bluuebunny/crossref_metadata_2025_split huggingface dataset:
G‐U base‐paired hpRNA confers potent inhibition of small RNA function in plants
Authors: Zhong Chengcheng , Smith Neil A. , Zhang Daai , Gou Xiuhong , Greaves Ian K. , Millar Anthony A. , Walsh Tom K. , Shan Weixing , Wang Ming‐Bo 
Published: December 2023

SUMMARYMicroRNA (miRNA) target mimicry technologies, utilizing naturally occurring miRNA decoy molecules, represent a potent tool for analyzing miRNA function. In this study, we present a highly efficient small RNA (sRNA) target mimicry design based on G‐U base‐paired hairpin RNA (hpG:U), which allows for the simultaneous targeting of multiple sRNAs. The hpG:U constructs consistently generate high amounts of intact, polyadenylated stem‐loop (SL) RNA outside the nuclei, in contrast to traditional hairpin RNA designs with canonical base pairing (hpWT), which were predominantly processed resulting in a loop. By incorporating a 460‐bp G‐U base‐paired double‐stranded stem and a 312–576 nt loop carrying multiple miRNA target mimicry sites (GUMIC), the hpG:U construct displayed effective repression of three Arabidopsis miRNAs, namely miR165/166, miR157, and miR160, both individually and in combination. Additionally, a GUMIC construct targeting a prominent cluster of siRNAs derived from cucumber mosaic virus (CMV) Y‐satellite RNA (Y‐Sat) effectively inhibited Y‐Sat siRNA‐directed silencing of the chlorophyll biosynthetic gene CHLI, thereby reducing the yellowing symptoms in infected Nicotiana plants. Therefore, the G‐U base‐paired hpRNA, characterized by differential processing compared to traditional hpRNA, acts as an efficient decoy for both miRNAs and siRNAs. This technology holds great potential for sRNA functional analysis and the management of sRNA‐mediated diseases.
Determination of Nonstationary Stochastic Response of Linear Oscillators With Fractional Derivative Elements of Rational Order
Authors: Di Matteo Alberto , Spanos Pol D. 
Published: December 2023

Abstract
In this paper, a technique is developed for determining the nonstationary response statistics of linear oscillators endowed with fractional derivative elements. Notably, fractional operators are particularly effective in modeling solid mechanics problems as they offer the option of influencing both the elasticity and the energy dissipation capacity of the system. In this paper, particular attention is devoted to the case of fractional derivatives of rational order that approximates reasonably well any real order model. The oscillators are subjected to stationary stochastic excitations, and the pertinent nonstationary response statistical moments are determined by first introducing a finite number of oscillator response related states; this is afforded by the rational number order of the fractional operator. Next, the technique involves proceeding to treating the problem in the Laplace transform domain. This leads to multiple convolution integrals determined by representing the transfer function of the oscillator in a partial fraction form by a pole-residue formulation. In this manner, the response evolutionary power spectral density of the fractional oscillator is derived in a closed form, while nonstationary second-order statistics can be obtained by mundane numerical integration in the frequency domain. Applications to oscillators comprising one or two fractional derivative elements are presented, considering the case of a white noise excitation and of a random process possessing the classical Kanai–Tajimi spectrum. Reliability of the developed technique is assessed by juxtaposing its analytical results with pertinent Monte Carlo simulation data.
Synthesizing Negative-Imaginary Systems With Closed-Loop H∞-Performance Via Static Output Feedback Control
Authors: Behera Pravin , Dey Arnab , Patra Sourav 
Published: December 2023

Abstract
This paper develops an algorithm for synthesizing negative imaginary (NI) systems with a specified H∞-norm bound by exploiting the convex relaxation technique in the static output-feedback (SOF) control design framework. This scheme improves the robustness objective since the present framework can handle both NI and H∞-norm-bounded unstructured uncertainty of the system. The non-strict inequality involved in the NI system description that creates a major difficulty in the SOF control design, can efficiently be tackled by the developed convex relaxation-based iterative algorithm. The advantages of the algorithm are shown using several examples and the results are compared with the existing works.
Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing
Authors: Qin Yujia , Wu Liyou , Zhang Qiuting , Wen Chongqin , Van Nostrand Joy D. , Ning Daliang , Raskin Lutgarde , Pinto Ameet , Zhou Jizhong 
Published: December 2023

ABSTRACT
Targeted amplicon sequencing is widely used in microbial ecology studies. However, sequencing artifacts and amplification biases are of great concern. To identify sources of these artifacts, a systematic analysis was performed using mock communities comprised of 16S rRNA genes from 33 bacterial strains. Our results indicated that while sequencing errors were generally isolated to low-abundance operational taxonomic units, chimeric sequences were a major source of artifacts. Singleton and doubleton sequences were primarily chimeras. Formation of chimeric sequences was significantly correlated with the GC content of the targeted sequences. Low-GC-content mock community members exhibited lower rates of chimeric sequence formation. GC content also had a large impact on sequence recovery. The quantitative capacity was notably limited, with substantial recovery variations and weak correlation between anticipated and observed strain abundances. The mock community strains with higher GC content had higher recovery rates than strains with lower GC content. Amplification bias was also observed due to the differences in primer affinity. A two-step PCR strategy reduced the number of chimeric sequences by half. In addition, comparative analyses based on the mock communities showed that several widely used sequence processing pipelines/methods, including DADA2, Deblur, UCLUST, UNOISE, and UPARSE, had different advantages and disadvantages in artifact removal and rare species detection. These results are important for improving sequencing quality and reliability and developing new algorithms to process targeted amplicon sequences.

IMPORTANCE
Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.
Diverse domain architectures of CheA histidine kinase, a central component of bacterial and archaeal chemosensory systems
Authors: Berry Marissa A. , Andrianova Ekaterina P. , Zhulin Igor B. 
Published: December 2023

ABSTRACT

Chemosensory systems in bacteria and archaea are complex, multi-protein pathways that enable rapid cellular responses to environmental changes. The CheA histidine kinase is a central component of chemosensory systems. In contrast to other histidine kinases, it lacks a sensor (input) domain and utilizes dedicated chemoreceptors for sensing. CheA is a multi-domain protein; in model organisms as diverse as
Escherichia coli
and
Bacillus subtilis
, it contains five single-copy domains. Deviations from this canonical domain architecture have been reported, however, a broad genome-wide analysis of CheA diversity is lacking. Here, we present the results of a genomic survey of CheA domain composition carried out using an unbiased set of thousands of CheA sequences from bacteria and archaea. We found that four out of five canonical CheA domains comprise a minimal functional unit (core domains), as they are present in all surveyed CheA homologs. The most common deviations from a classical five-domain CheA architecture are the lack of a P2/CheY-binding domain, which is missing from more than half of CheA homologs, and the acquisition of a response regulator receiver (CheY-like) domain, which is present in ~35% of CheA homologs. We also document other deviations from classical CheA architecture, including bipartite CheA proteins, domain duplications, and fusions, and reveal that phylogenetically defined CheA classes have pre-dominant domain architectures. This study lays a foundation for a better classification of CheA homologs and identifies targets for experimental investigations.

IMPORTANCE

We found that in contrast to the best-studied model organisms, such as
Escherichia coli
and
Bacillus subtilis
, most bacterial and archaeal species have a CheA protein with a different domain composition. We report variations in CheA architecture, such as domain duplication and acquisition as well as class-specific domain composition. Our results will be of interest to those working on signal transduction in bacteria and archaea and lay the foundation for experimental studies.
Petrogenesis of the early Permian Hongliujing granite complex in the Chinese Eastern Tianshan orogen: Evidence for crustal growth in the Central Tianshan microcontinent
Authors: He Zhen-Yu , Klemd Reiner , Lu Tian-Yu , Yan Li-Li , Xiang Hua 
Published: December 2023

Abstract
The generation and modification of silicic magma systems are essential processes in resolving the differentiation of continental crust. This understanding motivated the geochronological and geochemical study of the early Permian Hongliujing granite complex, consisting of quartz monzonite, granite, and leucogranite in the Central Tianshan microcontinent of the southern Central Asian Orogenic Belt. Laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) zircon U-Pb dating of the Hongliujing complex rock units revealed almost identical ages (279 ± 2 Ma to 270 ± 2 Ma). The high-silica leucogranite and granite are characterized by positive Rb and negative Eu anomalies and Ba, Sr, P, and Ti depletions. The zircon trace elements are characterized by relatively low Ti and Th/U and high Yb/Gd. In contrast, the quartz monzonite and its mafic microgranular enclaves display minor negative Ba, Sr, P, Ti, and Eu anomalies, while the zircon trace elements are characterized by relatively high Ti and Th/U and low Yb/Gd. The complex has similar zircon Hf and whole-rock Nd isotopic compositions, with Hf and Nd model ages younger than 1.4 Ga, suggesting that their magmas were derived from an isotopically depleted mantle, with some contributions from crustal melts. The leucogranites further showed relatively large variations of εHf(t) and lower εNd(t) values, implying that their magma was affected by higher amounts of crustal contamination. We suggest that crystal-melt segregation was the major mechanism responsible for the evolution of the magmatic system, and that the early Permian magmatism represents a crust-forming episode triggered by slab rollback of the subducting South Tianshan oceanic plate beneath the eastern Central Tianshan microcontinent. Thus, our study reveals that microcontinents with Precambrian crustal basement were major sites of juvenile continental growth during the accretionary evolution of the Central Asian Orogenic Belt.
Incremental value of machine learning for risk prediction in tetralogy of Fallot
Authors: Ishikita Ayako , McIntosh Chris , Roche S Lucy , Barron David J , Oechslin Erwin , Benson Lee , Nair Krishnakumar , Lee Myunghyun M , Gritti Michael N , Hanneman Kate , Karur Gauri Rani , Wald Rachel M 
Published: December 2023

ObjectiveMachine learning (ML) can facilitate prediction of major adverse cardiovascular events (MACEs) in repaired tetralogy of Fallot (rTOF). We sought to determine the incremental value of ML above expert clinical judgement for risk prediction in rTOF.MethodsAdult congenital heart disease (ACHD) clinicians (≥10 years of experience) participated (one cardiac surgeon and four cardiologists (two paediatric and two adult cardiology trained) with expertise in heart failure (HF), electrophysiology, imaging and intervention). Clinicians identified 10 high-yield variables for 5-year MACE prediction (defined as a composite of mortality, resuscitated sudden death, sustained ventricular tachycardia and HF). Risk for MACE (low, moderate or high) was assigned by clinicians blinded to outcome for adults with rTOF identified from an institutional database (n=25 patient reviews conducted by five independent observers). A validated ML model identified 10 variables for risk prediction in the same population.ResultsPrediction by ML was similar to the aggregate score of all experts (area under the curve (AUC) 0.85 (95% CI 0.58 to 0.96) vs 0.92 (0.72 to 0.98), p=0.315). Experts with ≥20 years of experience had superior discriminative capacity compared with <20 years (AUC 0.98 (95% CI 0.86 to 0.99) vs 0.80 (0.56 to 0.93), p=0.027). In those with <20 years of experience, ML provided incremental value such that the combined (clinical+ML) AUC approached ≥20 years (AUC 0.85 (95% CI 0.61 to 0.95), p=0.055).ConclusionsRobust prediction of 5-year MACE in rTOF was achieved using either ML or a multidisciplinary team of ACHD experts. Risk prediction of some clinicians was enhanced by incorporation of ML suggesting that there may be incremental value for ML in select circumstances.
Prehospital risk assessment and direct transfer to a percutaneous coronary intervention centre in suspected acute coronary syndrome
Authors: Demandt Jesse , Koks Arjan , Sagel Dennis , van Hattem Veerle A E , Haest Rutger J , Heijmen Eric , Thijssen H , Otterspoor Luuk C , van Veghel Dennis , Eerdekens Rob , el Farissi Mohamed , Teeuwen Koen , Wijnbergen Inge , van der Harst Pim , Pijls Nico H J , van 't Veer Marcel , Tonino Pim A L , Dekker Lukas R C , Vlaar Pieter J 
Published: December 2023

ObjectivePrehospital risk stratification and triage are currently not performed in patients suspected of non-ST-segment elevation acute coronary syndrome (NSTE-ACS). This may lead to prolonged time to revascularisation, increased duration of hospital admission and higher healthcare costs. The preHEART score (prehospital history, ECG, age, risk factors and point-of-care troponin score) can be used by emergency medical services (EMS) personnel for prehospital risk stratification and triage decisions in patients with NSTE-ACS. The aim of the current study was to evaluate the effect of prehospital risk stratification and direct transfer to a percutaneous coronary intervention (PCI) centre, based on the preHEART score, on time to final invasive diagnostics or culprit revascularisation.MethodsProspective, multicentre, two-cohort study in patients with suspected NSTE-ACS. The first cohort is observational (standard care), while the second (interventional) cohort includes patients who are stratified for direct transfer to either a PCI or a non-PCI centre based on their preHEART score. Risk stratification and triage are performed by EMS personnel. The primary endpoint of the study is time from first medical contact until final invasive diagnostics or revascularisation. Secondary endpoints are time from first medical contact until intracoronary angiography (ICA), duration of hospital admission, number of invasive diagnostics, number of inter-hospital transfers and major adverse cardiac events at 7 and 30 days.ResultsA total of 1069 patients were included. In the interventional cohort (n=577), time between final invasive diagnostics or revascularisation (42 (17–101) hours vs 20 (5–44) hours, p<0.001) and length of hospital admission (3 (2–5) days vs 2 (1–4) days, p=0.007) were shorter than in the observational cohort (n=492). In patients with NSTE-ACS in need for ICA or revascularisation, healthcare costs were reduced in the interventional cohort (€5599 (2978–9625) vs €4899 (2278–5947), p=0.02).ConclusionPrehospital risk stratification and direct transfer to a PCI centre, based on the preHEART score, reduces time from first medical contact to final invasive diagnostics and revascularisation, reduces duration of hospital admission and decreases healthcare costs in patients with NSTE-ACS in need for ICA or revascularisation.Trial registrationNCT05243485.
Cardiovascular disease risk in patients with inflammatory arthritis nowadays still substantially elevated
Authors: Raadsen Reinder , Hansildaar Romy , Pouw Lianne C , Hooijberg Femke , Boekel Laura , Wolbink Gerrit Jan , van Kuijk Arno W R , Nurmohamed Michael T 
Published: December 2023

ObjectivesThis study aims to assess current cardiovascular disease risk and prevalence of risk factors in patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA) and axial spondyloarthritis (SpA).Methods2050 consecutive patients with inflammatory arthritis (IA) and 939 controls were included, with 1308 patients with RA, 356 patients with PsA and 386 patients with SpA. In a prospective cohort setting, questionnaires regarding previous cardiovascular events and risk factors were used to assess cardiovascular risk and prevalence in patients with IA by calculating ORs using logistic regression models.Results‘Traditional’ cardiovascular (CV) risk factors were significantly elevated in patients with IA compared with controls. Cardiovascular disease (CVD) ORs were increased in patients with RA and PsA compared with controls, 1.61 (95% CI: 1.04 to 2.48) and 2.12 (95% CI: 1.23 to 3.66), respectively, and a trend towards increased odds was observed in patients with SpA (OR 1.43; 95% CI: 0.79 to 2.59). After adjusting for traditional risk factors, CV risk was not increased in patients with RA (OR; 0.95, 95% CI: 0.58 to 1.55), PsA (OR 1.19; 95% CI: 0.64 to 2.22) and SpA (OR; 0.91, 95% CI: 0.47 to 1.77).ConclusionCVD is currently still more prevalent in patients with IA compared with healthy controls and, more importantly, this elevated risk is highly influenced by an increased prevalence of ‘traditional’ CV risk factors. More attention to, as well as improvements in, identification and treatment of ‘traditional’ risk factors, need to be made for not only RA, but other IA conditions as well.
Lifestyle factors predict gout outcomes: Results from the NOR-Gout longitudinal 2-year treat-to-target study
Authors: Uhlig Till , Karoliussen Lars Fridtjof , Sexton Joseph , Kvien Tore K , Haavardsholm Espen A , Hammer Hilde Berner 
Published: December 2023

ObjectiveGout is associated with lifestyle, body mass index (BMI) and comorbidities, including dyslipidaemia. We studied how in actively treated patients, anthropometric measures and lipid levels changed over 2 years and whether they predicted gout outcomes.MethodsPatients with a recent gout flare and elevated serum urate (sUA) received gout education and treat-to-target urate-lowering therapy over 1 year. Anthropometric measures with BMI, waist circumference (WC) and waist–height ratio (WHR) as well as lipid levels were measured yearly over 2 years. We examined whether baseline anthropometric measures and lipid levels were related to flares and to achieving the sUA target.ResultsAt baseline, patients (n=211) were with mean age of 56.4 years and 95% were male. Over 2 years, anthropometric measures were largely unchanged while cholesterol and low-density lipoprotein cholesterol (LDL-C) were reduced at year 1. Anthropometric measures were associated with presence of tophi. Higher baseline WC (OR: 0.96 per cm, 95% CI: 0.93 to 0.99) decreased and high level of high-density lipoprotein cholesterol (OR: 5.1 per mmol/L, 95% CI: 1.2 to 22.1) increased the chance of sUA target achievement at year 2. High LDL-C (OR: 1.8 per mmol/L, 95% CI: 1.2 to 2.6) predicted the chance of having a gout flare during year 2.ConclusionIn actively treated patients with gout, anthropometric measures were largely unchanged over 2 years and lipid levels were reduced. High WC and lipid levels predicted unfavourable gout outcomes after 2 years.
Symptom-related screening programme for early detection of chronic thromboembolic pulmonary hypertension after acute pulmonary embolism: the SYSPPE study
Authors: Marin-Romero Samira , Ballaz-Quincoces Aitor , Gómez-Cuervo Covadonga , Marchena-Yglesias Pablo Javier , Lopez-Miguel Patricia , Francisco-Albesa Iria , Pedrajas-Navas Jose Maria , Lumbierres Marina , Aibar-Arregui Miguel Angel , Bosco Lopez-Saez Juan , Perez-Pinar Montserrat , Baeza-Martinez Carlos , Riera-Mestre Antoni , Peris-Sifre Marisa , Porras-Ledantes Jose Antonio , Criado-Garcia Juan , Elias-Hernandez Teresa , Otero Remedios , Barca-Hernando Maria , Muriel Alfonso , Klok Frederikus A , Jara-Palomares Luis 
Published: December 2023

BackgroundChronic thromboembolic pulmonary hypertension (CTEPH) is the most severe long-term complication of acute pulmonary embolism (PE). We aimed to evaluate the impact of a symptom screening programme to detect CTEPH in PE survivors.MethodsThis was a multicentre cohort study of patients diagnosed with acute symptomatic PE between January 2017 and December 2018 in 16 centres in Spain. Patients were contacted by phone 2 years after the index PE diagnosis. Those with dyspnoea corresponding to a New York Heart Association (NYHA)/WHO scale≥II, visited the outpatient clinic for echocardiography and further diagnostic tests including right heart catheterisation (RHC). The primary outcome was the new diagnosis of CTEPH confirmed by RHC.ResultsOut of 1077 patients with acute PE, 646 were included in the symptom screening. At 2 years, 21.8% (n=141) reported dyspnoea NYHA/WHO scale≥II. Before symptom screening protocol, five patients were diagnosed with CTEPH following routine care. In patients with NYHA/WHO scale≥II, after symptom screening protocol, the echocardiographic probability of pulmonary hypertension (PH) was low, intermediate and high in 76.6% (n=95), 21.8% (n=27) and 1.6% (n=2), respectively. After performing additional diagnostic test in the latter 2 groups, 12 additional CTEPH cases were confirmed.ConclusionsThe implementation of this simple strategy based on symptom evaluation by phone diagnosed more than doubled the number of CTEPH cases. Dedicated follow-up algorithms for PE survivors help diagnosing CTEPH earlier.Trial registration numberNCT03953560.