bluuebunny/crossref_metadata_2025_split huggingface dataset:
Avian influenza A (H5N1) virus in dairy cattle: origin, evolution, and cross-species transmission
Authors: Mostafa Ahmed , Naguib Mahmoud M. , Nogales Aitor , Barre Ramya S. , Stewart James P. , García-Sastre Adolfo , Martinez-Sobrido Luis 
Published: November 2024

ABSTRACT

Since the emergence of highly pathogenic avian influenza virus (HPAIV) H5N1 of clade 2.3.4.4b as a novel reassortant virus from subtype H5N8, the virus has led to a massive number of outbreaks worldwide in wild and domestic birds. Compared to the parental HPAIV H5N8 clade 2.3.4.4b, the novel reassortant HPAIV H5N1 displayed an increased ability to escape species barriers and infect multiple mammalian species, including humans. The virus host range has been recently expanded to include ruminants, particularly dairy cattle in the United States, where cattle-to-cattle transmission was reported. As with the avian 2.3.4.4.b H5N1 viruses, the cattle-infecting virus was found to transmit from cattle to other contact animals including cats, raccoons, rodents, opossums, and poultry. Although replication of the virus in cows appears to be mainly confined to the mammary tissue, with high levels of viral loads detected in milk, infected cats and poultry showed severe respiratory disease, neurologic signs, and eventually died. Furthermore, several human infections with HPAIV H5N1 have also been reported in dairy farm workers and were attributed to exposures to infected dairy cattle. This is believed to represent the first mammalian-to-human transmission report of the HPAIV H5N1. Fortunately, infection in humans and cows, as opposed to other animals, appears to be mild in most cases. Nevertheless, the H5N1 bovine outbreak represents the largest outbreak of the H5N1 in a domestic mammal close to humans, increasing the risk that this already mammalian adapted H5N1 further adapts to human-to-human transmission and starts a pandemic. Herein, we discuss the epidemiology, evolution, pathogenesis, and potential impact of the recently identified HPAIV H5N1 clade 2.3.4.4b in dairy cattle in the United States. Eventually, interdisciplinary cooperation under a One Health framework is required to be able to control this ongoing HPAIV H5N1 outbreak to stop it before further expansion of its host range and geographical distribution.
Type I interferon signaling in dendritic cells limits direct antigen presentation and CD8
+
T cell responses against an arthritogenic alphavirus
Authors: Bullock Christopher B. , Wang Leran , Ware Brian C. , Wagoner Ngan , Ohara Ray A. , Liu Tian-Tian , Desai Pritesh , Peters Bjoern , Murphy Kenneth M. , Handley Scott A. , Morrison Thomas E. , Diamond Michael S. 
Published: November 2024

ABSTRACT

Ross River virus (RRV) and other alphaviruses cause chronic musculoskeletal syndromes that are associated with viral persistence, which suggests deficits in immune clearance mechanisms, including CD8
+
T-cell responses. Here, we used a recombinant RRV-gp33 that expresses the immunodominant CD8
+
T-cell epitope of lymphocytic choriomeningitis virus (LCMV) to directly compare responses with a virus, LCMV, that strongly induces antiviral CD8
+
T cells. After footpad injection, we detected fewer gp33-specific CD8
+
T cells in the draining lymph node (DLN) after RRV-gp33 than LCMV infection, despite similar viral RNA levels in the foot. However, less RRV RNA was detected in the DLN compared to LCMV, with RRV localizing principally to the subcapsular region and LCMV to the paracortical T-cell zones. Single-cell RNA-sequencing analysis of adoptively transferred gp33-specific transgenic CD8
+
T cells showed rapid differentiation into effector cells after LCMV but not RRV infection. This defect in RRV-specific CD8
+
T effector cell maturation was corrected by local blockade of type I interferon (IFN) signaling, which also resulted in increased RRV infection in the DLN. Studies in
Wdfy4
−/−
, CD11c-Cre
B2m
fl/fl
, or Xcr1-Cre
Ifnar1
fl/fl
mice that respectively lack cross-presenting capacity, MHC-I antigen presentation by dendritic cells (DCs), or type I IFN signaling in the DC1 subset show that RRV-specific CD8
+
T-cell responses can be improved by enhanced direct antigen presentation by DCs. Overall, our experiments suggest that antiviral type I IFN signaling in DCs limits direct alphavirus infection and antigen presentation, which likely delays CD8
+
T-cell responses.

IMPORTANCE

Chronic arthritis and musculoskeletal disease are common outcomes of infections caused by arthritogenic alphaviruses, including Ross River virus (RRV), due to incomplete virus clearance. Unlike other viral infections that are efficiently cleared by cytotoxic CD8
+
T cells, RRV infection is surprisingly unaffected by CD8
+
T cells as mice lacking or having these cells show similar viral persistence in joint and lymphoid tissues. To elucidate the basis for this deficient response, we measured the RRV-specific CD8
+
T-cell population size and activation state relative to another virus known to elicit a strong T-cell response. Our findings reveal that RRV induces fewer CD8
+
T cells due to limited infection of immune cells in the draining lymph node. By increasing RRV susceptibility in antigen-presenting cells, we elicited a robust CD8
+
T-cell response. These results highlight antigen availability and virus tropism as possible targets for intervention against RRV immune evasion and persistence.
Comparative genomics of obligate predatory bacteria belonging to phylum
Bdellovibrionota
highlights distribution and predicted functions of lineage-specific protein families
Authors: Davis Sidney C. , Cerra Joseph , Williams Laura E. 
Published: November 2024

ABSTRACT

Comparative genomics of predatory bacteria is important to understand their ecology and evolution and explore their potential to treat drug-resistant infections. We compared chromosomes of 18 obligate predators from phylum
Bdellovibrionota
(16 intraperiplasmic, two epibiotic) and 15 non-predatory bacteria. Phylogenetics of conserved single-copy genes and analysis of genome-wide average amino acid identity provide evidence for at least five
Bdellovibrio
species and support recent reclassifications of predatory taxa. To define shared and differential genome content, we grouped predicted protein sequences into gene clusters based on sequence similarity. Few gene clusters are shared by all 33 bacteria or all 18 predatory bacteria; however, we identified gene clusters conserved within lineages, such as intraperiplasmic
Bdellovibrio
, and not found in other bacteria. Many of these are predicted to function in cell envelope biogenesis, signal transduction, and other roles important for predatory lifestyles. Among intraperiplasmic
Bdellovibrio
, we detected high abundance of gene clusters predicted to encode transglycosylases, endopeptidases, and lysozymes, and we identified six gene clusters (amidase, L,D-transpeptidase, four transglycosylases) with evidence of recent gene duplication and gene family expansion. Focusing on peptidoglycan metabolism, we defined a suite of gene clusters that include peptidoglycan-degrading and -modifying enzymes and occur only in predatory bacteria, suggesting these proteins may have evolved activities specific to predation. Our analyses highlight key genome content differences between obligate predatory bacteria and non-predatory relatives and identify gene clusters that may encode enzymes adapted to predatory lifestyles. These lineage-specific proteins are strong candidates for functional characterization to clarify their role in predation.

IMPORTANCE

Evolution of predation as a bacterial lifestyle involves selective pressure on and adaptation of enzymes that contribute to killing and digestion of prey bacteria, in some cases from within the prey itself. Such enzymes are a hallmark of obligate predatory bacteria belonging to phylum
Bdellovibrionota
, which includes the well-studied predator
Bdellovibrio
. By comparing protein sequences of obligate predatory bacteria and their non-predatory relatives, we define key genome content differences that distinguish bacterial predators and identify lineage-specific enzymes that may have evolved unique activities due to selective pressures related to a predatory lifestyle. In addition to providing insights into the ecology and evolution of predatory bacteria, comparative genomics studies, like this, can inform efforts to develop predatory bacteria and/or their enzymes as potential biocontrol agents to combat drug-resistant bacterial infections.
Influence of flow discharge and minibasin shape on the flow behavior and depositional mechanics of ponded turbidity currents
Authors: Reece J. Kevin , Dorrell Robert M. , Straub Kyle M. 
Published: November 2024

Abstract
The interplay between seafloor sediment-laden density-driven flows, turbidity currents, and topography helps to shape continental margins. However, these interactions are poorly understood, especially those within enclosed depressions termed minibasins. In this study, novel experiments quantify the three-dimensional (3-D) dynamics of turbidity currents interacting with a range of minibasin geometries that, for the first time, scale within the parameter space of natural systems. Controls on flow dynamics are quantified by measuring the evolving velocity and sediment transport fields, in addition to maps of bathymetry. This study focuses on three aspects of turbidity current interactions with minibasins. First, the results suggest that sediment transport and deposition in minibasins is likely dominated by evolving flow conditions. Contrary to earlier studies in two-dimensional (2-D) flumes, this study supports a time-to-flow equilibrium in minibasins that scales with the time to replace ambient fluid with turbid influx, and this replacement time likely takes days to achieve in many field-scale minibasins. Second, in all experiments, horizontal flow circulation is observed, which is critical for distributing sediment throughout minibasins. However, the strength of the horizontal circulation reduces as the ratio of minibasin length to width increases, which leads to stagnant or even upstream-directed flow near the bed, elevated height of the velocity maximum in flows, the lowering of near-bed shear stresses, and more homogeneous deposits through a reduction in bed reworking. Finally, the results indicate that fluid detrainment from minibasins significantly reduces sediment fall velocities, severely lowering the sediment-trapping efficiency for small or light particles. This reduction in effective fall velocities of sediments suggests a mechanism that fractionates fine particulates (e.g., clays), nutrients (e.g., organic carbon), and pollutants (e.g., microplastics) along transport paths down topographically complex margins.
Iron isotope fractionation during transcrustal magmatic differentiation: Implications for continental crustal formation in subduction zones
Authors: Xu Jian , Xia Xiao-Ping , Wang Qiang , Zhang Le , Cui Ze-Xian , Yang Qing , Zhang Wan-Feng 
Published: November 2024

Abstract
Earth’s continental crust is hypothesized to originate from mantle melting in subduction zones. However, mantle melts are typically Fe-rich, with light Fe isotopes (δ56Fe = 0.05‰), unlike the Fe-depleted and heavy Fe isotope (δ56Fe can be up to 0.2‰) compositions of continental crust. The mechanisms responsible for this paradox remain elusive. Here, we report Fe isotope data from a suite of co-magmatic Middle Triassic continental arc rocks in the Ailaoshan tectonic zone (Yunnan, SW China). Gabbroic diorites have light Fe isotopes (δ56Fe = 0.04‰–0.09‰), while granodiorites and normal-arc granites have slightly heavier values (δ56Fe = 0.07‰–0.14‰). Adakitic granites, with high Sr/Y (61–183) and La/Yb (47–90) ratios, exhibit the heaviest δ56Fe (0.16‰–0.19‰). Rayleigh fractionation modeling results suggest that fractionation of isotopically light Fe minerals (e.g., olivine, pyroxene, and amphibole) can reproduce the Fe isotopic variations in most samples, but fails to explain the high Sr/Y, La/Yb, and δ56Fe values of adakitic granites, which would require Fe-rich garnet fractionation. Notably, the different Fe isotopes of the adakitic granites and non-adakitic rocks reveal two distinct transcrustal magmatic differentiation pathways: lower crustal, high-pressure, garnet-dominated fractionation; and middle–upper crustal, amphibole-dominated fractionation. The heavy Fe isotopic and Fe-depleted characteristics of the Ailaoshan magmatic arc suites are more comparable to the calc-alkaline arc magmas from normal to thick crust arcs (e.g., the Andean arc), but remarkably different from the tholeiitic arc magmas from thin crust arcs (e.g., the Mariana arc). This study highlights the role of amphibole and garnet fractionation in magmatic calc-alkaline differentiation. We propose that a thickened crust would permit a longer magmatic differentiation column, thus facilitating felsic and Fe-depleted continental crustal formation. The fractionated Fe-rich, garnet-bearing arc cumulates with light Fe isotopes are density-unstable and may be recycled into the mantle by lower crustal foundering.
Long-term clinical follow-up of irritant-induced occupational asthma
Authors: Lantto Jussi , Suojalehto Hille , Jantunen Hanna , Lindström Irmeli 
Published: November 2024

BackgroundOccupational exposure to irritants is associated with poor asthma control, but the long-term clinical characteristics of irritant-induced occupational asthma (IIA) are poorly known.ObjectiveTo evaluate whether any distinguishable features contribute to IIA patients’ poor outcomes and whether clinical characteristics change over time.MethodsWe re-evaluated 28 IIA patients with a median of 6.8 years (IQR 4.6–11.1) after their diagnosis at the Finnish Institute of Occupational Health in 2004–2018. We measured their lung function, non-specific bronchial hyper-responsiveness, inflammation profile and exercise capacity using an ergometric bicycle test. The participants also underwent an Asthma Control Test (ACT) and responded to questionnaires assessing their laryngeal hypersensitivity (LHQ) and dysfunctional breathing (Nijmegen Questionnaires, NQ).ResultsAt follow-up, 22 (79%) participants used inhaled corticosteroids, 4 (14%) had asthma exacerbation within 1 year, 11 (39%) had ACT<20 (ie, poor asthma symptom control), 7 (26%) had abnormal spirometry and 8 (36%) had a positive methacholine challenge test result. 17 (61%) participants showed at least one elevated eosinophilic inflammation marker. Six (23%) had an abnormal LHQ score and 7 (26%) had an abnormal NQ score. 15 (58%) participants showed reduced physical capacity that was related to extensive asthma medication, poor asthma symptom control and acute IIA phenotype. A higher ACT score was the only significant change between diagnosis and follow-up (p=0.014).ConclusionMost of the IIA patients had normal lung function at follow-up, which had only changed a little over time. Reduced physical capacity was a common finding and appears to be related to poor asthma symptom control.
Routine radiographs of hands and feet do not have diagnostic or prognostic value in patients with clinically suspect arthralgia: a large longitudinal study
Authors: Dumoulin Quirine A , van der Helm - van Mil Annette H M , van Steenbergen Hanna W 
Published: November 2024

BackgroundConventional radiographs of hands and feet are used to depict structural damage in rheumatoid arthritis (RA). This is also commonly done in clinical practice in symptomatic patients at risk for RA (clinically suspect arthralgia (CSA)), but its rationale is unclear. We aimed to investigate the prevalence of radiographic erosive disease in patients with CSA and its progression over time.MethodsPatients with symptomatic arthralgia of the Leiden CSA cohort were studied during 2-year follow-up or until development of inflammatory arthritis (IA). Erosive disease was defined according to the radiologist, or according to the RA-specific erosive definition in light of the American College of Rheumatology (ACR)/European Alliance of Associations for Rheumatology (EULAR) 2010 RA criteria. Serial radiographs were evaluated according to the Sharp van der Heijde Scoring method (SHS) and radiographic erosive progression was determined. Additionally, it was evaluated if baseline erosive disease associated with IA development. Analyses were stratified for anticitrullinated protein antibody status.Results1497 radiographs of hands and feet of 749 patients with CSA were studied. Median SHS-erosion score at baseline was 0 (IQR 0–1). RA-specific erosive disease was present in 1.7% according to the radiologist, and 2.5% according to the ACR/EULAR criteria. No patients with CSA progressed ≥5 SHS-erosion points during follow-up. Erosive disease at CSA onset was not associated with IA development (HR 0.98 (95% CI 0.40 to 2.44)).ConclusionsAt CSA onset, radiographic erosive disease is rare. In addition, it is rarely progressive within the CSA phase and not predictive for IA development. Therefore, for clinical practice, routinely made radiographs of hands and feet (such as regularly done at RA diagnosis) can be omitted in the at-risk stage of arthralgia.
Tenecteplase thrombolytic therapy for acute ischaemic stroke in China: a real-world, multicentre, retrospective, controlled study
Authors: Liu Ye , Lu Guozhi , Li Dan , Wu Guang , Zhou Xiaoyu , Qu Rongbo , Fang Yongren , He ZhiJiao , Zhang Anqi , Hong Lan , Fang Kun , Cheng Xin , Dong Qiang 
Published: November 2024

Background and aimsTenecteplase (TNK) offers logistical advantages in stroke thrombolytic therapy with its single bolus administration compared with alteplase. We aim to investigate the real-world evidence regarding its safety and effectiveness in China.MethodsWe conducted a retrospective study on patients receiving alteplase or TNK for acute ischaemic stroke (AIS) within 4.5 hours of onset between 1 March 2019 and 1 October 2023, from 18 stroke centres in China. Using propensity score matching (PSM), TNK-treated patients were matched 1:1 with alteplase-treated patients. The primary outcome was the rate of symptomatic intracranial haemorrhage (sICH) within 72 hours post-thrombolysis. Secondary outcomes comprised the rate of parenchymal haemorrhage type 2, any intracranial haemorrhage, any systematic bleeding and mortality at 90 days, as well as 24-hour National Institutes of Health Stroke Scale (NIHSS), early neurological improvement at 24 hours, modified Rankin Scale (mRS) shift, percentage of mRS 0–1 and mRS 0–2 at 90 days.ResultsWe identified 1113 patients with AIS who received TNK and 2360 patients who received alteplase. Following PSM, 1113 TNK-treated patients with AIS were matched to 1113 patients treated with alteplase. No significant differences were observed in rates of sICH (1.8% vs 1.98%, p=0.864) or other safety outcomes. Moreover, TNK-treated patients demonstrated a lower rate of any intracranial haemorrhage (OR: 0.51, 95% CI: 0.31 to 0.86, p=0.012). A higher proportion of patients achieving early neurological improvement at 24 hours (OR: 1.76, 95% CI: 1.48 to 2.09, p=0.000), better 90-day mRS (OR: 0.67, 95% CI: 0.57 to 0.79, p=0.000) as well as higher percentages of 90-day mRS 0–1 (OR: 1.27, 95% CI: 1.05 to 1.54, p=0.012) and mRS 0–2 (OR: 1.41, 95% CI: 1.14 to 1.75, p=0.001) compared with alteplase.ConclusionsThrombolysis with TNK is not associated with an increased risk of sICH, and may result in better early neurological improvement and 90-day functional outcomes compared with alteplase in patients with AIS.
An interdisciplinary research field transformed into an intermedial science exploration programme: how to explore neurotronics research and development in a school student laboratory programme
Authors: Sacristán Daniel , Stamer Insa , Kohlstedt Hermann , Beyer Isabella , Parchmann Ilka 
Published: November 2024

Abstract
This work presents the development and implementation of an interdisciplinary and intermedial science outreach programme designed for school students. The programme integrates biological systems and technological advancements to provide students with hands-on laboratory experiences and immersive media, including virtual reality videos and augmented reality posters. Through a co-creation process involving scientists and educators, the programme aims to enhance students understanding of bio-inspired information pathways and neurogenesis. Preliminary evaluations indicate high engagement and educational value, suggesting that such interdisciplinary approaches can significantly enrich science education.

Graphical abstract
Triphasic Bone Scintigraphy Is Not Useful in Diagnosis and May Delay Surgical Treatment of CRPS of the Hand
Authors: PIÑAL Francisco del , LIM Jin Xi , WILLIAMS Daniel C. , RÚAS Jaime S. , STUDER Alexis T. 
Published: November 2024

Background: Triphasic bone scintigraphy (TPBS) is often used to diagnose complex regional pain syndrome (CRPS). The primary aim of this study is to determine if the diagnosis of CRPS in patients with a positive TPBS (TPBS +ve) is accurate. A secondary aim is to determine if there was delay in treatment of patients who underwent TPBS compared to those who did not have a TPBS. Methods: Of 225 consecutive patients presenting to the first author’s practice with a diagnosis of CRPS, 65 had TPBS performed before referral with 62 having TPBS +ve. The remaining 160 were clinically diagnosed and a TPBS was not done (TPBS-ND). Patients were classified into five categories – wrong diagnosis, dystonic-psychogenic hand, causalgia, flare reaction and irritative carpal tunnel syndrome (ICTS). Patients with flare reaction and ICTS were considered as having true CRPS and the rest were considered as misdiagnosis. The patients’ demographics, duration of symptoms, pre- and postoperative pain, functional score and patient satisfaction were compared. Results: Of the 62 TPBS +ve, there were 38 (61%) misdiagnosis. The proportion of misdiagnoses was fewer in the TPBS-ND group (45%; p = 0.036). Thirty-two of the 62 TPBS group (52%) and 92/160 (56%) of the TPBS-ND group had surgical treatment. At a mean follow-up of 19 months, pain dropped 6.5 ± 2.5 points in the TPBS +ve group. Disabilities of the arm, shoulder and hand (DASH) score fell by 56 ± 27. The mean single assessment numeric evaluation (SANE) score was 8.6 ± 2.3. These results did not differ substantially from those of the TPBS-ND group. Conclusions: A significant number of patients in this study who had TPBS +ve were misdiagnosed in this study. Outcomes after treatment of CRPS were consistently good despite the results of the TPBS. Patients with TPBS +ve had a significant delay to diagnosis. We conclude that TPBS is not useful in the management of CRPS. Level of Evidence: Level III (Therapeutic)