bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation of quantitative light-induced fluorescence and qualitative visual rating in infiltrated post-orthodontic white spot lesions
Authors: Knaup Isabel , Kobbe Celine , Ehrlich Eva-Elaine , Esteves-Oliveira Marcella , Abou-Ayash Bedram , Meyer-Lueckel Hendrik , Wolf Michael , Wierichs Richard J 
Published: September 2022

SummaryObjectivesThe aim of this prospective, clinical single-centre study was to evaluate the masking efficacy of post-orthodontic resin infiltration after 12-month follow-up and correlate quantitative and qualitative outcome measures.MethodsPatients with completed fixed orthodontic treatment and the presence of one or more vestibular active non-cavitated white spot lesion/s (WSL) [ICDAS 1 or 2 (International Caries Detection and Assessment System)] were provided with resin infiltration 3–12 months after bracket removal. All patients (n = 31) participating before (t0) intervention were invited again and examined after 12 months (t2). Enamel demineralization was scored using quantitative light-induced fluorescence [QLF (DeltaF[flourescence], DeltaQ[lesion volume], White Spot Area)] and qualitative visual rating [11-point Likert-scale from 0 (no lesions visible on any tooth) to 10 (all teeth affected on the entire vestibular surface)].ResultsIn 17 patients (7 female and 10 male) 112 WSL (ICDAS 1: n = 1; ICDAS 2: n = 111) in 112 teeth were (re)examined. Before treatment (t0) a significant, weak (DeltaF), and moderate (DeltaQ, White Spot Area) correlation was observed between the quantitative and the qualitative rating (P &lt; 0.002) [median DeltaF: −7.31 (−10.4/−6.58)%; DeltaQ:−2.25 (−10.8/−0.41)% mm2; White Spot Area: 0.34 (0.05/1.16) mm2; visual rating:3.7 ± 1.2]. Resin infiltration led to significantly increased fluorescence and decreased visual scores (P &lt; 0.001) 7 days (t1) and 12 months (t2) after treatment. No significant changes based on DeltaF [−6.55 (−7.29/−6.08)%] and on visual ratings [1.0 ± 1.0] were observed between t1 and t2 (P = 1.000). After 7 days (t1) the correlation between the quantitative and the qualitative ratings remained significant, weak to moderate (P &lt; 0.002). After 12 months (t2) the correlation was (non-)significant and weak for DeltaF, DeltaQ, and White Spot Area (P ≤ 0.097).LimitationsSince the overall masking efficacy of resin infiltration has been shown previously, an untreated control group was omitted.ConclusionsWhen assessing the masking efficacy of infiltrated post-orthodontic WSL only a weak to moderate correlation was found between QLF values and visual ratings. Furthermore, over time this correlation decreased. Thus, it remains unclear if QLF is a viable method to assess and quantify infiltrated post-orthodontic WSL over time.Trial registrationGerman Clinical Trials Register (DRKS-ID:DRKS00005067).
Plaque histology and myocardial disease in sudden coronary death: the Fingesture study
Authors: Holmström Lauri , Juntunen Samuli , Vähätalo Juha , Pakanen Lasse , Kaikkonen Kari , Haukilahti Anette , Kenttä Tuomas , Tikkanen Jani , Viitasalo Ville , Perkiömäki Juha , Huikuri Heikki , Myerburg Robert J , Junttila Juhani 
Published: September 2022

AbstractAimsAt least 50% of deaths due to coronary artery disease (CAD) are sudden cardiac deaths (SCDs), but the role of acute plaque complications on the incidence of sudden death in CAD is somewhat unclear. The present study aimed to investigate plaque histology and concomitant myocardial disease in sudden coronary death.Methods and resultsThe study population is derived from the Fingesture study, which has collected data from 5869 consecutive autopsy-verified SCD victims in Northern Finland (population ≈600 000) between 1998 and 2017. In this substudy, histological examination of culprit lesions was performed in 600 SCD victims whose death was due to CAD. Determination of the cause of death was based on the combination of medical records, police reports, and autopsy data. Plaque histology was classified as either (i) plaque rupture or erosion, (ii) intraplaque haemorrhage, or (iii) stable plaque. The mean age of the study subjects was 64.9 ± 11.2 years, and 82% were male. Twenty-four per cent had plaque rupture or plaque erosion, 24% had an intraplaque haemorrhage, and 52% had a stable plaque. Myocardial hypertrophy was present in 78% and myocardial fibrosis in 93% of victims. The presence of myocardial hypertrophy or fibrosis was not associated with specific plaque histology.ConclusionLess than half of sudden deaths due to CAD had evidence of acute plaque complication, an observation which is contrary to historical perceptions. The prevalence of concomitant myocardial disease was high and independent of associated plaque morphology.
Highly efficient transgenesis with miniMos in Caenorhabditis briggsae
Authors: Ding Qiutao , Ren Xiaoliang , Li Runsheng , Chan Luyan , Ho Vincy W S , Bi Yu , Xie Dongying , Zhao Zhongying 
Published: September 2022

Abstract
Caenorhabditis briggsae as a companion species for Caenorhabditis elegans has played an increasingly important role in study of evolution of development and genome and gene regulation. Aided by the isolation of its sister spices, it has recently been established as a model for speciation study. To take full advantage of the species for comparative study, an effective transgenesis method especially those with single-copy insertion is important for functional comparison. Here, we improved a transposon-based transgenesis methodology that had been originally developed in C. elegans but worked marginally in C. briggsae. By incorporation of a heat shock step, the transgenesis efficiency in C. briggsae with a single-copy insertion is comparable to that in C. elegans. We used the method to generate 54 independent insertions mostly consisting of a mCherry tag over the C. briggsae genome. We demonstrated the use of the tags in identifying interacting loci responsible for hybrid male sterility between C. briggsae and Caenorhabditis nigoni when combined with the GFP tags we generated previously. Finally, we demonstrated that C. briggsae tolerates the C. elegans toxin, PEEL-1, but not SUP-35, making the latter a potential negative selection marker against extrachromosomal array.
A high-quality genome assembly of Lactarius hatsudake strain JH5
Authors: Shen Airong , Luo Chen , Tan Yun , Shen Baoming , Liu Lina , Li Jilie , Tan Zhuming , Zeng Liangbin 
Published: September 2022

Abstract
Lactarius hatsudake is a species of Lactarius commonly found in pine forests, is edible with a delicious and nutritious fruiting body, and exhibits medicinal properties. It is an ideal natural multifunctional food with bioactive components including fungal polysaccharides, crude fiber, unsaturated fatty acids, nucleic acid derivatives, various amino acids, and vitamins. However, biological and genomic analyses of this mycorrhizal mushroom are sparse, thereby hindering large-scale cultivation. Previously, we isolated and screened L. hatsudake JH5 strains and have applied our garnered knowledge to the large-scale cultivation of mycorrhizal seedlings. In this study, we produced a high-quality genome assembly of L. hatsudake JH5 by combining Illumina paired-end and PacBio single molecule real-time sequencing, resulting in PacBio single molecule real-time reads of 7.67 Gb and Illumina Pair-End reads of 1,560 Mb. Based on the distribution of k-mer frequencies, the genome size of this strain was estimated to be 63.84 Mb (1.14% heterozygosity). Based on de novo genome assembly, the final genome size was determined to be 76.7 Mb, with scaffold N50 of 223.2 kb and N90 of 54.5 kb, and a GC content of 54.38%. BUSCO assessment showed that genome completeness was 89.0%. The N50 length of the JH5 genome was 43.6% longer than that of the previously published L. hatsudake MG20 genome. This high-quality L. hatsudake genome assembly will facilitate research on the functional genome, molecular breeding, yield enhancement, and sustainability of L. hatsudake cultivation.
Development and validation of novel models for the prediction of intravenous corticosteroid resistance in acute severe ulcerative colitis using logistic regression and machine learning
Authors: Yu Si , Li Hui , Li Yue , Xu Hui , Tan Bei , Tian Bo-Wen , Dai Yi-Min , Tian Feng , Qian Jia-Ming 
Published: September 2022

Abstract

Background
The early prediction of intravenous corticosteroid (IVCS) resistance in acute severe ulcerative colitis (ASUC) patients remains an unresolved challenge. This study aims to construct and validate a model that accurately predicts IVCS resistance.

Methods
A retrospective cohort was established, with consecutive inclusion of patients who met the diagnosis criteria of ASUC and received IVCS during index hospitalization in Peking Union Medical College Hospital between March 2012 and January 2020. The primary outcome was IVCS resistance. Classification models, including logistic regression and machine learning-based models, were constructed. External validation was conducted in an independent cohort from Shengjing Hospital of China Medical University.

Results
A total of 129 patients were included in the derivation cohort. During index hospitalization, 102 (79.1%) patients responded to IVCS and 27 (20.9%) failed; 18 (14.0%) patients underwent colectomy in 3 months; 6 received cyclosporin as rescue therapy, and 2 eventually escalated to colectomy; 5 succeeded with infliximab as rescue therapy. The Ulcerative Colitis Endoscopic Index of Severity (UCEIS) and C-reactive protein (CRP) level at Day 3 are independent predictors of IVCS resistance. The areas under the receiver-operating characteristic curves (AUROCs) of the logistic regression, decision tree, random forest, and extreme-gradient boosting models were 0.873 (95% confidence interval [CI], 0.704–1.000), 0.648 (95% CI, 0.463–0.833), 0.650 (95% CI, 0.441–0.859), and 0.604 (95% CI, 0.416–0.792), respectively. The logistic regression model achieved the highest AUROC value of 0.703 (95% CI, 0.473–0.934) in the external validation.

Conclusions
In patients with ASUC, UCEIS and CRP levels at Day 3 of IVCS treatment appeared to allow the prompt prediction of likely IVCS resistance. We found no evidence of better performance of machine learning-based models in IVCS resistance prediction in ASUC. A nomogram based on the logistic regression model might aid in the management of ASUC patients.
Long-read Sequencing Data Reveals Dynamic Evolution of Mitochondrial Genome Size and the Phylogenetic Utility of Mitochondrial DNA in Hercules Beetles (Dynastes; Scarabaeidae)
Authors: Morgan Brett , Wang Tzi-Yuan , Chen Yi-Zhen , Moctezuma Victor , Burgos Oscar , Le My Hanh , Huang Jen-Pan 
Published: September 2022

Abstract
The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, remain poorly explored due to technological constraints. Using a combination of long- and short-read sequencing data, we assembled ten complete mitogenomes from ten Hercules beetles. We found large-sized mitogenomes (from 24 to 28 kb), which are among the largest in insects. The variation in genome size can be attributed to copy-number evolution of tandem repeats in the control region. Furthermore, one type of tandem repeat was found flanking the conserved sequence block in the control region. Importantly, such variation, which made up around 30% of the size of the mitogenome, may only become detectable should long-read sequencing technology be applied. We also found that, although different mitochondrial loci often inferred different phylogenetic histories, none of the mitochondrial loci statistically reject a concatenated mitochondrial phylogeny, supporting the hypothesis that all mitochondrial loci share a single genealogical history. We on the other hand reported statistical support for mito-nuclear phylogenetic discordance in 50% of mitochondrial loci. We argue that long-read DNA sequencing should become a standard application in the rapidly growing field of mitogenome sequencing. Furthermore, mitochondrial gene trees may differ even though they share a common genealogical history, and ND loci could be better candidates for phylogenetics than the commonly used COX1.
Examining the Effects of Hibernation on Germline Mutation Rates in Grizzly Bears
Authors: Wang Richard J , Peña-Garcia Yadira , Bibby Madeleine G , Raveendran Muthuswamy , Harris R Alan , Jansen Heiko T , Robbins Charles T , Rogers Jeffrey , Kelley Joanna L , Hahn Matthew W 
Published: September 2022

AbstractA male mutation bias is observed across vertebrates, and, where data are available, this bias is accompanied by increased per-generation mutation rates with parental age. While continuing mitotic cell division in the male germline post puberty has been proposed as the major cellular mechanism underlying both patterns, little direct evidence for this role has been found. Understanding the evolution of the per-generation mutation rate among species requires that we identify the molecular mechanisms that change between species. Here, we study the per-generation mutation rate in an extended pedigree of the brown (grizzly) bear, Ursus arctos horribilis. Brown bears hibernate for one-third of the year, a period during which spermatogenesis slows or stops altogether. The reduction of spermatogenesis is predicted to lessen the male mutation bias and to lower the per-generation mutation rate in this species. However, using whole-genome sequencing, we find that both male bias and per-generation mutation rates are highly similar to that expected for a non-hibernating species. We also carry out a phylogenetic comparison of substitution rates along the lineage leading to brown bear and panda (a non-hibernating species) and find no slowing of the substitution rate in the hibernator. Our results contribute to accumulating evidence that suggests that male germline cell division is not the major determinant of mutation rates and mutation biases. The results also provide a quantitative basis for improved estimates of the timing of carnivore evolution.
On the recursive equivalence to Smith form of multivariate polynomial matrices
Authors: Liu Jinwang , Li Dongmei 
Published: September 2022

Abstract
The Smith form of an $n$-$D$ polynomial matrix plays an important role in many areas of mathematics and engineering. In this paper, we investigate the recursive equivalence problem of $n$-dimensional polynomial matrices, i.e. if diag$(1,B)$ is equivalent to diag$(1,1,C)$, is B equivalent to diag$(1,C)$? We give a negative answer to this question by explicitly constructing a four-dimensional polynomial matrix which is not equivalent to its Smith form.
Drug efflux transporters in Staphylococcus pseudintermedius: in silico prediction and characterization of resistance
Authors: Rampacci Elisa , Felicetti Tommaso , Pietrella Donatella , Sabatini Stefano , Passamonti Fabrizio 
Published: September 2022

Abstract

Objectives
To perform an in silico prediction of drug efflux pumps (EPs) in Staphylococcus pseudintermedius and investigate their role in conferring resistance to antibiotic and biocidal agents and biofilm formation.

Methods
A S. pseudintermedius efflux mutant was obtained by stimulating an isogenic line (ATCC 49444) with increasing concentrations of an efflux system substrate. Changes in antimicrobial susceptibility and biofilm-forming capability were evaluated in the presence/absence of the EP inhibitors (EPIs) thioridazine and reserpine and the efflux activity was assayed by fluorometry. Homologues of EPs of Staphylococcus aureus and Staphylococcus epidermidis were searched by exploratory GenBank investigations. Gene expression analyses and sequencing were then conducted on selected genes.

Results
Susceptibility to chlorhexidine, gentamicin and ciprofloxacin, but not enrofloxacin, was affected by the increased efflux and it was variably restored by the EPIs. The efflux mutant showed much greater biofilm formation that the original strain, which was significantly inhibited by thioridazine and reserpine at MIC/2. A high expression of norA, which was mgrA-independent, was found in the S. pseudintermedius efflux mutant, apparently regulated by an 11 bp deletion in its promoter region, whilst lmrB was transitorily overexpressed. icaA, which encodes the polysaccharide intercellular adhesin forming the extracellular matrix of staphylococcal biofilm, was also up-regulated.

Conclusions
EPs, particularly NorA, are supposed to have complex involvement in multiple stages of resistance development. Overexpression of EPs appears to be correlated with a remarkable increase of S. pseudintermedius biofilm production; however, the regulatory mechanisms remain to be explored.
High frequency of increased triclosan MIC among CC5 MRSA and risk of misclassification of the SCCmec into types
Authors: Viana Alice Slotfeldt , Botelho Ana Maria Nunes , Feder Andries , Moustafa Ahmed Magdi , Santos Silva Deborah Nascimento , Martini Caroline Lopes , Ferreira Adriana Lucia Pires , Silva-Carvalho Maria Cícera , Ferreira-Carvalho Bernadete Teixeira , Planet Paul Joseph , Sá Figueiredo Agnes Marie 
Published: September 2022

Abstract

Background
Typing of staphylococcal cassette chromosome mec (SCCmec) elements is commonly used for studies on the molecular epidemiology of MRSA.

Objectives
To perform an investigation centred on uncovering the reasons for misclassification of MRSA clonal complex 5 (CC5) SCCmec type II clinical isolates in our laboratory.

Methods
MRSA isolates from CC5 were subjected to WGS and SCCmec typing.

Results
This investigation led to the discovery that the classification failure was due to an insertion of IS1272 carrying the fabI gene on a transposable element (TnSha1) that confers increased MIC to the biocide triclosan. Genomic analysis revealed that fabI was present in 25% of the CC5 MRSA isolates sampled. The frequency of TnSha1 in our collection was much higher than that observed among publicly available genomes (0.8%; n = 24/3142 CC5 genomes). Phylogenetic analyses revealed that genomes in different CC5 clades carry TnSha1 inserted in different integration sites, suggesting that this transposon has entered CC5 MRSA genomes on multiple occasions. In at least two genotypes, ST5-SCCmecII-t539 and ST5-SCCmecII-t2666, TnSha1 seems to have entered prior to their divergence.

Conclusions
Our work highlights an important misclassification problem of SCCmecII in isolates harbouring TnSha1 when Boye’s method is used for typing, which could have important implications for molecular epidemiology of MRSA. The importance of increased-MIC phenotype is still a matter of controversy that deserves more study given the widespread use of triclosan in many countries. Our results suggest expanding prevalence that may indicate strong selection for this phenotype.
MDR carbapenemase-producing Klebsiella pneumoniae of the hypervirulence-associated ST23 clone in Poland, 2009–19
Authors: Biedrzycka M , Izdebski R , Urbanowicz P , Polańska M , Hryniewicz W , Gniadkowski M , Literacka E 
Published: September 2022

Abstract

Objectives
To characterize carbapenemase-producing isolates of the Klebsiella pneumoniae hypervirulent (hvKp) clone ST23 in Poland.

Methods
Fifteen K. pneumoniae ST23 isolates were identified by the Polish surveillance of carbapenemase-producing Enterobacterales. These comprised a cluster with KPC-2 + NDM-1 (n = 7), KPC-2 (n = 1) or NDM-1 (n = 1) enzymes from one hospital from 2018, and sporadic isolates with KPC-2 (n = 1), NDM-1 (n = 1), VIM-1 (n = 1) or OXA-48 (n = 3), recovered from 2009 to 2019 in different towns. The isolates were sequenced by Illumina MiSeq, followed by MinION for six representatives. Clonality, phylogeny, serotypes, virulomes, resistomes and plasmids of the isolates were analysed and compared with international ST23 strains, using various bioinformatic tools.

Results
Only two diverse isolates with KPC-2 or VIM-1 were of typical hvKp ST23 serotypes K1 and O1v.2, and its predominant phylogenetic clade. These contained multiple chromosomal (ybt, clb) and pK2044/KpVP-1 plasmid (iuc, iro, rmpADC, rmpA2) virulence loci, whereas carbapenemase and other antimicrobial resistance (AMR) genes were on single additional plasmids. All remaining isolates were of K57 and O2v.2 serotypes, and a minor, distant clade of unclear phylogeny, including also ∼10 isolates from other European countries. These had fewer virulence loci (ybt, iuc, rmpADC, rmpA2) but abounded in plasmids, which with several chromosomal AMR mutations conferred more extensive MDR phenotypes than in K1 O1v.2. Lower clonal diversity than in K1, and numerous common characteristics of the isolates supported the hypothesis of the emerging character of the ST23 K57 clade.

Conclusions
A new MDR ST23 lineage has emerged in Europe, causing a potential threat to public health.
In vitro activity of sulopenem against 1880 bacterial pathogens isolated from Canadian patients with urinary tract infections (CANWARD, 2014–21)
Authors: Walkty Andrew J , Karlowsky James A , Baxter Melanie R , Lagace-Wiens Philippe R S , Adam Heather J , Zhanel George G 
Published: September 2022

Abstract

Introduction
There are limited oral antimicrobial options for the treatment of urinary infections caused by ESBL-producing and MDR Enterobacterales. Sulopenem is an investigational thiopenem antimicrobial that is being developed as both an oral and IV formulation. The purpose of this study was to evaluate the in vitro activity of sulopenem versus bacterial pathogens recovered from the urine of patients admitted to or assessed at hospitals across Canada (CANWARD).

Materials and methods
The in vitro activity of sulopenem and clinically relevant comparators was determined for 1880 Gram-negative and Gram-positive urinary isolates obtained as part of the CANWARD study (2014 to 2021) using the CLSI broth microdilution method.

Results
Sulopenem demonstrated excellent in vitro activity versus members of the Enterobacterales, with MIC90 values ranging from 0.06 to 0.5 mg/L for all species tested. Over 90% of ESBL-producing, AmpC-producing and MDR (not susceptible to ≥1 antimicrobial from ≥3 classes) Escherichia coli were inhibited by ≤0.25 mg/L of sulopenem. Sulopenem had an identical MIC90 to meropenem for ESBL-producing and MDR E. coli. The MIC90 of sulopenem and meropenem versus MSSA was 0.25 mg/L. Sulopenem was not active in vitro versus Pseudomonas aeruginosa (similar to ertapenem), and it demonstrated poor activity versus Enterococcus faecalis (similar to meropenem).

Conclusions
Sulopenem demonstrated excellent in vitro activity versus bacterial pathogens recovered from the urine of Canadian patients. These data suggest that sulopenem may have a role in the treatment of urinary infections caused by antimicrobial-resistant Enterobacterales, but additional clinical studies are required.
When International Commercial Arbitration meets China’s sanction laws: living together but remaining apart?
Authors: Zhang Beibei , Shen Wei 
Published: September 2022

Abstract
In the light of China’s newly installed sanction laws recently being considered by Chinese court in a judicial review procedure for an arbitral award, this article examines two aspects of these laws that have been largely overlooked by previous research: their private international law nature and the impact they have on the enforcement of foreign arbitral awards. In their function, the Chinese sanction laws should neither fulfil the role of rules established to utilize private persons to implement Chinese state policy, nor, in their application, contradict China’s claimed role in the international legal and political framework. Accordingly, two routes are offered as to how these laws should be applied: first, the legal restrains on private enforcement of the sanction laws should be made available; and secondly, China should ensure that its sanction laws do not compromise the New York Convention’s remit.