bluuebunny/crossref_metadata_2025_split huggingface dataset:
The 5′UTR of porcine reproductive and respiratory syndrome virus strain JXwn06 harbors a uORF that regulates cellular inflammation
Authors: Liu Teng , Shao Qi , Cui Zhiying , Qing Pengkai , Gao Peng , Zhang Yongning , Zhou Lei , Ge Xinna , Guo Xin , Han Jun , Yang Hanchun 
Published: August 2024

ABSTRACT

The 5′ untranslated region (5′UTR) of many positive-stranded RNA viruses contain functional regulatory sequences. Here, we show that the porcine reproductive and respiratory syndrome virus (PRRSV), a member of arteriviruses, harbors small upstream open reading frames (uORFs) in its 5′UTR. Bioinformatics analysis shows that this feature is relatively well conserved among PRRSV strains and
Arteriviridae
. We also identified a uORF, namely uORF2, in the PRRSV strain JXwn06, that possesses translational activity and exerts a suppressive effect on the expression of the primary ORF evidenced by
in vitro
reporter assays. We tested its importance via reverse genetics by introducing a point mutation into the PRRSV infectious cDNA clone to inactivate the start codon of uORF2. The recovered mutant virus Mut2 surprisingly replicated to the same level as the wild-type virus (WT), but induced a higher level of inflammatory cytokines (e.g., TNF-
α
, IL-1
β
, and IL-6) both
in vitro
and in animal experiments, correlating well with more severe lung injury and higher death rate. In line with this, over-expression of uORF2 in transfected cells significantly inhibited poly(I:C)-induced expression of inflammatory cytokines. Together, our data support the idea that uORF2 encodes a novel, functional regulator of PRRSV virulence despite of its short size.

IMPORTANCE

PRRSV has remained a major challenge to the world swine industry, but we still do not know much about its biology and pathogenesis. Here, we provide evidence to show that the 5′UTR of PRRSV strain JXwn06 harbors a functional uORF that has the coding capacity and regulates induction of inflammation as demonstrated by
in vitro
assays and animal experiment. The findings reveal a novel viral factor that regulates cellular inflammation and provide insight into the understanding of PRRSV pathogenesis.
Protective role of cytosolic prion protein against virus infection in prion-infected cells
Authors: Hara Hideyuki , Chida Junji , Batchuluun Batzaya , Takahashi Etsuhisa , Kido Hiroshi , Sakaguchi Suehiro 
Published: August 2024

ABSTRACT

Production of the amyloidogenic prion protein, PrP
Sc
, which forms infectious protein aggregates, or prions, is a key pathogenic event in prion diseases. Functional prion-like protein aggregations, such as the mitochondrial adaptor protein MAVS and the inflammasome component protein ASC, have been identified to play a protective role in viral infections in mammalian cells. In this study, to investigate if PrP
Sc
could play a functional role against external stimuli, we infected prion-infected cells with a neurotropic influenza A virus strain, IAV/WSN. We found that prion-infected cells were highly resistant to IAV/WSN infection. In these cells, NF-κB nuclear translocation was disturbed; therefore, mitochondrial superoxide dismutase (mtSOD) expression was suppressed, and mitochondrial reactive oxygen species (mtROS) was increased. The elevated mtROS subsequently activated NLRP3 inflammasomes, leading to the suppression of IAV/WSN-induced necroptosis. We also found that prion-infected cells accumulated a portion of PrP molecules in the cytosol, and that the N-terminal potential nuclear translocation signal of PrP impeded NF-κB nuclear translocation. These results suggest that PrP
Sc
might play a functional role in protection against viral infections by stimulating the NLRP3 inflammasome-dependent antivirus mechanism through the cytosolic PrP-mediated disturbance of NF-κB nuclear translocation, which leads to suppression of mtSOD expression and consequently upregulation of the NLRP3 inflammasome activator mtROS.

IMPORTANCE
Cytosolic PrP has been detected in prion-infected cells and suggested to be involved in the neurotoxicity of prions. Here, we also detected cytosolic PrP in prion-infected cells. We further found that the nuclear translocation of NF-κB was disturbed in prion-infected cells and that the N-terminal potential nuclear translocation signal of PrP expressed in the cytosol disturbed the nuclear translocation of NF-κB. Thus, the N-terminal nuclear translocation signal of cytosolic PrP might play a role in prion neurotoxicity. Prion-like protein aggregates in other protein misfolding disorders, including Alzheimer's disease were reported to play a protective role against various environmental stimuli. We here showed that prion-infected cells were partially resistant to IAV/WSN infection due to the cytosolic PrP-mediated disturbance of the nuclear translocation of NF-κB, which consequently activated NLRP3 inflammasomes after IAV/WSN infection. It is thus possible that prions could also play a protective role in viral infections.
Probing Open Charm Hadron Production with the ALICE-3 Detector at the High-Luminosity Large Hadron Collider
Authors: Malaev M. V. , Riabov V. G. 
Published: August 2024

Abstract
ALICE-3 is a future upgrade of the current ALICE experiment to be operated at the high-luminosity Large Hadron Collider at CERN after 2030. One of the physics objectives of the experiment is to probe the hot and dense QCD matter produced in heavy-ion collisions by measuring the production of open charm hadrons. The ALICE-3 detector is equipped to measure the production of ground and excited states of D‑mesons in decay channels with charged particles in the final state. Results are presented from feasibility studies of recording of open charm hadrons in decay channels with neutral photons or mesons in the final state using the large acceptance electromagnetic calorimeter.
Trajectories of choriocapillaris perfusion in healthy individuals and patients with diabetes mellitus: a prospective cohort study
Authors: Zhong Xiaoying , Yang Shaopeng , Zhu Ziyu , Li Huangdong , Cheng Weijing , Wang Wei 
Published: August 2024

Purpose
To evaluate the longitudinal rate of choriocapillaris flow deficits (CFD) in healthy participants and patients with diabetes mellitus.

Methods
This prospective cohort study included healthy individuals and diabetic patients without diabetic retinopathy (non-DR) or with mild-to-moderate non-proliferative DR (NPDR). The swept-source optical coherence tomography angiography (OCTA) was adopted for quantifying CFD annually, and linear mixed models were used to analyse the CFD change and its 95% CI overtime.

Results
A total of 1025 individuals were included, including 465 healthy controls, 454 in the non-DR group and 106 in the NPDR group. Significant increase in CFDs was observed in NPDR group (0.423%, 95% CI 0.230% to 0.616%) and non-DR group (0.319%, 95% CI 0.225% to 0.412%), which were higher than the CFD in healthy controls (0.173%, 95% CI 0.079% to 0.266%). After adjusting for other factors, the non-DR and NPDR group had a greater annual elevation of CFD by 0.171% (95% CI 0.060% to 0.283%; p=0.003) and 0.258% (95% CI 0.068% to 0.449%; p=0.008) in comparisons with controls. Furthermore, higher serum creatinine and glycated haemoglobin levels, poorer best-corrected visual acuity, lower OCTA image quality scores and smaller CFD at baseline were independently related to accelerated CFD worsening (all p<0.05).

Conclusions
The CFD among healthy individuals and patients with diabetes increased consistently overtime, regardless of the presence or absence of DR, suggesting that CFD alterations could be an early indicator of microvascular complications, potentially aiding in the earlier DR detection.
Effects of reducing sedentary behaviour by increasing physical activity, on cognitive function, brain function and structure across the lifespan: a systematic review and meta-analysis
Authors: Feter Natan , Ligeza Tomasz S , Bashir Neha , Shanmugam Ramiya J , Montero Herrera Bryan , Aldabbagh Tamara , Usman Anne-Farah , Yonezawa Ayumi , McCarthy Shane , Herrera Danielle , Vargas Denise , Mir Emaad M , Syed Talha , Desai Sanam , Shi Hector , Kim William , Puhar Natalie , Gowda Kushi , Nowak Olivia , Kuang Jin , Quiroz Flor , Caputo Eduardo L , Yu Qian , Pionke JJ , Zou Liye , Raine Lauren B , Gratton Gabriele , Fabiani Monica , Lubans David R , Hallal Pedro C , Pindus Dominika M 
Published: August 2024

Objective
To examine the acute and chronic effects of reducing prolonged sedentary time (ST) with physical activity (PA) on cognitive and brain health.

Design
Systematic review and meta-analysis.

Data sources
PubMed, Scopus, CINAHL, PsycINFO, SPORTDiscus, Web of Science, and ProQuest Dissertation and Theses.

Eligibility criteria
Randomised controlled trials (RCTs) published from inception to 17 June 2024, with healthy participants without cognitive impairment or neurological conditions that affect cognitive functioning, aged ≥4 years, testing acute and chronic effects of reducing ST and/or prolonged ST by reallocating ST to PA on cognitive function, brain function, and structure.

Results

We included 25 RCTs (n=1289) investigating acute (21 studies) and chronic (4 studies) effects on cognitive function (acute: n=20, chronic: n=4) and brain function (acute: n=7, chronic: n=1); there were no studies on brain structure. Acutely interrupting continuous ST with either multiple or a single PA bout improved cognitive function measured from 3 hours to three consecutive days based on 91 effect sizes (
g
=0.17, 95% CI: 0.05 to 0.29, p=0.005,
I
2
=45.5%). When comparing single versus multiple PA bouts, only multiple PA bouts yielded a positive effect on cognitive function based on 72 effect sizes (
g
=0.20, 95% CI: 0.06 to 0.35, p=0.006;
I
2
=48.8%). Chronic studies reported null findings on cognitive function (n=4), with some evidence of improved neural efficiency of the hippocampus (n=1).

Conclusion
Interrupting ST with PA acutely improves cognitive function. The evidence from chronic studies remains inconclusive.

Systematic review registration
PROSPERO CRD42020200998.
Effect of henagliflozin on left ventricular mass index in dialysis patients with HFpEF (HELD-HF): protocol for a multicentre, randomised, double-blind, placebo-controlled trial
Authors: Yan Hao , Wang Wei , Li Ying , Qi Yinghui , Lu Renhua , Zhou Yijun , Zhang Weiming , Liu Shang , Pang Huihua , Fang Yan , Li Zhenyuan , Wang Jieying , Jiang Meng , Pu Jun , Gu Leyi , Fang Wei 
Published: August 2024

Introduction
Heart failure with preserved ejection fraction (HFpEF) is a prevalent comorbidity among patients with end-stage kidney disease. Although sodium-glucose cotransporter 2 inhibitors are validated in treating heart failure and ameliorating left ventricular hypertrophy among non-dialysis patients, the effects on dialysis patients are unknown. We previously investigated the pharmacokinetics of henagliflozin in patients undergoing haemodialysis (HD) or peritoneal dialysis (PD) and clarified its safety.

Methods and analysis

This multicentre, randomised, double-blind, placebo-controlled trial is being conducted at three hospitals in Shanghai, China. A target of 108 HD or PD patients with HFpEF are randomly allocated to treatment group (henagliflozin 5 mg/day in addition to standard therapy) or control group (placebo with standard therapy) at a ratio of 1:1. All subjects will be followed up for 24 weeks. The primary outcome is change in echocardiography-measured left ventricular mass index. The secondary interests include changes in left atrial volume index, E/e’, e’ and N-terminal pro-B-type natriuretic peptide (NT-proBNP). Intergroup comparisons of change in echocardiography-related outcomes from baseline to 24 weeks are based on a linear regression model adjusted for baseline values (analysis of covariance), and repeated measure analysis of variance with Bonferroni adjustment is employed for comparison of change in NT-proBNP. Subgroup analyses of the primary and secondary outcomes are conducted to determine whether the effect of henagliflozin varies according to dialysis modality. The χ
2
method is used to compare the occurrence of adverse events and severe adverse events.

Ethics and dissemination
This trial has been approved by the Ethics Committee of Renji Hospital, School of Medicine, Shanghai Jiao Tong University (LY2023-127-B). All participants provide written informed consent before screening. The results of the trial will be disclosed completely in international peer-reviewed journals. Both positive and negative results will be reported.

Trial registration number
ChiCTR2300073169.
Patterns of the left thalamus embedding into the connectome associated with reading skills in children with reading disabilities
Authors: Lou Chenglin , Cross Alexandra M. , Peters Lien , Ansari Daniel , Joanisse Marc F. 
Published: August 2024

Abstract
We examined how thalamocortical connectivity structure reflects children’s reading performance. Diffusion-weighted MRI at 3 T and a series of reading measures were collected from 64 children (33 girls) ages 8–14 years with and without dyslexia. The topological properties of the left and right thalamus were computed based on the whole-brain white matter network and a hub-attached reading network, and were correlated with scores on several tests of children’s reading and reading-related abilities. Significant correlations between topological metrics of the left thalamus and reading scores were observed only in the hub-attached reading network. Local efficiency was negatively correlated with rapid automatized naming. Transmission cost was positively correlated with phonemic decoding, and this correlation was independent of network efficiency scores; follow-up analyses further demonstrated that this effect was specific to the pulvinar and mediodorsal nuclei of the left thalamus. We validated these results using an independent dataset and demonstrated that that the relationship between thalamic connectivity and phonemic decoding was specifically robust. Overall, the results highlight the role of the left thalamus and thalamocortical network in understanding the neurocognitive bases of skilled reading and dyslexia in children.
Pushing the Limits of Participatory Video: Exploring Transgressive Voices through Researcher-Participant Minor Video-Making as a Non-Representational Practice
Authors: Iwase Masayuki 
Published: August 2024

Abstract
This article inquires into participatory researchers’ ‘representational’ practices in relation to sharing power with minority participants through collaborative video-making processes. The author argues that there is a limit to attaining such a political and ethical end because a ‘representational’ logic seemingly operates as the theoretical and methodological underpinning for participatory video, which undercuts its ability to represent the voices of collaborators. This article takes into account Shannon Walsh’s (2014) emphasis that “if participatory video is to be a significant method within a project for social change, we must push its limits, and its politics” (p. 140). This article does so by drawing on a ‘non-representational’ approach (Vannini, 2015) and the concept of ‘transgressive voices’ (Jackson & Mazzei, 2009). The author discusses his experience with Deleuze-inspired ‘minor video-making’ as a relational and affective practice in which participants, tangible and intangible research objects and environments, and the researcher himself became relationally entangled to falsify any predetermined essentialized identity and to compose a powerful new body. In the unfolding of transgressive voices in the specific liminal space or moments during the minor video-making, the author ‘intensively and immanently reads’ (Masny & Cole, 2012) the entanglements during storyboarding, rehearsing, shooting, and editing.
DINEOF Interpolation of Global Ocean Color Data: Error Analysis and Masking
Authors: Zhao Haipeng , Matsuoka Atsushi , Manizza Manfredi , Winter Amos 
Published: August 2024

Abstract
The Data Interpolation Empirical Orthogonal Function (DINEOF) algorithm is used to reconstruct datasets of geophysical and biological variables such as sea surface temperature (SST) and chlorophyll a (Chl a). In this study, we analyze the impact of both the quantity and distribution of missing data on the performance of DINEOF demonstrating how DINEOF plus a connectivity mask can be used for future data reconstruction tasks. We propose an enhanced version of DINEOF (DINEOF+) by adding two steps: 1) Using a 75% threshold of missing data for reconstructing incomplete datasets and 2) masking interpolated points that lack sufficient space–time observations in the original dataset. We successfully apply DINEOF+ to the Ocean Color Climate Change Initiative (OC-CCI) global daily Chl a dataset and validate the results using in situ datasets. We find that the recovery rate varies across ocean basins and years. In oligotrophic waters, the daily data coverage increased by 40%–50% during the period from 2003 to 2020. Using DINEOF+ allows us to obtain a significantly higher temporal resolution of global Chl a data, which will improve understanding of marine phytoplankton dynamics in response to changing environments.

Significance Statement
We perform an error analysis on the application of DINEOF for reconstructing a global Chl a dataset. The results of this analysis illustrate the impact of missing data—both in terms of quantity and distribution—on the performance of DINEOF. We propose using DINEOF+, an enhanced version of DINEOF that adds an editing step to mask out interpolated points based on the number of surrounding observations in the original input. The performance of DINEOF+ was validated using both simulated and in situ datasets. The results indicate that employing this masking technique effectively reduces biased estimates of missing data. DINEOF+ can be applied to other biogeochemical variables. However, caution is advised when dealing with observations characterized by high variance.
Analytical performance evaluation of the GreenCare A1c and Cera-Stat HbA1c point-of-care testing assays
Authors: Lee Joon Hee , Jun Sun-Hee , Lee Jikyo , Song Sang Hoon , Lee Kyunghoon 
Published: August 2024

Background The escalating prevalence of diabetes underscores the need for precise diagnostic tools to facilitate effective management. Hemoglobin A1c (HbA1c) is a crucial biomarker for long-term glycemic control in diabetic patients. Point-of-care testing (POCT) for HbA1c offers rapid, accessible alternatives to conventional laboratory methods, but uncertainties persist regarding the accuracy and reliability of POCT assays. Methods This study evaluates the analytical performance of two boronate-affinity based HbA1c POCT assays, the GreenCare A1c and Cera-Stat HbA1c. Various analytical parameters including precision, linearity, comparison, and accuracy are assessed following guidelines from Clinical and Laboratory Standards Institute (CLSI), with results applied to certification criteria from the National Glycohemoglobin Standardization Program (NGSP) and International Federation of Clinical Chemistry and Laboratory Medicine (IFCC). Furthermore, 52 and 13 frozen EDTA whole blood samples were respectively used for additional evaluation of accuracy and interference due to Hb variants for the GreenCare A1c assay. Results Both GreenCare and Cera-Stat demonstrated good precision (repeatability CV% 1.5-1.9 and total imprecision CV% 1.6–2.2), linearity (R2 = 0.9996 & 0.9990), and correlation (r = 0.982 & 0.978) with an established HbA1c analyzer, the Bio-Rad D100. The GreenCare also exhibited good accuracy with frozen EDTA samples with known HbA1c values. Both assays met the certification criteria from NGSP and IFCC, classifying them as “standard” according to IFCC model for quality targets for HbA1c. Conclusions This evaluation affirms the reliability of GreenCare and Cera-Stat POCT assays for HbA1c measurements, which can potentially reduce unnecessary referrals and enhance the overall quality of diabetes diagnosis and treatment.
Driver Situation Awareness for Regaining Control from Conditionally Automated Vehicles: A Systematic Review of Empirical Studies
Authors: Tan Xiaomei , Zhang Yiqi 
Published: August 2024

Objective An up-to-date and thorough literature review is needed to identify factors that influence driver situation awareness (SA) during control transitions in conditionally automated vehicles (AV). This review also aims to ascertain SA components required for takeovers, aiding in the design and evaluation of human–vehicle interfaces (HVIs) and the selection of SA assessment methodologies. Background Conditionally AVs alleviate the need for continuous road monitoring by drivers yet necessitate their reengagement during control transitions. In these instances, driver SA is crucial for effective takeover decisions and subsequent actions. A comprehensive review of influential SA factors, SA components, and SA assessment methods will facilitate driving safety in conditionally AVs but is still lacking. Method A systematic literature review was conducted. Thirty-four empirical research articles were screened out to meet the criteria for inclusion and exclusion. Results A conceptual framework was developed, categorizing 23 influential SA factors into four clusters: task/system, situational, individual, and nondriving-related task factors. The analysis also encompasses an examination of pertinent SA components and corresponding HVI designs for specific takeover events, alongside an overview of SA assessment methods for conditionally AV takeovers. Conclusion The development of a conceptual framework outlining influential SA factors, the examination of SA components and their suitable design of presentation, and the review of SA assessment methods collectively contribute to enhancing driving safety in conditionally AVs. Application This review serves as a valuable resource, equipping researchers and practitioners with insights to guide their efforts in evaluating and enhancing driver SA during conditionally AV takeovers.
Tract embolization with gelatin sponge after percutaneous transhepatic portal vein intervention
Authors: Shibata Eisuke , Takao Hidemasa , Abe Osamu 
Published: August 2024

Background Bleeding from the puncture tract after percutaneous transhepatic portal vein intervention can become life-threatening. To date, studies about tract embolization with gelatin sponge after percutaneous transhepatic portal vein intervention are only with small numbers of patients, or non-consecutive or pediatric patients with a relatively small sheath in diameter. Purpose To evaluate the safety and efficacy of tract embolization with gelatin sponge strips after percutaneous transhepatic poral vein access. Material and Methods Between September 2017 and February 2024, 100 consecutive patients (61 men, 39 women; mean age = 53 ± 15 years) underwent a total of 105 portal vein interventions using a percutaneous transhepatic approach. Tract embolization for the removal of 6–8 Fr sheath was performed using gelatin sponge strips in all procedures, including 71 portal vein embolization before major hepatectomy, 27 portal balloon venoplasty or stent placement after liver transplantation, and seven other interventions. Results No bleeding occurred after tract embolization with gelatin sponge strips. Minor portal vein thrombosis was detected in three procedures after liver transplantation and in one procedure for portal vein stenosis caused by essential thrombocytopenia. Thrombosis occurred in the punctured portal vein branch in all procedures. Thrombosis was not clinically relevant in any patient, and it was difficult to differentiate whether thrombosis was caused by sheath placement or the inserted gelatin sponge. Conclusion Tract embolization with gelatin sponge strips after percutaneous transhepatic portal vein intervention is a safe and feasible method for preventing hemorrhage from the puncture tract.