bluuebunny/crossref_metadata_2025_split huggingface dataset:
Field-evolved pyrethroid resistance in Tychius picirostris (Coleoptera: Curculionidae) populations in Oregon white clover seed crops
Authors: Tiwari Grace , Kaur Navneet , Anderson Nicole P , Tanner K Christy , Lightle Danielle M , Willette Alison R , Otani Jennifer K , Jorgensen Amanda M , Yoder Calvin , Dorman Seth J 
Published: January 2024

Abstract
The clover seed weevil, Tychius picirostris Fabricius, a serious pest of white clover, Trifolium repens L., grown for seed in western Oregon, causing feeding damage to flowers and developing seeds. Since 2017, white clover seed producers have anecdotally reported T. picirostris control failures using foliar pyrethroid insecticide applications. This mode of action (MoA) is an important chemical control option for T. picirostris management. To evaluate insecticide resistance selection to pyrethroids (bifenthrin) and other MoAs labeled for T. picirostris management (malathion and chlorantraniliprole), adult populations were collected from 8 commercial white clover grown for seed fields in the Willamette Valley, OR, in 2022 and 2023. Among collected Oregon populations, very high resistance ratios (RR50 = 178.00–725.67) were observed to technical grade bifenthrin and low to high resistance ratios (RR50 = 7.80–32.80) to malathion in surface contact assays compared to a susceptible Canadian field population. Moreover, &gt;2.73 times the labeled rate of formulated product containing bifenthrin as the sole MoA was required to kill &gt;50% of T. picirostris in topical assays. Synergistic assays with a mixed-function oxidase inhibitor, an esterase inhibitor, and a glutathione-S-transferase inhibitor revealed phase I and II detoxification enzymes are present in Oregon T. picirostris populations and confer metabolic resistance to bifenthrin. This is the first report of T. picirostris insecticide resistance selection to pyrethroid and organophosphate insecticides. Results will inform continued monitoring and insecticide resistance management strategies to slow the evolution of T. picirostris insecticide resistance selection in Oregon’s white clover seed production.
Round-up of national decisions on copyright protection of works of applied art 2023
Authors:   The Bird & Bird Ip Team, Shehana Wijesena , Dang Katrina , Chloupek Vojtêch , Kalenský Petr , Martin Taimr , Lutzhőft Niels , Hendel Christoph , Hembt Simon , Milanesi Luisa Moavero , Ripa-monti Margherita , Boonen Edzard , Molle Clemens , Rieger-Jansen Manon , Lipski Paweł , Morawska-Zakroczymska Zuzanna , Balcer-Kopka Karina , Lahoz David Fuentes , Vilceanu Sorin 
Published: January 2024

Abstract
Following the judgments of the Court of Justice of the European Union (CJEU) in Cofemel, C-683/17 and Brompton, C-833/18, the treatment of works of applied art under copyright law has (re-)gained central attention. At the time of writing, the CJEU has just received two new referrals for a preliminary ruling (Mio, C-580/23 and USM Haller [case number pending; I ZR 96/22]), asking how the assessment of originality—including having regard to such works—is to be conducted. In 2023, national courts in the Czech Republic, Finland, France, Hungary, Italy, the Netherlands, and Spain delivered a series of important rulings in connection with the copyright treatment of works of applied art. This contribution provides a round-up of the most significant judgments issued in the period 1 January—31 December 2023. The analysis is divided by area (subsistence of copyright; infringement and enforcement aspects; exceptions and limitations; interplay between copyright and other rights in works of applied art) and country (Czech Republic, Finland, France, Hungary, Italy, the Netherlands, and Spain).
Agreement of methods to assess antimicrobial susceptibility using Escherichia coli isolates as target models
Authors: Andretta Milimani , Tavares Rafaela de Melo , Fusieger Andressa , Yamatogi Ricardo Seiti , Nero Luís Augusto 
Published: January 2024

Abstract
Antimicrobial susceptibility tests (AST) conducted in vitro offer a range of methods to assess the antimicrobial resistance (AMR) of microorganisms. Escherichia coli, a widely distributed bacterium, is closely linked to the issue of AMR. In this way, the present study aimed to assess the agreement among different in vitro AST methods, including disk diffusion in agar, broth dilution, and agar dilution method. A total of 100 E. coli isolates were analyzed for their resistance levels against six antibiotics: amoxicillin, ceftiofur, ciprofloxacin, chloramphenicol, tetracycline, and sulfamethoxazole + trimethoprim, using the aforementioned AST methods. Standard breakpoint values were employed to classify isolates as resistant, intermediate, or susceptible, and comparisons among the AST methods were conducted by McNemar’s test (P &lt; .05). The obtained data demonstrated equivalence among the AST methods, highlighting the reliability of these standardized classical methodologies. This standardization aids in preventing the inappropriate use of antimicrobials and the dissemination of antimicrobial-resistant microorganisms.
Machine Learning Refinement of In Situ Images Acquired by Low Electron Dose LC-TEM
Authors: Katsuno Hiroyasu , Kimura Yuki , Yamazaki Tomoya , Takigawa Ichigaku 
Published: January 2024

Abstract
We have studied a machine learning (ML) technique for refining images acquired during in situ observation using liquid-cell transmission electron microscopy. Our model is constructed using a U-Net architecture and a ResNet encoder. For training our ML model, we prepared an original image dataset that contained pairs of images of samples acquired with and without a solution present. The former images were used as noisy images, and the latter images were used as corresponding ground truth images. The number of pairs of image sets was 1,204, and the image sets included images acquired at several different magnifications and electron doses. The trained model converted a noisy image into a clear image. The time necessary for the conversion was on the order of 10 ms, and we applied the model to in situ observations using the software Gatan DigitalMicrograph (DM). Even if a nanoparticle was not visible in a view window in the DM software because of the low electron dose, it was visible in a successive refined image generated by our ML model.
An Assessment of Clinical Accuracy of Vital Sign–based Triage Tools Among U.S. and Coalition Forces
Authors: Vernon Tate E , April Michael D , Fisher Andrew D , Rizzo Julie A , Long Brit J , Schauer Steven G 
Published: January 2024

ABSTRACT

Introduction
Early appropriate allocation of resources for critically injured combat casualties is essential. This is especially important when inundated with an overwhelming number of casualties where limited resources must be efficiently allocated, such as during mass casualty events. There are multiple scoring systems utilized in the prehospital combat setting, including the shock index (SI), modified shock index (MSI), simple triage and rapid treatment (START), revised trauma score (RTS), new trauma score (NTS), Glasgow Coma Scale + age + pressure (GAP), and the mechanism + GAP (MGAP) score. The optimal score for application to the combat trauma population remains unclear.

Materials and Methods
This is a secondary analysis of a previously described dataset from the Department of Defense Trauma Registry from January 1, 2007 through March 17, 2020. We constructed univariable analyses to determine the area under the receiving operator characteristic (AUROC) for the scoring systems of interest. Our primary outcomes were early death (within 24 hours) or early massive transfusion, as defined by ≥3 units.

Results
There were 12,268 casualties that met inclusion criteria. There were 168 (1%) who died within the first 24 hours and 2082 (17%) that underwent significant transfusion within the first 24 hours. When assessing the predictive capabilities for death within 24 hours, the AUROCs were 0.72 (SI), 0.69 (MSI), 0.89 (START), 0.90 (RTS), 0.83 (NTS), 0.90 (GAP), and 0.91 (MGAP). The AUROCs for massive transfusion were 0.89 (SI), 0.89 (MSI), 0.82 (START), 0.81 (RTS), 0.83 (NTS), 0.85 (MGAP), and 0.86 (GAP).

Conclusions
This study retrospectively applied seven triage tools to a database of 12,268 cases from the Department of Defense Trauma Registry to evaluate their performance in predicting early death or massive transfusion in combat. All scoring systems performed well with an AUROC &gt;0.8 for both outcomes. Although the SI and MSI performed best for predicting massive transfusion (both had an AUROC of 0.89), they ranked last for assessment of mortality within 24 hours, with the other tools performing well. START, RTS, NTS, MGAP and GAP reliably identified early death and need for massive transfusion, with MGAP and GAP performing the best overall. These findings highlight the importance of assessing triage tools to best manage resources and ultimately preserve lives of traumatically wounded warfighters. Further studies are needed to explain the surprising performance discrepancy of the SI and MSI in predicting early death and massive transfusion.
Performance of Mucorales spp. qPCR in bronchoalveolar lavage fluid for the diagnosis of pulmonary mucormycosis
Authors: Brousse Xavier , Imbert Sébastien , Issa Nahéma , Forcade Edouard , Faure Maxime , Chambord Jeremy , Ramaroson Hanta , Kaminski Hannah , Dumas Pierre-Yves , Blanchard Elodie 
Published: January 2024

Abstract
To estimate the diagnostic performance of Mucorales polymerase chain reaction (PCR) in Bronchoalveolar lavage fluid (BALF) in routine practice. This was a single-center retrospective study including all consecutive patients &gt;18 years who underwent Mucorales PCR assay in BALF between January 2021 and May 2022. Index testing was prospectively performed using the MycoGENIE Aspergillus spp.–Mucorales spp. PCR. The reference was the diagnosis of pulmonary mucormycosis by the Adjudication Committee. Mucorales PCR in BALF was performed for 938 patients and was positive for 21 of 938 (2.2%). Eleven pulmonary mucormycosis (including one disseminated) were diagnosed. Among them, one (9.1%) was classified as proven mucormycosis, three (27.3%) as probable, and seven (63.6%) as possible according to the EORTC/MSGERC 2019 criteria. The main host factor was hematological malignancy (10 of 11, 90.9%). Mucorales PCR was positive in serum for eight patients (72.7%). Three patients had positive PCR in BALF, but negative in serum. The mean cycle threshold value was significantly lower in mucormycosis than false-positive cases. Sensitivity was 72.7% (95% confidence interval [CI], 43.4–90.3%), and specificity was 98.6% (95% CI, 97.6–99.2%). The positive and negative predictive values were 38.1% (95% CI, 20.8–59.1%) and 99.7% (95% CI, 99.1–99.9%), respectively. Mucorales PCR in BALF showed good diagnostic performance for mucormycosis, particularly in combination with serum PCR. A positive result should be interpreted with caution, given the possibility of carriage in the airway. However, its high negative predictive value and specificity suggest the utility of Mucorales PCR in BALF in the diagnosis of pulmonary mucormycosis.
Mapping dust in the giant molecular cloud Orion A
Authors: Gration Amery , Magorrian John 
Published: January 2024

ABSTRACT
The Sun is located close to the Galactic mid-plane, meaning that we observe the Galaxy through significant quantities of dust. Moreover, the vast majority of the Galaxy’s stars also lie in the disc, meaning that dust has an enormous impact on the massive astrometric, photometric and spectroscopic surveys of the Galaxy that are currently underway. To exploit the data from these surveys we require good three-dimensional maps of the Galaxy’s dust. We present a new method for making such maps in which we form the best linear unbiased predictor of the extinction at an arbitrary point based on the extinctions for a set of observed stars. This method allows us to avoid the artificial inhomogeneities (so-called ‘fingers of God’) and resolution limits that are characteristic of many published dust maps. Moreover, it requires minimal assumptions about the statistical properties of the interstellar medium. In fact, we require only a model of the first and second moments of the dust density field. The method is suitable for use with directly measured extinctions, such as those provided by the Rayleigh–Jeans colour excess method, and inferred extinctions, such as those provided by hierarchical Bayesian models like StarHorse. We test our method by mapping dust in the region of the giant molecular cloud Orion A. Our results indicate a foreground dust cloud at a distance of 350 pc, which has been identified in work by another author.
Saturation of spiral instabilities in disc galaxies
Authors: Hamilton Chris 
Published: January 2024

ABSTRACT
Spiral density waves can arise in galactic discs as linear instabilities of the underlying stellar distribution function. Such an instability grows exponentially in amplitude at some fixed growth rate β before saturating non-linearly. However, the mechanisms behind saturation, and the resulting saturated spiral amplitude, have received little attention. Here, we argue that one important saturation mechanism is the non-linear trapping of stars near the spiral’s corotation resonance. Under this mechanism, we show analytically that an m-armed spiral instability will saturate when the libration frequency of resonantly trapped orbits reaches $\omega _\mathrm{lib} \sim \mathrm{a\, \, few}\times m^{1/2} \beta$. For a galaxy with a flat rotation curve, this implies a maximum relative spiral surface density $\vert \delta \Sigma /\Sigma _0\vert \sim \mathrm{a\, \, few} \times (\beta /\Omega _\mathrm{p})^2 \cot \alpha$, where Ωp is the spiral pattern speed and α is its pitch angle. This result is in reasonable agreement with recent N-body simulations, and suggests that spirals driven by internally-generated instabilities reach relative amplitudes of at most a few tens of per cent; higher amplitude spirals, like in M51 and NGC 1300, are likely caused by very strong bars and/or tidal perturbations.
Why dust pressure matters in debris discs
Authors: Lynch Elliot M , Lovell Joshua B , Sefilian Antranik A 
Published: January 2024

ABSTRACT
There is a common assumption in the particulate disc community that the pressure in particulate discs is essentially zero and that the disc streamlines follow Keplerian orbits, in the absence of self-gravity or external perturbations. It is also often assumed that the fluid description of particulate discs is not valid in the presence of crossing orbits (e.g. from non-zero free eccentricities). These stem from the misconception that fluid pressure arises due to the (typically rare) collisions between particles and that the velocity of particles in fluids are single-valued in space. In reality, pressure is a statistical property of the particle distribution function which arises precisely because there is a distribution of velocities at a given position. In this letter we demonstrate, with simple examples, that pressure in particulate discs is non-zero and is related to the inclination and free eccentricity distributions of the constituent particles in the discs. This means many common models of debris discs implicitly assume a non-zero, and potentially quite significant, dust pressure. We shall also demonstrate that the bulk motion of the dust is not the same as the particle motion and that the presence of pressure gradients can lead to strong departures from Keplerian motion.
A large-scale study of peptide features defining immunogenicity of cancer neo-epitopes
Authors: Wan Yat-tsai Richie , Koşaloğlu-Yalçın Zeynep , Peters Bjoern , Nielsen Morten 
Published: January 2024

Abstract
Accurate prediction of immunogenicity for neo-epitopes arising from a cancer associated mutation is a crucial step in many bioinformatics pipelines that predict outcome of checkpoint blockade treatments or that aim to design personalised cancer immunotherapies and vaccines. In this study, we performed a comprehensive analysis of peptide features relevant for prediction of immunogenicity using the Cancer Epitope Database and Analysis Resource (CEDAR), a curated database of cancer epitopes with experimentally validated immunogenicity annotations from peer-reviewed publications. The developed model, ICERFIRE (ICore-based Ensemble Random Forest for neo-epitope Immunogenicity pREdiction), extracts the predicted ICORE from the full neo-epitope as input, i.e. the nested peptide with the highest predicted major histocompatibility complex (MHC) binding potential combined with its predicted likelihood of antigen presentation (%Rank). Key additional features integrated into the model include assessment of the BLOSUM mutation score of the neo-epitope, and antigen expression levels of the wild-type counterpart which is often reflecting a neo-epitope's abundance. We demonstrate improved and robust performance of ICERFIRE over existing immunogenicity and epitope prediction models, both in cross-validation and on external validation datasets.
Analysis of the inter-domain orientation of tandem RRM domains with diverse linkers: connecting experimental with AlphaFold2 predicted models
Authors: Roca-Martínez Joel , Kang Hyun-Seo , Sattler Michael , Vranken Wim 
Published: January 2024

Abstract
The RNA recognition motif (RRM) is the most prevalent RNA binding domain in eukaryotes and is involved in most RNA metabolism processes. Single RRM domains have a limited RNA specificity and affinity and tend to be accompanied by other RNA binding domains, frequently additional RRMs that contribute to an avidity effect. Within multi-RRM proteins, the most common arrangement are tandem RRMs, with two domains connected by a variable linker. Despite their prevalence, little is known about the features that lead to specific arrangements, and especially the role of the connecting linker. In this work, we present a novel and robust way to investigate the relative domain orientation in multi-domain proteins using inter-domain vectors referenced to a stable secondary structure element. We apply this method to tandem RRM domains and cluster experimental tandem RRM structures according to their inter-domain and linker-domain contacts, and report how this correlates with their orientation. By extending our analysis to AlphaFold2 predicted structures, with particular attention to the inter-domain predicted aligned error, we identify new orientations not reported experimentally. Our analysis provides novel insights across a range of tandem RRM orientations that may help for the design of proteins with a specific RNA binding mode.
A compact regulatory RNA element in mouse Hsp70 mRNA
Authors: Wang Wenshuai , Liu Fei , Ugalde Maria Vera , Pyle Anna Marie 
Published: January 2024

Abstract
Hsp70 (70 kDa heat shock protein) performs molecular chaperone functions by assisting the folding of newly synthesized and misfolded proteins, thereby counteracting various cell stresses and preventing multiple diseases, including neurodegenerative disorders and cancers. It is well established that, immediately after heat shock, Hsp70 gene expression is mediated by a canonical mechanism of cap-dependent translation. However, the molecular mechanism of Hsp70 expression during heat shock remains elusive. Intriguingly, the 5′ end of Hsp70 messenger RNA (mRNA) appears to form a compact structure with the potential to regulate protein expression in a cap-independent manner. Here, we determined the minimal length of the mHsp70 5′-terminal mRNA sequence that is required for RNA folding into a highly compact structure. This span of this RNA element was mapped and the secondary structure characterized by chemical probing, resulting in a secondary structural model that includes multiple stable stems, including one containing the canonical start codon. All of these components, including a short stretch of the 5′ open reading frame (ORF), were shown to be vital for RNA folding. This work provides a structural basis for future investigations on the role of translational regulatory structures in the 5′ untranslated region and ORF sequences of Hsp70 during heat shock.
“It changes everything”: Understanding how people experience the impact of living with a lower-grade glioma
Authors: Rimmer Ben , Balla Michelle , Dutton Lizzie , Williams Sophie , Lewis Joanne , Gallagher Pamela , Finch Tracy , Burns Richéal , Araújo-Soares Vera , Menger Fiona , Sharp Linda ,   Ways Ahead Study Team, Erridge Sara , Sturdy Pauline , McBain Catherine 
Published: January 2024

Abstract

Background
Quantitative studies show people living with a lower-grade glioma (LGG) often report low health-related quality of life. However, it is unclear how this impact is experienced; resulting supportive care needs are also poorly understood. We explored how people experience the impact of living long-term with an LGG, to help identify potential supportive care needs.

Methods
We conducted semi-structured interviews with a diverse group of people with LGG (n = 28) across the United Kingdom, who had completed primary treatment (male n = 16, female n = 12, mean age 54.6 years, mean time since diagnosis 8.7 years). Interviews were transcribed and inductive thematic analysis was conducted.

Results
Four themes relating to the impact experiences of people with LGG were generated: “Emotional response to the diagnosis,” “Living with the ‘What ifs’,” “Changing relationships,” and “Faltering independence.” These reflect participants’ experiences with symptoms (eg, fatigue, seizures) and impairments (eg, motor dysfunction, cognitive deficits), and how these, in turn, drive impacts on daily living (including on work, relationships, social activities, and transport). Participants spoke about their experiences with profound emotion throughout.

Conclusions
People with LGG can experience wide-ranging everyday impacts and may have extensive supportive care needs. This study highlights how this impact is experienced and what it means to people with LGG. Best practice suggestions for conducting comprehensive needs assessments tailored to those with LGG, and the development of personalized plans to meet those needs, would be a critical step to ensure that people with LGG are best supported in living with their condition.
Traumatic optic neuropathy from an air gun pellet injury: a case report.
Authors: Anis Iqra , Baig Muhammad Akbar 
Published: January 2024

Abstract
Orbital apex fractures are a debilitating condition that can cause vision problems and are often associated with intracranial injury. Traumatic Optic Neuropathy (TON), which results in vision loss following a traumatic injury to the optic nerve, can be caused by various mechanisms, but most cases involve injuries to the globe, orbit, or adnexa. We are reporting a case of an 18 year old male with a history of an air gun being accidentally discharged into his left eye. He was evaluated and found to have an Orbital apex fracture with left eye TON. Patient was administered high dose steroids. Detailed evaluation by Ophthalmology revealed a left eye traumatic stage I macular hole which was conservatively treated with visual improvement reported during patient follow up.