bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of salinity in recovery of white sturgeon (Acipenser transmontanus) from stimulated angling stress
Authors: Shartau Ryan B , Shu Jacelyn , Baker Daniel W 
Published: March 2023

AbstractWhite sturgeon (Acipenser transmontanus) in the Lower Fraser River are the focus of a catch-and-release angling fishery in British Columbia, Canada. However, the lower region of the catch area includes areas where tidal waters invade, and the consequence of salinity levels on recovery from an angling challenge are not characterized in sturgeon, despite theoretical implications of its import. We acclimated white sturgeon to various salinities (0, 10 and 20‰ (parts per thousand)) to investigate the effects of acclimation on recovery from stimulated angling stress that was induced through manual chasing. This challenge elicited the traditional physiological responses such as ion homeostasis disturbance, increases in secondary stress indicators and metabolic acidosis; however, environmental salinity altered the timing of recovery in some of the parameters measured. In addition, the severity of the intracellular pH disturbance in both heart and red blood cell seemed to be mediated in fresh water, yet the recovery pattern of plasma chloride and bicarbonate ions seemed to be facilitated by higher salinity. In general, responses were similar but not identical, leading us to conclude that the role of salinity on recovery from exercise is complex but not insignificant. Salinity may be important to behaviours exhibited by white sturgeon (such as migrations) in their respective saline environments, but less so around the impact of an angling stressor. Further exploration of this response may provide insight on whether the current tidal boundaries for angling white sturgeon are appropriate.
Periodontitis exacerbates atherosclerosis through Fusobacterium nucleatum-promoted hepatic glycolysis and lipogenesis
Authors: Zhou Lu-Jun , Lin Wen-Zhen , Meng Xiao-Qian , Zhu Hong , Liu Ting , Du Lin-Juan , Bai Xue-Bing , Chen Bo-Yan , Liu Yan , Xu Yuanzhi , Xie Yufeng , Shu Rong , Chen Fa-Ming , Zhu Ya-Qin , Duan Sheng-Zhong 
Published: March 2023

Abstract

Aims
Positive associations between periodontitis (PD) and atherosclerosis have been established, but the causality and mechanisms are not clear. We aimed to explore the causal roles of PD in atherosclerosis and dissect the underlying mechanisms.

Methods and results
A mouse model of PD was established by ligation of molars in combination with application of subgingival plaques collected from PD patients and then combined with atherosclerosis model induced by treating atheroprone mice with a high-cholesterol diet (HCD). PD significantly aggravated atherosclerosis in HCD-fed atheroprone mice, including increased en face plaque areas in whole aortas and lesion size at aortic roots. PD also increased circulating levels of triglycerides and cholesterol, hepatic levels of cholesterol, and hepatic expression of rate-limiting enzymes for lipogenesis. Using 16S ribosomal RNA (rRNA) gene sequencing, Fusobacterium nucleatum was identified as the most enriched PD-associated pathobiont that is present in both the oral cavity and livers. Co-culture experiments demonstrated that F. nucleatum directly stimulated lipid biosynthesis in primary mouse hepatocytes. Moreover, oral inoculation of F. nucleatum markedly elevated plasma levels of triglycerides and cholesterol and promoted atherogenesis in HCD-fed ApoE−/− mice. Results of RNA-seq and Seahorse assay indicated that F. nucleatum activated glycolysis, inhibition of which by 2-deoxyglucose in turn suppressed F. nucleatum-induced lipogenesis in hepatocytes. Finally, interrogation of the molecular mechanisms revealed that F. nucleatum-induced glycolysis and lipogenesis by activating PI3K/Akt/mTOR signalling pathway in hepatocytes.

Conclusions
PD exacerbates atherosclerosis and impairs lipid metabolism in mice, which may be mediated by F. nucleatum-promoted glycolysis and lipogenesis through PI3K/Akt/mTOR signalling in hepatocytes. Treatment of PD and specific targeting of F. nucleatum are promising strategies to improve therapeutic effectiveness of hyperlipidaemia and atherosclerosis.
In perspective: the patient at the heart of research in acute cardiovascular care
Authors: Thomson Ross J , Warren Alex , Pimento Steven , Fan Eddy , Proudfoot Alastair 
Published: March 2023

AbstractPatient and public involvement is a fundamental part of research design and is increasingly required by research funders and regulators. In addition to the moral and ethical arguments in its favour, it has the potential to improve the accessibility and transparency of research and to optimize study recruitment and retention. Whilst clinical trials in acute cardiovascular care have traditionally focussed on ‘hard’ outcomes, such as mortality or major adverse cardiovascular events, there is increasing recognition that these fail to capture the full breadth of patient experience. Patient-centred outcomes aim to measure things of greater value to patients, using validated tools to quantify symptoms, patient self-reports, or novel outcomes such as days alive and outside hospital. This In Perspective commentary explores the rationale behind patient and public involvement and the background to and evidence supporting the use of patient-centred outcomes and discusses potential challenges and how they can be mitigated.
Mid-regional pro-adrenomedullin and lactate levels for risk stratification in patients with out-of-hospital cardiac arrest
Authors: Zelniker Thomas A , Schwall Dominik , Hamidi Fardin , Steinbach Simone , Scheller Pascal , Spaich Sebastian , Michels Guido , Giannitsis Evangelos , Katus Hugo A , Frey Norbert , Preusch Michael R 
Published: March 2023

Abstract

Aims
Adrenomedullin (ADM) is a free-circulating peptide that regulates endothelial barrier function and vascular tone. Here, we sought to study the relationship of ADM in combination with lactate and the risk of death in patients with out-of-hospital cardiac arrest (OHCA).

Methods and results
Mid-regional pro-adrenomedullin (MR-proADM) and lactate concentrations were measured in patients with OHCA who survived at least 24 h after the return of spontaneous circulation. The outcome of interest was all-cause death. Patients were characterized by the quartiles (Q) of MR-proADM and lactate concentrations. Cox models were adjusted for age, sex, shockable rhythm, bystander resuscitation, simplified acute physiology score II (SAPS II), and estimated glomerular filtration rate (eGFR). A total of 232 patients were included in the present study (28% women, 67 years, SAPS II 80). The median MR-proADM and lactate levels at 24 h were 1.4 nmol/L [interquartile range (IQR) 0.8–2.8 nmol/L] and 1.8 mmol/L (IQR 1.3–3.4 mmol/L), respectively. Mid-regional pro-adrenomedullin concentrations correlated weakly with lactate levels (r = 0.36, P &lt; 0.001). High (Q4) vs. low (Q1–Q3) MR-proADM concentrations were significantly associated with an increased rate of death at 28 days (75.9 vs. 45.4%; P &lt; 0.001). After multivariable adjustment (including lactate levels at 24 h), higher MR-proADM levels were significantly associated with an increased risk of death [Q4 vs. Q1–Q3: adjusted hazard ratio (adj-HR) 1.67, 95% confidence interval (CI) 1.12–2.50; adj-HR for a 1-unit increase in a standardized biomarker 1.44, 95% CI 1.19–1.73]. This relationship remained significant even after further adjustment for baseline NT-proBNP and high-sensitivity troponin T levels. The combination of high MR-proADM and high lactate (Q4) concentrations identified patients at a particularly elevated risk (adj-HR 3.50; 95% CI 1.92–6.39).

Conclusion
Higher MR-proADM concentrations are associated with an increased risk of death in patients with OHCA, and the combination of high MR-proADM and lactate levels identifies patients at a distinctly elevated risk.
Postoperative myocardial fibrosis assessment in aortic valvular heart diseases—a cardiovascular magnetic resonance study
Authors: Pires Lucas T , Rosa Vitor E E , Morais Thamara C , Bello Juliana H S M , Fernandes Joao R C , de Santis Antonio , Lopes Mariana P , Gutierrez Paulo S , Rochitte Carlos E , Nomura Cesar H , Pomerantzeff Pablo M A , Sampaio Roney O , Tarasoutchi Flávio 
Published: March 2023

Abstract

Aims
Left ventricular remodelling occurs during the chronic course of aortic regurgitation (AR) and aortic stenosis (AS), leading to myocardial hypertrophy and fibrosis. Several studies have shown that extracellular volume fraction (ECV) and indexed extracellular volume (iECV) are important surrogate markers of diffuse myocardial fibrosis (MF). Postoperative data on these cardiovascular magnetic resonance (CMR) extracellular expansion parameters for either AS or AR are scarce. This study aimed to demonstrate the postoperative changes that occur in diffuse MF, and the influence of preoperative MF on the reversal of LV remodelling, in patients with AR or AS.

Methods and results
Patients with severe AR or AS and indications for surgery were prospectively enrolled. Patients underwent pre- and postoperative CMR, and ECV and iECV were quantified. Data from 99 patients were analysed (32 with AR and 67 with AS). After surgery, the left ventricle mass index decreased in both groups (AR: 110 vs. 91 g/m2; AS: 86 vs. 68 g/m2, both P &lt; 0.001). The late gadolinium enhancement fraction (AR: preoperative 1.9% vs. postoperative 1.7%, P = 0.575; AS: preoperative 2.4% vs. postoperative 2.4%, P = 0.615) and late gadolinium enhancement mass (AR: preoperative 3.8 g vs. postoperative 2.5 g, P = 0.635; AS: preoperative 3.4 g vs. postoperative 3.5 g, P = 0.575) remained stable in both groups. Preoperative iECV and ECV were greater in the AR group (iECV: 30 mL/m2 vs. 22 mL/m2, P = 0.001; ECV: 28.4% vs. 27.2%, P = 0.048). Indexed extracellular volume decreased after surgery in both groups (AR: 30–26.5 mL/m2, AS: 22–18.2 mL/m2, both P &lt; 0.001); it was still greater in the AR group (AR: 26.5 mL/m2 vs. AS: 18.2 mL/m2, P &lt; 0.001). Postoperative ECV remained stable in the AR group (preoperative 28.4% vs. postoperative 29.9%; P = 0.617) and increased in the AS group (preoperative 27.2% vs. postoperative 28.6%; P = 0.033).

Conclusion
Patients with both AR or AS presented reduction in iECV after surgery, unfolding the reversible nature of diffuse MF. In contrast to patients with AS, those with AR developed postoperative iECV regression with stable ECV, suggesting a balanced reduction in both intracellular and extracellular myocardial components.
Prediction of coronary artery disease using urinary proteomics
Authors: Wei Dongmei , Melgarejo Jesus D , Van Aelst Lucas , Vanassche Thomas , Verhamme Peter , Janssens Stefan , Peter Karlheinz , Zhang Zhen-Yu 
Published: March 2023

Abstract

Aims
Coronary artery disease (CAD) is multifactorial, caused by complex pathophysiology, and contributes to a high burden of mortality worldwide. Urinary proteomic analyses may help to identify predictive biomarkers and provide insights into the pathogenesis of CAD.

Methods and results
Urinary proteome was analysed in 965 participants using capillary electrophoresis coupled with mass spectrometry. A proteomic classifier was developed in a discovery cohort with 36 individuals with CAD and 36 matched controls using the support vector machine. The classifier was tested in a validation cohort with 115 individuals who progressed to CAD and 778 controls and compared with two previously developed CAD-associated classifiers, CAD238 and ACSP75. The Framingham and SCORE2 risk scores were available in 737 participants. Bioinformatic analysis was performed based on the CAD-associated peptides. The novel proteomic classifier was comprised of 160 urinary peptides, mainly related to collagen turnover, lipid metabolism, and inflammation. In the validation cohort, the classifier provided an area under the receiver operating characteristic curve (AUC) of 0.82 [95% confidence interval (CI): 0.78–0.87] for the CAD prediction in 8 years, superior to CAD238 (AUC: 0.71, 95% CI: 0.66–0.77) and ACSP75 (AUC: 0.53 and 95% CI: 0.47–0.60). On top of CAD238 and ACSP75, the addition of the novel classifier improved the AUC to 0.84 (95% CI: 0.80–0.89). In a multivariable Cox model, a 1-SD increment in the novel classifier was associated with a higher risk of CAD (HR: 1.54, 95% CI: 1.26–1.89, P &lt; 0.0001). The new classifier further improved the risk reclassification of CAD on top of the Framingham or SCORE2 risk scores (net reclassification index: 0.61, 95% CI: 0.25–0.95, P = 0.001; 0.64, 95% CI: 0.28–0.98, P = 0.001, correspondingly).

Conclusion
A novel urinary proteomic classifier related to collagen metabolism, lipids, and inflammation showed potential for the risk prediction of CAD. Urinary proteome provides an alternative approach to personalized prevention.
ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids
Authors: Sotcheff Stephanea , Zhou Yiyang , Yeung Jason , Sun Yan , Johnson John E , Torbett Bruce E , Routh Andrew L 
Published: March 2023

Abstract

Background
Genetic recombination is a tremendous source of intrahost diversity in viruses and is critical for their ability to rapidly adapt to new environments or fitness challenges. While viruses are routinely characterized using high-throughput sequencing techniques, characterizing the genetic products of recombination in next-generation sequencing data remains a challenge. Viral recombination events can be highly diverse and variable in nature, including simple duplications and deletions, or more complex events such as copy/snap-back recombination, intervirus or intersegment recombination, and insertions of host nucleic acids. Due to the variable mechanisms driving virus recombination and the different selection pressures acting on the progeny, recombination junctions rarely adhere to simple canonical sites or sequences. Furthermore, numerous different events may be present simultaneously in a viral population, yielding a complex mutational landscape.

Findings
We have previously developed an algorithm called ViReMa (Virus Recombination Mapper) that bootstraps the bowtie short-read aligner to capture and annotate a wide range of recombinant species found within virus populations. Here, we have updated ViReMa to provide an “error density” function designed to accurately detect recombination events in the longer reads now routinely generated by the Illumina platforms and provide output reports for multiple types of recombinant species using standardized formats. We demonstrate the utility and flexibility of ViReMa in different settings to report deletion events in simulated data from Flock House virus, copy-back RNA species in Sendai viruses, short duplication events in HIV, and virus-to-host recombination in an archaeal DNA virus.
Preparation of water-quenched manganese slag and fly ash ultrafine mineral admixture and its application in UHPC
Authors: Li Hang , Ming Yang , Li Ling , Chen Ping , Zhang Zhanqiang , Zhou Libo , Li Juntong , Yao Kai , Dun Linan 
Published: March 2023

Abstract
In this paper, S95 grade ultrafine mineral admixture (UMA) was prepared by water quenched manganese slag and fly ash 1:1 compound mechanical ball milling to a specific surface area of 714 m2/kg. Its activity index was 86.8% at 7d and 96.3% at 28d. The S95 UMA prepared by ball milling has the characteristics of small particle size, high specific surface and high activity. Mixing with powders of different particle sizes, such as cement and silica fume (SF), is helpful to improve particle gradation, reduce its pore structure and increase its compacting property for ultra-high performance concrete (UHPC) whose raw materials are fine aggregate. UHPC was prepared by using the obtained UMA based on orthogonal test. The effects of different factors on the workability, mechanical properties, hydration heat and microstructure of UHPC were studied. The results show that when the SF content is 10%, the mineral admixture content is 10%, the binder–sand ratio is 1.1, and the water–binder ratio is 0.17, the fluidity of UHPC slurry can reach 261 mm, the compressive strength of 7d and 28d age can reach 128 MPa and 154.6 MPa, respectively. The hydration heat release of cementitious materials in 3d was 139.8 J/g. In terms of solid waste resource utilization, S95 grade UMA prepared by water-quench manganese slag and fly ash can replace 10% SF for the preparation of UHPC. It can not only solve the utilization problem of high added value of water quench manganese slag but also reduce the preparation cost of UHPC to a certain extent.
Local Viterbi property in decoding
Authors: Lember Jüri 
Published: March 2023

Abstract
The article studies the decoding problem (also known as the classification or the segmentation problem) with pairwise Markov models (PMMs). A PMM is a process where the observation process and the underlying state sequence form a two-dimensional Markov chain, a natural generalization of hidden Markov model. The standard solutions to the decoding problem are the so-called Viterbi path—a sequence with maximum state path probability given the observations—or the pointwise maximum a posteriori (PMAP) path that maximizes the expected number of correctly classified entries. When the goal is to simultaneously maximize both criterions—conditional probability (corresponding to Viterbi path) and pointwise conditional probability (corresponding to PMAP path)—then they are combined into one single criterion via the regularization parameter $C$. The main objective of the article is to study the behaviour of the solution—called the hybrid path—as $C$ grows. Increasing $C$ increases the conditional probability of the hybrid path and when $C$ is big enough then every hybrid path is a Viterbi path. We show that hybrid paths also approach the Viterbi path locally: we define $m$-locally Viterbi paths and show that the hybrid path is $m$-locally Viterbi whenever $C$ is big enough. This all might lead to an impression that when $C$ is relatively big then any hybrid path that is not yet Viterbi differs from the Viterbi path by a few single entries only. We argue that this intuition is wrong, because when unique and $m$-locally Viterbi, then different hybrid paths differ by at least $m$ entries. Thus, when $C$ increases then the different hybrid paths tend to differ from each other by larger and larger intervals. Hence the hybrid paths might offer a variety of rather different solutions to the decoding problem.
Eco-efficiency considering NetZero and data envelopment analysis: a critical literature review
Authors: Emrouznejad Ali , Marra Marianna , Yang Guo-liang , Michali Maria 
Published: March 2023

Abstract
We highlight the state of the art in the eco-efficiency measurement using data envelopment analysis, including Malmquist–Luenberger productivity index. We also consider productivity change over time, provide directions for future studies in the field and gather the most recent policy suggestions for governments, organizations and sectors for reducing CO2 emissions. A structured literature search of the Web of Science academic database reveals 311 papers published between 1989 and 2022. We carry out network analysis of citations to show the evolution of the literature in this research topic. In doing so, we (a) examine the key-route main path of knowledge flows, (b) provide basic bibliometric information about the most active journals and authors, (c) conduct a qualitative in-depth analysis of the identified most important studies and (d) identify the research fronts and relate them to the emerging issues on the topic researched, focusing on the most recent period between 2000 and 2022. Based on the insights of the literature review, the second part of this paper critically analyses the papers on the key-route (main path) of this subject. This review can be used as guidance and a starting point for researchers and practitioners who want to further investigate optimal policies to reach NetZero.
Optimal Regularity for Elliptic Equations With Measurable Nonlinearities Under Nonstandard Growth
Authors: Byun Sun-Sig , Lee Ho-Sik 
Published: March 2023

Abstract
We are concerned with weak solutions of elliptic equations involving measurable nonlinearities with Orlicz growth to address what would be the weakest regularity condition on the associated nonlinearity for the Calderón–Zygmund theory. We prove that the gradient of weak solution is as integrable as the nonhomogeneous term under the assumption that the nonlinearity is only measurable in one of the variables while it has a small BMO assumption in the other variables. To this end, we develop a nonlinear Moser-type iteration argument for such a homogeneous reference problem with one variable–dependent nonlinearity under Orlicz growth to establish $W^{1,q}$–regularity for every $q&gt;1$. Our results open a new path into the comprehensive understanding of the problem with nonstandard growth in the literature of optimal regularity theory in highly nonlinear elliptic and parabolic equations.
SPIDR is required for homologous recombination during mammalian meiosis
Authors: Huang Tao , Wu Xinyue , Wang Shiyu , Bao Ziyou , Wan Yanling , Wang Ziqi , Li Mengjing , Yu Xiaochen , Lv Yue , Liu Zhaojian , Chen Xiangfeng , Chan Wai-Yee , Gao Fei , Lu Gang , Chen Zi-Jiang , Liu Hongbin 
Published: March 2023

Abstract
Meiotic recombinases RAD51 and DMC1 mediate strand exchange in the repair of DNA double-strand breaks (DSBs) by homologous recombination. This is a landmark event of meiosis that ensures genetic diversity in sexually reproducing organisms. However, the regulatory mechanism of DMC1/RAD51-ssDNA nucleoprotein filaments during homologous recombination in mammals has remained largely elusive. Here, we show that SPIDR (scaffold protein involved in DNA repair) regulates the assembly or stability of RAD51/DMC1 on ssDNA. Knockout of Spidr in male mice causes complete meiotic arrest, accompanied by defects in synapsis and crossover formation, which leads to male infertility. In females, loss of Spidr leads to subfertility; some Spidr−/− oocytes are able to complete meiosis. Notably, fertility is rescued partially by ablation of the DNA damage checkpoint kinase CHK2 in Spidr−/− females but not in males. Thus, our study identifies SPIDR as an essential meiotic recombination factor in homologous recombination in mammals.
Cavity hairpin ThT-light nucleic acid switches: the construction of label- and enzyme-free sensing and imaging platforms
Authors: Lan Xinyue , Zhu Longjiao , Zhang Yangzi , Chen Keren , Wang Jia , Du Zaihui , Li Shuting , Chen Xu , Xu Wentao 
Published: March 2023

Abstract
Thioflavin T (ThT) is a classical fluorescent dye gaining prominence in current research regarding nucleic acid conformations (NACs). However, most NACs with the ability to excite ThT fluorescent are unique or form in demanding conditions, limiting the extensiveness and depth of ThT application in sensing and imaging. Therefore, this study proposed CGG-AAA mismatched cavity hairpin ThT-light nucleic acid switches (CHTLNAS) with excellent fluorescence excitation over 500-fold higher than spontaneous, 17∼20-fold higher than ssDNA and 2.5∼5-fold higher than complementary duplex. Based on the excellent fluorescence excitation, convenient conformation formation, good sequence programmability, and flexible allosteric ability (known as the Worm-crack pod mechanism mediated by the target), it achieved the label- and enzyme-free detection of tetracycline (TET) and berberine (BB) at the pM level within 10 min. Moreover, it was found enable to realize the sensitive tracking of intracellular carriers at the nM level of ThT entry concentration, and prolongated its cell nuclear-entry time of ThT over 8 h, overcoming the non-specific high background signal interference of ThT in the nuclear region, and expanding the diversified application of ThT in cell biology research. Therefore, CHTLNAS is a more universal, practical tool than G-quadruplex or other kinds of NACs for ThT development and utilization in sensing and imaging platforms.