and future pediatric anesthesia providers and increase overall acceptance of POCUS use.