bluuebunny/crossref_metadata_2025_split huggingface dataset:
A yeast-based reverse genetics system to generate HCoV-OC43 reporter viruses encoding an eighth subgenomic RNA
Authors: Duguay Brett A. , Tooley Trinity H. , Pringle Eric S. , Rohde John R. , McCormick Craig 
Published: January 2025

ABSTRACT

Coronaviruses have large, positive-sense single-stranded RNA genomes that challenge conventional strategies for mutagenesis. Yeast genetics has been used to manipulate large viral genomes, including those of herpesviruses and coronaviruses. This method, known as transformation-associated recombination (TAR), involves assembling complete viral genomes from dsDNA copies of viral genome fragments via homologous recombination in
Saccharomyces cerevisiae
. Here, we report our development of a TAR assembly and mutagenesis system for the endemic, seasonal human coronavirus (HCoV) strain OC43. HCoV-OC43 generally causes mild respiratory symptoms and is classified as a biosafety level 2 agent, making it useful for studying fundamental aspects of coronavirus biology and for comparative studies of more highly pathogenic betacoronaviruses. Following cDNA synthesis from HCoV-OC43 viral RNA, we generated five plasmids encompassing ~7.2 kb portions of the
ORF1ab
gene, the
NS2
to
M
segment, or the
N
gene and structured to facilitate reporter gene insertions in the
M
-to-
N
intergenic region. Using these plasmids, we completed independent assemblies of yeast centromeric plasmids encoding
ORF1ab
,
NS2a
to
N
, as well as full-length HCoV-OC43 plasmids. A wild-type virus (OC43
YA
), as well as mClover3-H2B (OC43-mClo
YA
), mRuby3-H2B (OC43-mRuby
YA
), and mCardinal (OC43-mCard
YA
) reporter viruses, were rescued. The OC43-mClo
YA
reporter virus replicated comparably to an OC43 reference strain and produced the mClover3-H2B protein from a novel subgenomic RNA through insertion of an eighth body transcription regulatory sequence, preventing the need to delete or mutate viral genes. This updated HCoV-OC43 reverse genetics system will contribute to a better understanding of betacoronavirus host-pathogen interactions and can accelerate studies of novel antivirals.

IMPORTANCE
Coronaviruses are ubiquitous pathogens that infect humans resulting in both mild and severe respiratory infections. Human coronavirus strain OC43 (HCoV-OC43) is one of many viruses responsible for common colds and is a useful model of more severe coronavirus infections. In this study, we describe an updated HCoV-OC43 mutagenesis system that uses yeast to capture six DNA fragments of the viral RNA genome and assemble them into full-length genomes in yeast/bacterial plasmids. The design of this system allowed for the rapid assembly and rescue of functional HCoV-OC43 viruses, including fluorescent reporter viruses with expanded genetic capacity. This updated reverse genetics system will enhance our ability to monitor viral replication, through building new reporter viruses, while also enhancing the study of betacoronavirus biology through the generation of mutant HCoV-OC43 viruses.
Robotic Congenital Cardiac Surgery Practice Worldwide: A Systematic Review
Authors: Lee Madonna E. , Amabile Andrea , Hameed Irbaz , Antonios James , Awad Ahmed K. , Brackett Alexandria , Krane Markus , Gruber Peter J. , Geirsson Arnar 
Published: January 2025

Background: With the increasing adoption of robotic technology in adult cardiac surgery patients, improved surgeon experience and wider utilization have been reported. However, interpreting trends in robotic congenital surgery is more challenging. By performing a systematic review, the authors aim to evaluate the current literature on robotic congenital operations.Methods: The protocol was registered with PROSPERO. The inclusion and exclusion criteria were established based on the population, intervention, comparison, and outcome (PICO) framework. A comprehensive literature search was conducted from January 1998 to December 2021. Studies involving patients undergoing congenital cardiac surgery operations performed with robotic assistance were included. Two independent reviewers screened titles/abstracts and then full text of eligible studies. A third reviewer resolved any discrepancies. The Newcastle–Ottawa Scale was applied to quantify quality assessment for nonrandomized observational studies.Results: A total of one‐hundred twenty‐eight publications underwent full‐text review, and 66 studies were included. Overwhelmingly, the majority are from single institutions and observational and retrospective studies. The population was mostly adults with only 10.6% (7/66) studies solely reporting pediatric patients. About 50% of the studies were case reports (28/66). Selective reporting of outcomes varied widely across studies. Cumulative mortality rates were 0.3%. The highest incidence of morbidities included pleural effusion (12.3%), reoperation for bleeding (10.7%), atrial fibrillation (10.7%), heart block (9.5%), and peripheral cannulation–related complications (8.6%). The overall quality of the studies was unsatisfactory, with the majority of studies receiving a score of 3 out of 9.Conclusions: Most publications were case reports or small case series performed in adults and restricted to a few international institutions. To address these clinical challenges, technological improvements and advanced training will be mandatory before wider application to children and complex congenital diagnoses. Unfortunately, the overall quality of studies is poor, with inconsistent outcomes reporting. Improved and standardized reporting will be necessary before an appropriate evaluation of robotics in the treatment of congenital heart disease is feasible.
Infection‐Related Hospitalization and Incident Heart Failure: The Atherosclerosis Risk in Communities Study
Authors: Molinsky Rebecca L. , Shah Amil , Yuzefpolskaya Melana , Yu Bing , Misialek Jeffrey R. , Bohn Bruno , Vock David , MacLehose Richard , Borlaug Barry A. , Colombo Paolo C. , Ndumele Chiadi E. , Ishigami Junichi , Matsushita Kunihiro , Lutsey Pamela L. , Demmer Ryan T. 
Published: January 2025

Background
The immune response to infections may become dysregulated and promote myocardial damage contributing to heart failure (HF). We examined the relationship between infection‐related hospitalization (IRH) and HF, HF with preserved ejection fraction, and HF with reduced ejection fraction.

Methods and Results

We studied 14 468 adults aged 45 to 64 years in the ARIC (Atherosclerosis Risk in Communities) Study who were HF free at visit 1 (1987–1989). IRH was identified using select
International Classification of Diseases
(
ICD
) codes in hospital discharge records and was treated as a time‐varying exposure. HF incidence was defined as the first occurrence of either a hospitalization that included an
ICD, Ninth Revision
(
ICD‐9
) discharge code of 428 (428.0–428.9) among the primary or secondary diagnoses or a death certificate with an
ICD‐9
code of 428 or an
ICD, Tenth Revision
(
ICD‐10
) code of I50 among any of the listed diagnoses or underlying causes of death. We used multivariable‐adjusted Cox proportional hazards models to assess the association between IRH and incident HF, HF with reduced ejection fraction, and HF with preserved ejection fraction. Median follow‐up time was 27 years, 55% were women, 26% were Black, mean age at baseline was 54±6 years, 46% had an IRH, and 3565 had incident HF. Hazard ratio (HR) for incident HF events among participants who had an IRH compared with those who did not was 2.35 (95% CI, 2.19–2.52). This relationship was consistent across different types of infections. Additionally, IRH was associated with both HF with reduced ejection fraction and HF with preserved ejection fraction: 1.77 (95% CI, 1.35–2.32) and 2.97 (95% CI, 2.36–3.75), respectively.

Conclusions
IRH was associated with incident HF, HF with reduced ejection fraction, and HF with preserved ejection fraction. IRH might represent a modifiable risk factor for HF pathophysiology.
Abstract TP351: Evidence of sustained monocytosis during chronic stroke recovery
Authors: Verma Rajkumar , DiMauro Sharon , Gamiotea Turro Daylin , Yadav Sanjeev , Mittal Sanjay , Zhou Beiyan , Liang Bruce 
Published: January 2025

An acute ischemic stroke (AIS) triggers rapid mobilization of immune cells from bone marrow, leading to the infiltration of circulating immune cells into the brain. Among these immune cells, monocytes, which are pivotal in both adaptive and innate immune responses, play a crucial role in stroke injury and recovery in a temporal manner. Previous research indicates that tissue injury such as AIS causes acute monocytosis. However, it remains unclear if this upregulation persists during the recovery phase. Given the diverse roles of monocytes during post-stroke recovery, we hypothesize that their numbers remain elevated during chronic recovery.
In this study, we will analyze the effect of stroke duration on monocytosis and the factors affecting this process after AIS.
We recruited consecutive AIS patients (58-90 years) undergoing endovascular clot retrieval and age-matched healthy control subjects of both sexes, with informed consent obtained from all participants. Flow cytometric analysis of whole blood-derived immune cells, including monocytes, was performed at 0–2 days (acute, n=20), 3–7 days (subacute, n=20), and 65±20 days (chronic, n=14) after stroke onset. These were compared with healthy subjects (n=20 per age group). A pure monocyte population was isolated using a side and forward scatter plot with cell-surface markers, such as HLA-DR, CD45, CD11b, CD14, and CD16, along with a negative gating strategy. Plasma samples were analyzed for various secreted cytokine levels using the Millipore multiplex array. scRNA-seq analysis was employed to support the evidence of monocytosis using total immune cells of these subjects.
We found that the total monocyte count (% of total immune cells) progressively increased during recovery in AIS patients (P<0.05), which was corroborated by unbiased scRNA-seq analysis data. Cytokine analysis indicated that the levels of M-CSF and G-CSF also progressively increased, further supporting the evidence of monocytosis after stroke. Subclassification of monocyte clusters from RNA-seq data suggested that specific monocyte subsets are the major contributors to monocytosis.
In summary, our data support the evidence of continued monocytosis after ischemic stroke, indicating diverse roles for monocytes beyond the acute inflammatory response. Detailed molecular characterization of monocytes, their subpopulations, and their genetic composition over time may provide novel insights into their pathophysiological roles during stroke recovery.
Abstract TP375: Ischemic Insult Under Hyperhomocysteinemic Condition Triggers Early Onset Of Inflammatory Response Causing Exacerbation Of Brain Injury
Authors: Deep Satyanarayan , Seelig Sarah , Gomez Madelyn , Paul Surojit , Poddar Ranjana 
Published: January 2025

Hyperhomocysteinemia, a metabolic disorder characterized by systemic elevation of amino acid homocysteine, is linked to deficiency in vitamins and enzymes involved in homocysteine metabolism. The incidence of hyperhomocysteinemia is high in the elderly population due to reduced micronutrient absorption and metabolism. Recent preclinical studies in animal models of stroke showed that predisposition to hyperhomocysteinemia exacerbates ischemic brain injury and worsens behavioral deficits, establishing hyperhomocysteinemia as a potential comorbidity for stroke. These studies further showed that hyperhomocysteinemia-induced stimulation of GluN2A subunit containing NMDA receptors (GluN2A-NMDARs) in conjunction with glutamate-induced stimulation of GluN2B subunit containing NMDARs (GluN2B-NMDARs) exacerbates stroke pathology. However, the precise intracellular mechanisms involved in such exacerbation of ischemic brain injury is not known. The current study sought to investigate whether under hyperhomocysteinemic condition GluN2A-NMDAR mediated early activation of the transcription factor Nuclear Factor-κB (NFκB) and subsequent expression of the pro-inflammatory chemokine Monocyte chemoattractant protein-1 (MCP-1) enhances post-ischemic inflammatory response and exacerbation of brain damage.
Adult male Wistar rats were made hyperhomocysteinemic by implantation of Alzet osmotic pumps containing L-homocysteine. The animals were hyperhomocysteinemic within 3 days with a total plasma homocysteine level of ~24 μM. Acute ischemic stroke was induced by middle cerebral artery occlusion for 60 min followed by reperfusion (6h). Brain tissues were processed for MCP-1 ELISA and RT-PCR. A significant increase in MCP-1 mRNA and protein levels were observed in the ipsilateral cortex of hyperhomocysteinemic rats compared to control rats within 6h of reperfusion. An accelerated brain damage was also observed at this time in the hyperhomocysteinemic rats. Inhibition of GluN2A-NMDAR (NVP-AAM077, i.v.) and NFκB (BMS345541, IKK inhibitor; i.p) at the onset of ischemic insult attenuated increase in MCP-1 mRNA and protein levels, as well as exacerbation of brain injury under hyperhomocysteinemic condition. The study provides compelling evidence for a novel role of GluN2A-NMDAR in promoting neuro-inflammatory response that contributes to exacerbation of stroke pathology under hyperhomocysteinemic condition.
Thrombolysis for Ischemic Stroke Beyond the 4.5-Hour Window: A Meta-Analysis of Randomized Clinical Trials
Authors: Günkan Ahmet , Ferreira Marcio Yuri , Vilardo Marina , Scarcia Luca , Bocanegra-Becerra Jhon E. , Cardoso Leonardo Januario Campos , Fabrini Paleare Luis F. , de Oliveira Almeida Gustavo , Semione Gabriel , Ferreira Christian , Ciccio Gabriele , Mujanovic Adnan , Jabbour Pascal , Serulle Yafell , Nguyen Thanh N. , Baron Jean-Claude 
Published: January 2025

BACKGROUND:
A minority of patients with stroke qualify for intravenous thrombolysis (IVT) within 4.5-hour window. The safety and efficacy of IVT beyond this period have not been well studied.

METHODS:

We systematically searched MEDLINE, Embase, Cochrane, and
ClinicalTrials.gov
for relevant randomized clinical trials. Randomized clinical trials comparing IVT versus standard medical care in patients with ischemic stroke beyond 4.5 hours of symptom onset or last known well without mechanical thrombectomy (MT) were included. Primary outcomes were excellent (modified Rankin Scale score of 0–1) and good (modified Rankin Scale score of 0–2) functional outcomes at 90 days, symptomatic intracerebral hemorrhage (sICH), and death at 90 days. Pooled odds ratios (ORs) with 95% CIs were calculated using a random-effects model. Heterogeneity was assessed by
Q
test and quantified by
I
² values.

RESULTS:

Eight randomized clinical trials (1742 patients; mean age, 69.8±9 years, 63.5% men) were included. Compared with standard medical care, IVT achieved higher rates of excellent (OR, 1.43 [95% CI, 1.17–1.75];
Q
=2.30;
P
=0.94;
I
2
=0%) and good functional outcomes (OR, 1.36 [95% CI, 1.12–1.66];
Q
=2.07;
P
=0.96;
I
2
=0%) at 90 days but also increased sICH rates (OR, 4.25 [95% CI, 1.67–10.84],
Q
=0.48;
P
=0.99;
I
2
=0%). Mortality at 90 days did not significantly differ between treatment groups (OR, 1.28 [95% CI, 0.87–1.89];
Q
=4.63;
P
=0.59;
I
2
=0%). Subanalyses yielded numerically higher odds of excellent functional outcomes when patients were selected with perfusion imaging (3 studies, OR, 1.45 [95% CI, 1.08–1.94]) compared with diffusion-weighted imaging–fluid-attenuated inversion recovery mismatch (3 studies, OR, 1.34 [95% CI, 0.94–1.91]) and when treated with tenecteplase (3 studies, OR, 1.47 [95% CI, 1.06–2.04]) compared with alteplase (5 studies, OR, 1.38 [95% CI, 1.08–1.78]).

CONCLUSIONS:
IVT for ischemic stroke beyond 4.5 hours, without MT, led to increased odds of excellent and good functional outcomes compared with standard medical care, despite higher odds of sICH, and a nonsignificant numerical increase in mortality.
Peers Affect Personality Development
Authors: Shan Xiaoyue , Zölitz Ulf 
Published: January 2025

Abstract
Do people around us influence our personality? We investigate this question through a field experiment where we randomly assign university students to study groups. We find personality spillovers along three dimensions: students become more conscientious when assigned to conscientious peers, more open-minded when assigned to open-minded peers, and more competitive when assigned to competitive peers. We find no effects for peers' extraversion, agreeableness, or neuroticism. Our findings are consistent with students' adopting peer traits that are predictive of academic achievement. Our paper provides novel evidence on spillovers in noncognitive skills and establishes that socialization with peers affects personality development.
Pauronemoides lorestanensis n. sp. (Tylenchomorpha, Paurodontidae), from the rhizosphere of grasses in Lorestan province, western Iran
Authors: Mirzaie Fouladvand Zeinab , Atighi Mohammad Reza , Pourjam Ebrahim , Kanzaki Natsumi , Giblin-Davis Robin M. , Pedram Majid 
Published: January 2025

Summary
Pauronemoides lorestanensis n. sp., the fifth species of the newly established genus Pauronemoides, is described and illustrated based on morphological, morphometric and molecular data. The new species was recovered from a soil sample collected from the rhizosphere of grasses in Lorestan province. It is characterised by having a medium-sized body (868-1092 μm, females; 714, 710 μm, males), four incisures in lateral fields, asymmetrical knobs of stylet, vulva at 87.9-90.2%, post-vulval uterine sac (PUS) absent, intestine with extension over rectum, and tail dimorphism of sexes and bursa of males reaching near tail end in lateral view. It was morphologically compared with four currently known species of the genus viz. P. siddiqii, P. iranicus, P. mucronatus and P. macrocellus, and is regarded as the cryptic form of P. iranicus, both of which could be separated using some morphological characters and molecular data. Phylogenetic analyses of the partial small and large subunit ribosomal DNA (SSU, LSU D2-D3 rDNA) sequences of the new species were conducted, and the resulting topologies discussed.
Our Markets, Our Selves
Authors: Damrosch David 
Published: January 2025

Abstract
Reflecting on several recurring themes in the contributions to this special issue, this essay discusses the interplay between an individual’s scholarly formation and the markets in which our work circulates, both within academia and beyond. The examples of Matthew Arnold and Michel Foucault can exemplify what Kenneth Burke described as “perspective by incongruity,” with which we can approach the widely disparate works now circulating within world literature, and challenge our own ingrained biases and assumptions in the process.
East-West Cross-Cultural Encounters of the Lyric
Authors: Harper Elizabeth 
Published: January 2025

Abstract
Adorno described the lyric as “a philosophical sundial telling the time of history”. Here I read two poets whose continued cultural dominance make their work an ideal site for defining the privileged access of lyric to the nature of things. Horace and Tao body forth deep-rooted cultural thinking in a specific language at a specific time, but share universal concerns with the art of living well. Horace’s Odes suggest the freedom that art confers; the continual return of Chinese poets to Tao’s oeuvre suggests they found there a touchstone for their own questing voice. These small lyrics enshrine theories of the natural world, the self and society which present an enlarged vision of the good life. Articulating variously the realities of sacrifice and struggle, the pull of necessity and freedom, the path of beauty and the role of poetry, Horace and Tao open up horizons for reading empathetically across cultures.
Before Fandom in Japanese-Indonesian Film: the Roots of Globalization from Japan to Indonesia
Authors: Purwaning Tyas Agnes Siwi , Darumukti Georgius Benardi 
Published: January 2025

Abstract
The establishment of Japan Motion Picture (Nippon Eigasha) Indonesian branch and Cultural Center both in 1943 during Japanese occupation served as a driving force to develop Indonesia’s national film. Sending their film experts, Japan introduced national film standardization and taught systematic film-making techniques to Indonesian young directors. Usmar Ismail, later known as the founding father of Indonesian film, also learned about film-making from Japanese side, and eventually his first film was named the first Indonesian national film. Despite its major influence on Indonesian filmography, analysis on its internal elements and how much the education from Japan affected his film has been overlooked. Therefore, this study aims to identify the roots of globalization brought during the cultural imperialism era of Japan. An analysis by looking at cinematic elements in two Japanese and two Indonesian films will be made to find film-making principles and ideologies laid by Japan in Indonesia.
The Impact of Transience in the Interaction between Orographic Gravity Waves and Mean Flow
Authors: Jochum Felix , Chew Ray , Lott François , Voelker Georg S. , Weinkaemmerer Jan , Achatz Ulrich 
Published: January 2025

Abstract
A Lagrangian gravity wave parameterization [Multiscale Gravity Wave Model (MS-GWaM)] that allows for fully transient wave–mean-flow interaction and horizontal propagation is applied to orographic gravity waves for the first time. Both linear and nonlinear mountain waves are modeled in idealized simulations within the pseudoincompressible flow solver PincFlow. Two-dimensional flows over monochromatic orographies are considered, using MS-GWaM either in its fully transient implementation or in a steady-state implementation that represents classic mountain-wave parameterizations. Comparisons of wave-resolving simulations (not using MS-GWaM) and coarse-resolution simulations (using MS-GWaM) show that allowing for transience leads to a significantly more accurate forcing of the resolved mean flow. The parameterization is able to reproduce the transient forcing of linearly generated mountain waves that slowly propagate upward, in contrast to the instantaneous distribution of wave energy in classic parameterizations. At high altitudes, wave breaking induces a wind reversal that is captured by the transient parameterization but inhibited in steady-state simulations, due to the assumption of critical level formation. This shows that transience can have a substantial impact on the interaction between mountain waves and mean flow.