bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recommendations for Setting a Criterion and Assessing Commutability of Sample Materials Used in External Quality Assessment/Proficiency Testing Schemes
Authors: Sandberg Sverre , Fauskanger Pernille , Johansen Jesper V , Keller Thomas , Budd Jeffrey , Greenberg Neil , Rej Robert , Panteghini Mauro , Delatour Vincent , Ceriotti Ferruccio , Deprez Liesbet , Camara Johanna E , MacKenzie Finlay , Lyle Alicia N , van der Hagen Eline , Burns Chris , Greg Miller W ,   for the IFCC Working Group on Commutability in Metrological Traceability
Published: September 2023

Abstract
It is important for external quality assessment materials (EQAMs) to be commutable with clinical samples; i.e., they should behave like clinical samples when measured using end-user clinical laboratory in vitro diagnostic medical devices (IVD-MDs). Using commutable EQAMs makes it possible to evaluate metrological traceability and/or equivalence of results between IVD-MDs.
The criterion for assessing commutability of an EQAM between 2 IVD-MDs is that its result should be within the prediction interval limits based on the statistical distribution of the clinical sample results from the 2 IVD-MDs being compared. The width of the prediction interval is, among other things, dependent on the analytical performance characteristics of the IVD-MDs. A presupposition for using this criterion is that the differences in nonselectivity between the 2 IVD-MDs being compared are acceptable. An acceptable difference in nonselectivity should be small relative to the analytical performance specifications used in the external quality assessment scheme. The acceptable difference in nonselectivity is used to modify the prediction interval criterion for commutability assessment.
The present report provides recommendations on how to establish a criterion for acceptable commutability for EQAMS, establish the difference in nonselectivity that can be accepted between IVD-MDs, and perform a commutability assessment. The report also contains examples for performing a commutability assessment of EQAMs.
Conventional and non-conventional antigen presentation by mast cells
Authors: Tung Chi-Ching , Rathore Abhay P S , St. John Ashley L 
Published: September 2023

Summary
Mast cells (MCs) are multifunctional immune cells that express a diverse repertoire of surface receptors and pre-stored bioactive mediators. They are traditionally recognized for their involvement in allergic and inflammatory responses, yet there is a growing body of literature highlighting their contributions to mounting adaptive immune responses. In particular, there is growing evidence that MCs can serve as antigen-presenting cells, owing to their often close proximity to T cells in both lymphoid organs and peripheral tissues. Recent studies have provided compelling support for this concept, by demonstrating the presence of antigen processing and presentation machinery in MCs and their ability to engage in classical and non-classical pathways of antigen presentation. However, there remain discrepancies and unresolved questions regarding the extent of the MC’s capabilities with respect to antigen presentation. In this review, we discuss our current understanding of the antigen presentation by MCs and its influence on adaptive immunity.
Cardiorespiratory fitness and the incidence of surgery for aortic valve stenosis—the HUNT study
Authors: Nystøyl Benedikte Therese Smenes , Letnes Jon Magne , Nes Bjarne Martens , Slagsvold Katrine Hordnes , Wisløff Ulrik , Wahba Alexander 
Published: September 2023

Abstract

OBJECTIVES
Aortic valve stenosis (AVS) shares many risk factors with coronary disease, the latter being strongly and inversely associated with physical activity (PA) and cardiorespiratory fitness (CRF). However, the relationship between PA, CRF and AVS needs to be established. We explored whether PA habits and estimated CRF affect the risk of developing AVS demanding aortic valve replacement (AVR) and how these factors affect postoperative mortality.

METHODS
Participants from the second and third waves of Trøndelag Health Study were cross-linked with a local heart surgery registry and the Norwegian Cause of Death Registry. Estimated CRF was calculated through a developed algorithm based on clinical and self-reported data. Fine-Gray competing risk analyses were used to investigate how PA habits and estimated CRF were associated with the risk of AVR across CRF quintiles, PA groups and per 1-metabolic equivalent task (MET) (3.5 ml/min/kg).

RESULTS
In a study population of 57 214 participants, we found a 15% [95% confidence interval (CI) 1–27] reduced risk of AVR per 1-MET estimated CRF increment. Those in the highest CRF quintile had a 56% (95% CI 14–77) lower risk of surgery compared to the lowest quintile. Analyses on PA groups did not show significant results. Finally, we found a 37% (95% CI 17–53) lower risk of postoperative mortality per 1-MET increased estimated CRF.

CONCLUSIONS
Our findings indicate a strong and inverse relationship between estimated CRF and incidence of AVR due to AVS. Higher estimated CRF was associated with lower mortality after surgery.
Surgery for ventricular tachycardia originating from the left ventricular summit
Authors: Nitta Takashi , Sakamoto Shun-ichiro , Murata Hiroshige , Suzuki Kenji , Yamada Naoki , Iwasaki Yuki , Ishii Yosuke 
Published: September 2023

Abstract

OBJECTIVES
Ventricular tachycardia (VT) originating from the left ventricular summit region, the most superior region of the left ventricle surrounded by the major coronary arteries and veins, is frequently refractory to pharmacological therapies and endocardial and epicardial catheter ablation.

METHODS
Eleven patients with an age from 31 to 79 (median 56) years old, underwent map-guided surgery for left ventricular summit VT. All patients had undergone 1–5 unsuccessful sessions of catheter ablation for incessant VT, preoperatively. Five patients had suffered VT storm and 1 had a history of cardiopulmonary resuscitation. Four patients had implanted with a defibrillator. Epicardium to endocardium transmural cryothermia was applied at the VT origin determined by intraoperative epicardial mapping with electro-anatomical mapping system. Harmonic scalpel was used to remove the epicardial fat and cryothermia was applied directly to the myocardium, avoiding thermal or mechanical injuries to the coronary vessels. Additional endocardial cryothermia at the VT origin was performed by a cryoprobe introduced into the left ventricular cavity through an aortotomy.

RESULTS
There was no surgical mortality or long-term mortality related to VT during a median follow-up period of 60 months (interquartile range: 34–82). Five-year freedom from preoperatively documented left ventricular summit VT and non-documented VT was 91% and 73%, respectively. All the patients with postoperative VT underwent successful catheter ablation. Other patients were free from VT during the follow-up period.

CONCLUSIONS
Epicardial to endocardial transmural cryothermia at the VT origin guided by intraoperative electro-anatomical mapping with a close collaboration with electrophysiologists was crucial in successful surgery for left ventricular summit VT.
Lack of association between fluoroquinolone and aortic aneurysm or dissection
Authors: Huh Kyungmin , Kang Minsun , Jung Jaehun 
Published: September 2023

Abstract

Background and Aims
An increased risk of aortic aneurysm and aortic dissection (AA/AD) has been reported with fluoroquinolone (FQ) use. However, recent studies suggested confounding factors by indication. This study aimed to investigate the risk of AA/AD associated with FQ use.

Methods
This nationwide population-based study included adults aged ≥20 years who received a prescription of oral FQ or third-generation cephalosporins (3GC) during outpatient visits from 2005 to 2016. Data source was the National Health Insurance Service reimbursement database. The primary outcome was hospitalization or in-hospital death with a primary diagnosis of AA/AD. A self-controlled case series (SCCS) and Cox proportional hazards model were used. Self-controlled case series compared the incidence of the primary outcome in the risk period vs. the control periods.

Results
A total of 954 308 patients (777 109 with FQ and 177 199 with 3GC use) were included. The incidence rate ratios for AA/AD between the risk period and the pre-risk period were higher in the 3GC group [11.000; 95% confidence interval (CI) 1.420–85.200] compared to the FQ group (2.000; 95% CI 0.970–4.124). The overall incidence of AA/AD among the patients who received FQ and 3GC was 5.40 and 8.47 per 100 000 person-years. There was no significant difference in the risk between the two groups (adjusted hazard ratio 0.752; 95% CI 0.515–1.100) in the inverse probability of treatment-weighted Cox proportional hazards model. Subgroup and sensitivity analysis showed consistent results.

Conclusions
There was no significant difference in the risk of AA/AD in patients who were administered oral FQ compared to those administered 3GC. The study findings suggest that the use of FQ should not be deterred when clinically indicated.
Genome streamlining and clonal erosion in nutrient-limited environments: a test using genome-size variable populations
Authors: Stelzer Claus-Peter , Pichler Maria , Stadler Peter 
Published: September 2023

Abstract
Some selection-based theories propose that genome streamlining, favoring smaller genome sizes, is advantageous in nutritionally limited environments, particularly under P-limitation. To test this prediction, we conducted several experimental evolution trials on clonal populations of a facultatively asexual rotifer that exhibits intraspecific variation in genome size. Most trials showed a rapid decline in clonal diversity, which was accelerated in populations that were initially nonadapted. Populations consisting of three rotifer clones often became monoclonal within a few weeks, while populations starting with 120 clones eroded to 10 multilocus genotypes, of which only five were abundant in higher numbers. While P-limitation affected population growth during the experiments, it did not affect the outcome of clonal competition or the speed at which clonal diversity was lost. Common garden transplant experiments revealed that the evolved populations were better adapted to the experimental conditions than the ancestral controls. However, contrary to expectations, the evolved populations did not show an overrepresentation of small genomes. Intermediate genomes were also frequently abundant, although very large genomes were rare. Our findings suggest that fitness is more influenced by genotypic differences among clones than by differences in GS, and indicate that such differences might hinder genome streamlining during early adaptation to a new environment.
Aspergillus SUMOylation mutants exhibit chromosome segregation defects including chromatin bridges
Authors: Zhang Jun , Qiu Rongde , Bieger Baronger D , Oakley C Elizabeth , Oakley Berl R , Egan Martin J , Xiang Xin 
Published: September 2023

Abstract
Functions of protein SUMOylation remain incompletely understood in different cell types. Via forward genetics, here we identified ubaBQ247*, a loss-of-function mutation in a SUMO activation enzyme UbaB in the filamentous fungus Aspergillus nidulans. The ubaBQ247*, ΔubaB, and ΔsumO mutants all produce abnormal chromatin bridges, indicating the importance of SUMOylation in the completion of chromosome segregation. The bridges are enclosed by nuclear membrane containing peripheral nuclear pore complex proteins that normally get dispersed during mitosis, and the bridges are also surrounded by cytoplasmic microtubules typical of interphase cells. Time-lapse sequences further indicate that most bridges persist through interphase prior to the next mitosis, and anaphase chromosome segregation can produce new bridges that persist into the next interphase. When the first mitosis happens at a higher temperature of 42°C, SUMOylation deficiency produces not only chromatin bridges but also many abnormally shaped single nuclei that fail to divide. UbaB-GFP localizes to interphase nuclei just like the previously studied SumO-GFP, but the nuclear signals disappear during mitosis when the nuclear pores are partially open, and the signals reappear after mitosis. The nuclear localization is consistent with many SUMO targets being nuclear proteins. Finally, although the budding yeast SUMOylation machinery interacts with LIS1, a protein critical for dynein activation, loss of SUMOylation does not cause any obvious defect in dynein-mediated transport of nuclei and early endosomes, indicating that SUMOylation is unnecessary for dynein activation in A. nidulans.
Living Longer But Frailer? Temporal Trends in Life Expectancy and Frailty in Older Swedish Adults
Authors: Tazzeo Clare , Rizzuto Debora , Calderón-Larrañaga Amaia , Dekhtyar Serhiy , Zucchelli Alberto , Xia Xin , Fratiglioni Laura , Vetrano Davide Liborio 
Published: September 2023

Abstract

Background
This study aims to examine temporal trends in frailty state transitions, and years spent frail, in older Swedish adults.

Methods
We followed the Swedish National Study on Aging and Care in Kungsholmen participants from baseline (2001–2004) for 15 (median: 9.6) years. A 40-deficit frailty index (FI) was constructed to identify 3 frailty states: robust (FI ≤ 0.125), mild frailty (0.125 &lt; FI ≤ 0.25), and moderate and severe frailty (FI  &gt; 0.25). Multistate survival analyses were implemented to obtain hazard ratios (HRs) for frailty state transitions, with birth year and sex as predictors. To examine temporal trends, frailty state-specific life expectancies at age 60 were forecasted for robust persons born in different years (1900, 1910, 1920, 1930, and 1940), also by sex.

Results
At baseline, the 2 941 participants’ mean age was 75 years and 65% were women. Predicted life expectancy and time spent frail from age 60 followed an increasing trend by birth year. Hazards of transitioning from mild frailty to death (HR: 0.89; 95% confidence interval [CI]: 0.83–0.97) and moderate and severe frailty to death (HR: 0.98; 95% CI: 0.97–1.00) were lower for those born later. Women were less likely to transition from robust to mild frailty (HR: 0.81; 95% CI: 0.70–0.93), mild frailty to moderate and severe frailty (HR: 0.80; 95% CI: 0.68–0.93), and moderate and severe frailty to death (HR: 0.68; 95% CI: 0.59–0.78), but spent more time frail.

Conclusions
Our results point to an expansion of time spent frail among older Swedish adults over time.
Workforce Participation and Mortality Risk Among Chinese Older Adults: A Nationwide Population-Based Prospective Study
Authors: Guo Yujia , Qian Dongfu 
Published: September 2023

Abstract

Objectives
This study examines the association between workforce participation and mortality among Chinese older adults.

Methods
6,138 participants aged 60 and older from the 2011 to 2018 China Health and Retirement Longitudinal Study were studied and 79.5% of the sample were rural Hukou. Cox proportional hazard models were used to estimate hazard ratios (HRs) for the associations of work status, work types, and changes in work status with all-cause mortality. Cox models with penalized splines were performed to explore the dose–response relationship for hours worked per week and mortality.

Results
37,235.3 person-years observed 1,165 deaths (19.0%). Working reduced the mortality risk in older adults by 41% compared with those who did not work (HR: 0.59, 95% confidence interval: 0.50–0.69). This effect was consistent across subgroups. The mortality risk was lowest among self-employed older adults, followed by nonagricultural employment and then agricultural work, with adjusted HRs of (0.38, 0.21–0.70), (0.58, 0.36–0.93), and (0.61, 0.51–0.72), respectively. The mortality risk decreased with increasing hours of work per week and appeared to reach a threshold of about 45 hr of work per week. Compared with the older adults who continuously did not work, those who started and kept working had 28% (0.72, 0.53–0.97) and 48% (0.52, 0.41–0.65) lower mortality risks, respectively. When older adults transitioned from working to not working, the mortality risk would no longer be significantly different from that of older adults who were continuously not working (0.86, 0.65–1.12, p = 0.3).

Discussion
Workforce participation was associated with survival benefits among older adults in China.
PbrChiA: a key chitinase of pear in response to Botryosphaeria dothidea infection by interacting with PbrLYK1b2 and down-regulating ROS accumulation
Authors: Chen Qiming , Dong Huizhen , Li Qionghou , Sun Xun , Qiao Xin , Yin Hao , Xie Zhihua , Qi Kaijie , Huang Xiaosan , Zhang Shaoling 
Published: September 2023

Abstract
Pear ring rot, caused by the pathogenic fungi Botryosphaeria dothidea, seriously affects pear production. While the infection-induced reactive oxygen species (ROS) burst of infected plants limits the proliferation of B. dothidea during the early infection stage, high ROS levels can also contribute to their growth during the later necrotrophic infection stage. Therefore, it is important to understand how plants balance ROS levels and resistance to pathogenic B. dothidea during the later stage. In this study, we identified PbrChiA, a glycosyl hydrolases 18 (GH18) chitinase-encoding gene with high infection-induced expression, through a comparative transcriptome analysis. Artificial substitution, stable overexpression, and virus induced gene silencing (VIGS) experiments demonstrated that PbrChiA can positively regulate pear resistance as a secreted chitinase to break down B. dothidea mycelium in vitro and that overexpression of PbrChiA suppressed infection-induced ROS accumulation. Further analysis revealed that PbrChiA can bind to the ectodomain of PbrLYK1b2, and this interaction suppressed PbrLYK1b2-mediated chitin-induced ROS accumulation. Collectively, we propose that the combination of higher antifungal activity from abundant PbrChiA and lower ROS levels during later necrotrophic infection stage confer resistance of pear against B. dothidea.
Hybrid neural-network FEM approximation of diffusion coefficient in elliptic and parabolic problems
Authors: Cen Siyu , Jin Bangti , Quan Qimeng , Zhou Zhi 
Published: September 2023

Abstract
In this work we investigate the numerical identification of the diffusion coefficient in elliptic and parabolic problems using neural networks (NNs). The numerical scheme is based on the standard output least-squares formulation where the Galerkin finite element method (FEM) is employed to approximate the state and NNs act as a smoothness prior to approximate the unknown diffusion coefficient. A projection operation is applied to the NN approximation in order to preserve the physical box constraint on the unknown coefficient. The hybrid approach enjoys both rigorous mathematical foundation of the FEM and inductive bias/approximation properties of NNs. We derive a priori error estimates in the standard $L^2(\varOmega )$ norm for the numerical reconstruction, under a positivity condition which can be verified for a large class of problem data. The error bounds depend explicitly on the noise level, regularization parameter and discretization parameters (e.g., spatial mesh size, time step size and depth, upper bound and number of nonzero parameters of NNs). We also provide extensive numerical experiments, indicating that the hybrid method is very robust for large noise when compared with the pure FEM approximation.
Gardnerella Vaginolysin Potentiates Glycan Molecular Mimicry by Neisseria gonorrhoeae
Authors: Morrill Sydney R , Saha Sudeshna , Varki Ajit P , Lewis Warren G , Ram Sanjay , Lewis Amanda L 
Published: September 2023

Abstract
Bacterial vaginosis (BV) is a dysbiotic condition of the vaginal microbiome associated with higher risk of infection by Neisseria gonorrhoeae—the cause of gonorrhea. Here we test if one known facet of BV—the presence of bacterial cytolysins—leads to mobilization of intracellular contents that enhance gonococcal virulence. We cloned and expressed recombinant vaginolysin (VLY), a cytolysin produced by the BV-associated bacterium Gardnerella, verifying that it liberates contents of cervical epithelial (HeLa) cells, while vector control preparations did not. We tested if VLY mediates a well-known gonococcal virulence mechanism—the molecular mimicry of host glycans. To evade host immunity, N. gonorrhoeae caps its lipooligosaccharide (LOS) with α2-3-linked sialic acid. For this, gonococci must scavenge a metabolite made inside host cells. Flow cytometry-based lectin-binding assays showed that gonococci exposed to vaginolysin-liberated contents of HeLa cells displayed greater sialic acid capping of their LOS. This higher level of bacterial sialylation was accompanied by increased binding of the complement regulatory protein factor H, and greater resistance to complement attack. Together these results suggest that cytolytic activities present during BV may enhance the ability of N. gonorrhoeae to capture intracellular metabolites and evade host immunity via glycan molecular mimicry.
Ebola Virus Uses Tunneling Nanotubes as an Alternate Route of Dissemination
Authors: Djurkovic Marija A , Leavitt Carson G , Arnett Eusondia , Kriachun Valeriia , Martínez-Sobrido Luis , Titone Rossella , Sherwood Laura J , Hayhurst Andrew , Schlesinger Larry S , Shtanko Olena 
Published: September 2023

Abstract
Ebola virus (EBOV) disease is marked by rapid virus replication and spread. EBOV enters the cell by macropinocytosis and replicates in the cytoplasm, and nascent virions egress from the cell surface to infect neighboring cells. Here, we show that EBOV uses an alternate route to disseminate: tunneling nanotubes (TNTs). TNTs, an actin-based long-range intercellular communication system, allows for direct exchange of cytosolic constituents between cells. Using live, scanning electron, and high-resolution quantitative 3-dimensional microscopy, we show that EBOV infection of primary human cells results in the enhanced formation of TNTs containing viral nucleocapsids. TNTs promote the intercellular transfer of nucleocapsids in the absence of live virus, and virus could replicate in cells devoid of entry factors after initial stall. Our studies suggest an alternate model of EBOV dissemination within the host, laying the groundwork for further investigations into the pathogenesis of filoviruses and, importantly, stimulating new areas of antiviral design.
Viral Interference During Influenza A–SARS-CoV-2 Coinfection of the Human Airway Epithelium and Reversal by Oseltamivir
Authors: Cheemarla Nagarjuna R , Watkins Timothy A , Mihaylova Valia T , Foxman Ellen F 
Published: September 2023

Abstract
To gain insight into interactions among respiratory viruses, we modeled influenza A virus (IAV)-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coinfections using differentiated human airway epithelial cultures. Replicating IAV induced a more robust interferon response than SARS-CoV-2 and suppressed SARS-CoV-2 replication in both sequential and simultaneous infections, whereas SARS-CoV-2 did not enhance host cell defense during influenza infection or suppress IAV replication. Oseltamivir, an antiviral targeting influenza, reduced IAV replication during coinfection but also reduced the host antiviral response and restored SARS-CoV-2 replication. These results demonstrate how perturbations in one viral infection can impact its effect on a coinfecting virus.