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The taxonomy of the Listeriaceae family has undergone substantial revisions, expanding the Listeria genus from 6 to 29 species since 2009. However, these classifications have relied on 16S rRNA gene sequences and conventional polyphasic taxonomy, with limited use of genomic approaches. This study aimed to employ genomic tools, including phylogenomics, Overall Genomic Relatedness Indices (OGRIs), and core-genome phylogenomic analyses, to reevaluate the taxonomy of the Listeriaceae family. The analyses involved the construction of phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and core genomes from 34 type strain genomes belonging to Listeriaceae family. OGRIs, which encompass Average Amino acid Identity (AAI), core-proteome AAI (cAAI), and Percentage of Conserved Proteins (POCP), were calculated, and specific threshold values of 70%, 87%, and 72–73% were established, respectively, to delimitate genera in the Listeriaceae family. These newly proposed OGRI thresholds unveiled distinct evolutionary lineages. The outcomes of this taxonomic re-evaluation were: (i): the division of the Listeria genus into an emended Listeria genus regrouping only Listeria senso stricto species; (ii): the remaining Listeria senso lato species were transferred into three newly proposed genera: Murraya gen. nov., Mesolisteria gen. nov., and Paenilisteria gen. nov. within Listeriaceae; (iii): Brochothrix was transferred to the newly proposed family Brochothricaceae fam. nov. within the Caryophanales order; (iiii): Listeria ivanovii subsp. londonensis was elevated to the species level as Listeria londonensis sp. nov.; and (iiiii): Murraya murrayi comb. nov. was reclassified as a later heterotypic synonym of Murraya grayi comb. nov. This taxonomic framework enables more precise identification of pathogenic Listeriaceae species, with significant implications for important areas such as food safety, clinical diagnostics, epidemiology, and public health. [ABSTRACT FROM AUTHOR]

City populations grow due to natural change, migration, and areas that are reclassified as part of a city. Because a time series of city boundaries was not available, most analyses ignore reclassification. This paper measures reclassification in a harmonized and transparent manner by applying a new harmonized definition of cities, towns, and rural areas, called the degree of urbanization, to gridded population data between 1980 and 2020. Ignoring reclassification would attribute city population growth equally to natural change and migration. Including the effects of reclassification reveals that two‐thirds of the growth is due to natural change, followed by reclassification (29 percent), and the remainder to migration (4 percent). This demonstrates the importance of accounting for reclassification. It also underlines that discouraging migration to cities will not significantly reduce city population growth. [ABSTRACT FROM AUTHOR]

Butirosins are naturally occurring aminoglycoside (AG) antibiotics featuring a 4,5-disubstituted 2-deoxystreptamine (2-DOS) with a (2S)-4-amino-2-hydroxybutyrate (AHBA) side chain. This side chain has been shown to confer resistance against AG-modifying enzymes, leading to ongoing studies on the butirosin biosynthetic pathway and the corresponding enzymes. Butirosin is produced by Niallia (formerly Bacillus) circulans and Bacillus vitellinus, with most research focused on the first strain. To date, no whole-genome analysis has been performed on B. vitellinus. In this study, we sequenced the complete genome of B. vitellinus NBRC 13296 and performed a comparative analysis of different butirosin biosyntheric gene clusters (BGCs), including those from N. circulans. The complete genome of B. vitellinus NBRC 13296 comprises a 6,331,192-base circular chromosome with GC content of 52.68%. The annotation revealed the presence of 5605 CDSs, 70 tRNA genes, 30 rRNA genes, and 3 ncRNA genes in NBRC 13296. The highest dDDH and ANI values between NBRC 13296 and the most closely related type strain, Paenibacillus chitinolyticus KCCM 41,400, were 97.8% and 98.66%, respectively. Based on these genome-based comparative analyses, we propose reclassifying B. vitellinus NBRC 13296 as P. chitinolyticus. Genome mining revealed 18 gene clusters encoding the biosynthesis of diverse secondary metabolites in the genome of B. vitellinus NBRC 13296, indicating the enormous biosynthetic potential of this strain. The predicted structural diversity of the secondary metabolites includes aminoglycosides, PKS, NRPS, PKS–NRPS hybrids, metallophores, phosphonates, terpenes, β-lactones, and RiPP peptides. We then comparatively characterized the butirosin BGCs previously studied in several N. circulans strains. Additionally, the comparative genome analysis revealed complete butirosin BGCs identified from P. chitinolyticus KCCM 41,400, P. chitinolyticus NRRL B-23119, P. chitinolyticus NRRL B-23120, P. chitinolyticus B-14908, P. chitinolyticus YSY-3.1, P. chitinolyticus JMW06, Paenibacillus sp. GbtcB18, Paenibacillus sp. HGH0039, and Paenibacillus sp. MZ04-78.2. Finally, we identified the core region consisting of BtrS, BtrN, BtrM, BtrL, BtrA, BtrB, BtrC, BtrD, BtrD, BtrE, BtrF, BtrG, BtrH, BtrI, BtrI, BtrJ, BtrK, BtrO, BtrP, and BtrV, followed by an upstream region organizing BtrQ, BtrW, BtrX, BtrY, and BtrZ in the same transcriptional direction and sequential genetic arrangement, and a downstream region organizing various proteins based on BtrT, BtrR2, BtrU, and BtrR1. Our study provides insights into the reclassification of B. vitellinus NBRC 13296 to P. chitinolyticus and suggests the need for continued studies on butirosin biosynthesis from an enzymatic perspective. [ABSTRACT FROM AUTHOR]

Antarctica is renowned as the most inhospitable environment where microorganisms are thriving in the frontiers of life. In the past few years, many novel bacterial species have been reported from the Antarctic environment. During taxonomic re-evaluation of novel bacterial species from Antarctica, it was noticed that Kocuria polaris shared high 16S rRNA gene sequence similarity with Kocuria rosea. In the present study, the taxonomic position, metabolic potentials, and stress survival strategy of K. polaris were evaluated through genome analysis. K. polaris encodes genes for glycolysis, citrate cycle, pentose phosphate pathway, dissimilatory nitrate reduction, assimilatory sulfate reduction, etc. In addition, K. polaris also encodes genes for cold and salt stress. The 16S rRNA gene sequence extracted from K. polaris and K. rosea genomes showed 99.7% similarity. In the phylogenomic tree, K. polaris and K. rosea clustered together. The average nucleotide identity and digital DNA-DNA hybridization values between K. polaris and K. rosea exceeded the threshold (95-96% for ANI and 70% for dDDH) value for distinguishing species, showing that they are similar species. The present study shed light on K. polaris survival strategy in extreme conditions. We further propose to reclassify Kocuria polaris as a later heterotypic synonym of Kocuria rosea. [ABSTRACT FROM AUTHOR]

Background: Indexed left ventricular end‐diastolic volume (LVEDVi) is a left ventricle (LV) size marker. The "Recommendations for Chamber Quantification" guideline was published in 2006 and updated in 2015. Although the previous guideline maintained uniform cutoff points for both men and women, the latest revision introduced new thresholds that vary between genders. We evaluated the extent of change in labeled indexed LV diastolic volumes in men and women following the adoption of the 2015 guideline. Methods: Data were extracted from a web‐based registry from March 2020 to October 2022. LV indexed volume variables were categorized on the basis of the 2006 and 2015 guidelines. Results: Among the 7598 individuals, the classification of LVEDVi differed in 910 (12.0%) individuals. In 213 (5.5%) female subjects, substantial reclassification (i.e., transitioning from normal to moderate LV enlargement to mild to severe LV enlargement) occurred on the basis of the 2015 guideline. All females classified as having moderately abnormal LVEDVi according to the 2006 guideline were reclassified as having severely abnormal LVEDVi according to the 2015 guideline. Age, LV ejection fraction (LVEF), and significant aortic regurgitation (AR) were common factors contributing to the observed discrepancy in both men and women. Significant mitral regurgitation (MR) and regional or global motion abnormality were correlated with the reclassification of LVEDVi to higher abnormal partitions only in women. Conclusion: The observed disparities underscore the importance of ongoing dedicated research to reassess the range of indexed echocardiographic parameters, considering various outcomes and differences in countries. [ABSTRACT FROM AUTHOR]

A tsunami is a sequence of powerful waves or surges primarily resulting from underwater earthquakes. Creating tsunami vulnerability maps is of utmost importance to develop effective strategies for mitigating potential damage caused by future tsunamis. This article focuses on areas (Indian subcontinent) severely affected by the 2004 Indian Ocean tsunami. Utilizing geographic information system (GIS)-based tools, the authors employed geospatial cell-based modeling and used a multicriteria decision-making tool, an analytical hierarchy process (AHP), to develop the final inundation map. Using the digital elevation model and Environmental Systems Research Institute (ESRI) land-cover data, the authors created the elevation, slope, coastal proximity, flow accumulation, and land-use land-cover (parameters) map. Areas with a higher risk of tsunami impact are predominantly situated along the coastline with a descending terrain. The presence of waterways and lower elevations intensifies the impact of tsunamis. Regions classified under very high or high vulnerability are more likely to be inundated by the tsunami. The final vulnerability map of Nagapattinam shows that 166.455 km2 of the region is highly vulnerable to a tsunami. Similarly, Kanyakumari, Cuddalore, Karaikal, and Chennai show 37.6516 km2 , 245.641 km2 , 35.7128 km2 , and 35.6306 km2 , respectively, under very high vulnerability. The findings of this study serve as fundamental information for disaster mitigation and urban planning in coastal regions. The research introduces a novel approach to assess areas susceptible to tsunami inundation, utilizing a vulnerability map generated through remote sensing and spatial multicriteria analysis. Furthermore, the parameters employed closely resemble those used in actual inundation mapping, adding to the practicality and reliability of the results. Village maps of the selected area are superimposed on the final vulnerability map to understand the villages vulnerable to tsunamis better. The final vulnerability maps can be used for strategic mitigation during an actual event and to be prepared for future disasters. [ABSTRACT FROM AUTHOR]

Abstract Introduction Variants of uncertain significance (VUS) are commonly reported in cancer with the widespread adoption of diagnostic massive parallel sequencing. The rate of reclassification of VUS in patients with haematological malignancy is not known and we evaluated this retrospectively. We also investigated whether re‐evaluating VUS in 12–24 months or greater than 24 months post‐initial classification was significant. Method A retrospective audit of patients with haematological malignancies referred to the Molecular Medicine Department at the John Hunter Hospital in Newcastle, Australia between September 2018 and December 2021. Data was analysed for VUS, which was then re‐analysed in standard software using current somatic variant guidelines. Proportions of VUS at baseline were compared to post‐re‐analysis. Results The most common diagnoses in the patient cohort (n = 944) were acute myelogenous leukaemia (41%), myelodysplastic syndrome (31%), and chronic myelomonocytic leukaemia (7%). A total of 210 VUS were re‐analysed. The most common VUS were in the TET2 (20%), RUNX1 (10%) and DNMT3A (9%) genes. A total of 103 were re‐analysed at 24–39 months post‐initial classification and 107 variants were re‐analysed between 12 and 24 months post‐initial classification. Of these, 33 (16%) of VUS were re‐classified at 24–39 months and 12 (11%) were re‐classified at 12–24 months post‐initial classification. The most common variants that were re‐classified in both groups were CSF3R (32%), TET2 (29%), ASXL1 (11%) and ZRSR2 (11%). Conclusion This study on reclassification of VUS in blood cancers demonstrated that one in seven VUS were re‐classified 12 months post initial classification. This can inform practice guidelines and potentially impact the prognosis, diagnosis and treatment of haematological malignancies.

Antarctica is renowned as the most inhospitable environment where microorganisms are thriving in the frontiers of life. In the past few years, many novel bacterial species have been reported from the Antarctic environment. During taxonomic re-evaluation of novel bacterial species from Antarctica, it was noticed that Kocuria polaris shared high 16S rRNA gene sequence similarity with Kocuria rosea. In the present study, the taxonomic position, metabolic potentials, and stress survival strategy of K. polaris were evaluated through genome analysis. K. polaris encodes genes for glycolysis, citrate cycle, pentose phosphate pathway, dissimilatory nitrate reduction, assimilatory sulfate reduction, etc. In addition, K. polaris also encodes genes for cold and salt stress. The 16S rRNA gene sequence extracted from K. polaris and K. rosea genomes showed 99.7% similarity. In the phylogenomic tree, K. polaris and K. rosea clustered together. The average nucleotide identity and digital DNA–DNA hybridization values between K. polaris and K. rosea exceeded the threshold (95-96% for ANI and 70% for dDDH) value for distinguishing species, showing that they are similar species. The present study shed light on K. polaris survival strategy in extreme conditions. We further propose to reclassify Kocuria polaris as a later heterotypic synonym of Kocuria rosea.

Butirosins are naturally occurring aminoglycoside (AG) antibiotics featuring a 4,5-disubstituted 2-deoxystreptamine (2-DOS) with a (2S)-4-amino-2-hydroxybutyrate (AHBA) side chain. This side chain has been shown to confer resistance against AG-modifying enzymes, leading to ongoing studies on the butirosin biosynthetic pathway and the corresponding enzymes. Butirosin is produced by Niallia (formerly Bacillus) circulans and Bacillus vitellinus, with most research focused on the first strain. To date, no whole-genome analysis has been performed on B. vitellinus. In this study, we sequenced the complete genome of B. vitellinus NBRC 13296 and performed a comparative analysis of different butirosin biosyntheric gene clusters (BGCs), including those from N. circulans. The complete genome of B. vitellinus NBRC 13296 comprises a 6,331,192-base circular chromosome with GC content of 52.68%. The annotation revealed the presence of 5605 CDSs, 70 tRNA genes, 30 rRNA genes, and 3 ncRNA genes in NBRC 13296. The highest dDDH and ANI values between NBRC 13296 and the most closely related type strain, Paenibacillus chitinolyticus KCCM 41,400, were 97.8% and 98.66%, respectively. Based on these genome-based comparative analyses, we propose reclassifying B. vitellinus NBRC 13296 as P. chitinolyticus. Genome mining revealed 18 gene clusters encoding the biosynthesis of diverse secondary metabolites in the genome of B. vitellinus NBRC 13296, indicating the enormous biosynthetic potential of this strain. The predicted structural diversity of the secondary metabolites includes aminoglycosides, PKS, NRPS, PKS–NRPS hybrids, metallophores, phosphonates, terpenes, β-lactones, and RiPP peptides. We then comparatively characterized the butirosin BGCs previously studied in several N. circulans strains. Additionally, the comparative genome analysis revealed complete butirosin BGCs identified from P. chitinolyticus KCCM 41,400, P. chitinolyticus NRRL B-23119, P. chitinolyticus NRRL B-23120, P. chitinolyticus B-14908, P. chitinolyticus YSY-3.1, P. chitinolyticus JMW06, Paenibacillus sp. GbtcB18, Paenibacillus sp. HGH0039, and Paenibacillus sp. MZ04-78.2. Finally, we identified the core region consisting of BtrS, BtrN, BtrM, BtrL, BtrA, BtrB, BtrC, BtrD, BtrD, BtrE, BtrF, BtrG, BtrH, BtrI, BtrI, BtrJ, BtrK, BtrO, BtrP, and BtrV, followed by an upstream region organizing BtrQ, BtrW, BtrX, BtrY, and BtrZ in the same transcriptional direction and sequential genetic arrangement, and a downstream region organizing various proteins based on BtrT, BtrR2, BtrU, and BtrR1. Our study provides insights into the reclassification of B. vitellinus NBRC 13296 to P. chitinolyticus and suggests the need for continued studies on butirosin biosynthesis from an enzymatic perspective.

The research subject is the application of geographic information systems (GIS) in assessing land suitability for agriculture in the Sana River Basin in Bosnia and Herzegovina. The aim of the research is to apply the analytic hierarchy process (AHP) in identifying suitable areas for agricultural production. Within the AHP framework, the following factors were considered: pedology, land use, elevation, slope, aridity index, and distance from rivers. The results of the suitability assessment underwent reclassification (RP) and cluster analysis processes (CAPs). It was found that very unsuitable land (1) covers an area of 0.15% (RP) or 5.83% (CAP), unsuitable land (2) covers 3.44% (RP) or 17.52% (CAP), conditionally suitable land (3) covers 32.11% or 28.47% (CAP), suitable land (4) covers 56.29% or 28.57% (CAP), and very suitable land (5) covers 7.98% (RP) or 19.59% (CAP). At the study area level, a supervised classification process was conducted to identify land use classes: meadows/pastures, water, forest, agricultural, and built-up areas. RP and CAP results were overlaid with supervised classification results to determine the amount of land used for agricultural purposes within each suitability class. It was determined that currently, for agricultural purposes, 0.04 km2 (RP) or 0.88 km2 (CAP) of very unsuitable land (1) is used, 0.41 km2 (RP) or 7.28 km2 (CAP) of unsuitable land (2), 15.75 km2 (RP) or 27.52 km2 (CAP) of conditionally suitable land (3), 185.15 km2 (RP) or 107.06 km2 (CAP) of suitable land (4), and 42.99 km2 (RP) or 101.65 km2 (CAP) of very suitable land (5). The research findings hold substantial importance in elucidating both the potential and constraints of land use practices as a vital natural resource within agriculture. They also have practical importance for relevant institutions in terms of agricultural sector development and making timely land use planning decisions for sustainable development.

Abstract Background Genetic diagnostics support the diagnosis of hereditary arrhythmogenic diseases, but variants of uncertain significance (VUS) complicate matters, emphasising the need for regular reassessment. Our study aims to reanalyse rare variants in different genes in order to decrease VUS diagnoses and thus improve risk stratification and personalized treatment for patients with arrhythmogenic disorders. Methods Genomic DNA was analysed using Sanger sequencing and next-generation sequencing (NGS). The Data was evaluated using various databases and in silico prediction tools and classified according to current ACMG standards by two independent experts. Results We identified 53 VUS in 30 genes, of which 17 variants (32%) were reclassified. 13% each were downgraded to likely benign (LB) and benign (B) and 6% were upgraded to likely pathogenic (LP). Reclassifications mainly occurred among variants initially classified in 2017–2019, with rates ranging from 50 to 60%. Conclusion The results support the assumption that regular reclassification of VUS is important, as it provides new insights for genetic diagnostics, that benefit patients and guide therapeutic approach.

Background: Genetic diagnostics support the diagnosis of hereditary arrhythmogenic diseases, but variants of uncertain significance (VUS) complicate matters, emphasising the need for regular reassessment. Our study aims to reanalyse rare variants in different genes in order to decrease VUS diagnoses and thus improve risk stratification and personalized treatment for patients with arrhythmogenic disorders. Methods: Genomic DNA was analysed using Sanger sequencing and next-generation sequencing (NGS). The Data was evaluated using various databases and in silico prediction tools and classified according to current ACMG standards by two independent experts. Results: We identified 53 VUS in 30 genes, of which 17 variants (32%) were reclassified. 13% each were downgraded to likely benign (LB) and benign (B) and 6% were upgraded to likely pathogenic (LP). Reclassifications mainly occurred among variants initially classified in 2017–2019, with rates ranging from 50 to 60%. Conclusion: The results support the assumption that regular reclassification of VUS is important, as it provides new insights for genetic diagnostics, that benefit patients and guide therapeutic approach. [ABSTRACT FROM AUTHOR]

A significant amount of European basic and clinical neuroscience research includes the use of transcranial magnetic stimulation (TMS) and low intensity transcranial electrical stimulation (tES), mainly transcranial direct current stimulation (tDCS). Two recent changes in the EU regulations, the introduction of the Medical Device Regulation (MDR) (2017/745) and the Annex XVI have caused significant problems and confusions in the brain stimulation field. The negative consequences of the MDR for non-invasive brain stimulation (NIBS) have been largely overlooked and until today, have not been consequently addressed by National Competent Authorities, local ethical committees, politicians and by the scientific communities. In addition, a rushed bureaucratic decision led to seemingly wrong classification of NIBS products without an intended medical purpose into the same risk group III as invasive stimulators. Overregulation is detrimental for any research and for future developments, therefore researchers, clinicians, industry, patient representatives and an ethicist were invited to contribute to this document with the aim of starting a constructive dialogue and enacting positive changes in the regulatory environment. [ABSTRACT FROM AUTHOR]

Genetic testing in the inherited arrhythmia clinic informs risk stratification, clinical management, and family screening. Periodic review of variant classification is recommended as supporting evidence accrues over time. However, there is limited reporting of real-world data on the frequency and impact of variant reclassification. The purpose of this study was to determine the burden of variant reclassification in our inherited arrhythmia clinic and the impact on clinical management. Genetic testing reports for patients referred to our clinic from 2004–2020 were reviewed. Reported variants were reinvestigated using ClinVar, VarSome, and a literature review. Classification was updated using the American College of Medical Genetics and Genomics (ACMG) criteria and tested for association with arrhythmic events and modification of medical management. We identified 517 patients (median age 37 years) who underwent gene panel testing. A variant of uncertain significance (VUS) was reported for 94 patients (18.2%) and more commonly identified when using large gene panels (P <.001). A total of 28 of 87 unique VUSs (32.2%) were reclassified to pathogenic/likely pathogenic (n = 11) or benign/likely benign (n = 17). Of 138 originally reported pathogenic variants, 7 (5.1%) lacked support using ACMG criteria. Variant reclassification was not associated with arrhythmic events; however, it did impact genotype-specific counseling and future therapeutic options. In our large real-world patient cohort, we identify a clinically important proportion of both pathogenic variants and VUSs with evidence for reclassification. These findings highlight the need for informed pretest counseling, a regular structured review of variants reported in genetic testing, and the potential benefits to patients for supporting genotype-guided therapy. [ABSTRACT FROM AUTHOR]

Objectives: To report oncological outcomes of active surveillance (AS) at a single non‐academic institution adopting the standardised Prostate Cancer Research International Active Surveillance (PRIAS) protocol. Patients and Methods: Competing risk analyses estimated the incidence of overall mortality, metastases, conversion to treatment, and grade reclassification. The incidence of reclassification and adverse pathological findings at radical prostatectomy were compared between patients fulfilling all PRIAS inclusion criteria vs those not fulfilling at least one. Results: We analysed 341 men with Grade Group 1 prostate cancer (PCa) followed on AS between 2010 and 2022. There were no PCa deaths, two patients developed distant metastases and were alive at the end of the study period. The 10‐year cumulative incidence of metastases was 1.9% (95% confidence interval [CI] 0.33–6.4%). A total of 111 men were reclassified, and 127 underwent definitive treatment. Men not fulfilling at least one PRIAS inclusion criteria (n = 43) had a higher incidence of reclassification (subdistribution hazards ratio 1.73, 95% CI 1.07–2.81; P = 0.03), but similar rates of adverse pathological findings at radical prostatectomy. Conclusion: Metastases in men on AS at a non‐academic institution are as rare as those reported in established international cohorts. Men followed without stringent inclusion criteria should be counselled about the higher incidence of reclassification and reassured they can expect rates of adverse pathological findings comparable to those fulfilling all criteria. Therefore, AS should be proposed to all men with low‐grade PCa regardless of whether they are followed at academic institutions or smaller community hospitals. [ABSTRACT FROM AUTHOR]

Abstract Backgroud The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. Results The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40–80.91% and 83.98–86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. Conclusion The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.

Backgroud: The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. Results: The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40–80.91% and 83.98–86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. Conclusion: The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex. [ABSTRACT FROM AUTHOR]

This paper introduces a novel procedure that can increase the signal-to-noise ratio in psychological experiments that use accuracy as a selection variable for another dependent variable. This procedure relies on the fact that some correct responses result from guesses and reclassifies them as incorrect responses using a trial-by-trial reclassification evidence such as response time. It selects the optimal reclassification evidence criterion beyond which correct responses should be reclassified as incorrect responses. We show that the more difficult the task and the fewer the response alternatives, the more to be gained from this reclassification procedure. We illustrate the procedure on behavioral and ERP data from two different datasets (Caplette et al. NeuroImage 218, 116994, 2020; Faghel-Soubeyrand et al. Journal of Experimental Psychology: General 148, 1834–1841, 2019) using response time as reclassification evidence. In both cases, the reclassification procedure increased signal-to-noise ratio by more than 13%. Matlab and Python implementations of the reclassification procedure are openly available (https://github.com/GroupeLaboGosselin/Reclassification). [ABSTRACT FROM AUTHOR]

This article investigates the syntax of sluicing in Mandarin Chinese, including the syntactic constraints on predicates that might appear in sluicing, the reclassification of wh-phrases, the syntactic status of shi 'be' and you 'have,' and the syntactic derivation of typical sluicing and pseudo-sluicing. This article argues that there are both pseudo-sluicing and typical sluicing in Chinese, with each involving different structures and derivations and requiring different analysis. [ABSTRACT FROM AUTHOR]

The purple sulfur bacterium Thiocapsa roseopersicina BBS is interesting from both fundamental and practical points of view. It possesses a thermostable HydSL hydrogenase, which is involved in the reaction of reversible hydrogen activation and a unique reaction of sulfur reduction to hydrogen sulfide. It is a very promising enzyme for enzymatic hydrogenase electrodes. There are speculations that HydSL hydrogenase of purple bacteria is closely related to sulfur metabolism, but confirmation is required. For that, the full genome sequence is necessary. Here, we sequenced and assembled the complete genome of this bacterium. The analysis of the obtained whole genome, through an integrative approach that comprised estimating the Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (DDH) parameters, allowed for validation of the systematic position of T. roseopersicina as T. bogorovii BBS. For the first time, we have assembled the whole genome of this typical strain of a new bacterial species and carried out its functional description against another purple sulfur bacterium: Allochromatium vinosum DSM 180T. We refined the automatic annotation of the whole genome of the bacteria T. bogorovii BBS and localized the genomic positions of several studied genes, including those involved in sulfur metabolism and genes encoding the enzymes required for the TCA and glyoxylate cycles and other central metabolic pathways. Eleven additional genes coding proteins involved in pigment biosynthesis was found. [ABSTRACT FROM AUTHOR]

Objective: In 2016 a group of expert endocrine pathologists proposed a new terminology, NIFTP (Non-invasive follicular thyroid neoplasm with papillary-like nuclear features) for a histological subtype of thyroid carcinoma (encapsulated follicular variant of papillary thyroid carcinoma, non-invasive type). In this study, we aimed to assess on a retrospective basis the epidemiological trend and overall incidence of NIFTP in Mureș county, Romania, over a six-year period (2016-2021).

Introduction: The proposed evolutionary origins and corresponding nomenclature of bilaterian gonadotropin-releasing hormone (GnRH)-related neuropeptides have changed tremendously with the aid of receptor deorphanization. However, the reclassification of the GnRH and corazonin (CRZ) signaling systems in Lophotrochozoa remains unclear. Methods: We characterized GnRH and CRZ receptors in the mollusk Pacific abalone, Haliotis discus hannai (Hdh), by phylogenetic and gene expression analyses, bioluminescence-based reporter, Western blotting, substitution of peptide amino acids, in vivo neuropeptide injection, and RNA interference assays. Results: Two Hdh CRZ-like receptors (Hdh-CRZR-A and Hdh-CRZR-B) and three Hdh GnRH-like receptors (Hdh-GnRHR1-A, Hdh-GnRHR1-B, and Hdh-GnRHR2) were identified. In phylogenetic analysis, Hdh-CRZR-A and -B grouped within the CRZ-type receptors, whereas Hdh-GnRHR1-A/-B and Hdh-GnRHR2 clustered within the GnRH/adipokinetic hormone (AKH)/CRZ-related peptide-type receptors. Hdh-CRZR-A/-B and Hdh-GnRHR1-A were activated by Hdh-CRZ (pQNYHFSNGWHA-NH2) and Hdh-GnRH (pQISFSPNWGT-NH2), respectively. Hdh-CRZR-A/-B dually coupled with the Gαq and Gαs signaling pathways, whereas Hdh-GnRHR1-A was linked only with Gαq signaling. Analysis of substituted peptides, [I2S3]Hdh-CRZ and [N2Y3H4]Hdh-GnRH, and in silico docking models revealed that the N-terminal amino acids of the peptides are critical for the selectivity of Hdh-CRZR and Hdh-GnRHR. Two precursor transcripts for Hdh-CRZ and Hdh-GnRH peptides and their receptors were mainly expressed in the neural ganglia, and their levels increased in starved abalones. Injection of Hdh-CRZ peptide into abalones decreased food consumption, whereas Hdh-CRZR knockdown increased food consumption. Moreover, Hdh-CRZ induced germinal vesicle breakdown in mature oocytes. Conclusion: Characterization of Hdh-CRZRs and Hdh-GnRHRs and their cognate peptides provides new insight into the evolutionary route of GnRH-related signaling systems in bilaterians. [ABSTRACT FROM AUTHOR]

Oral contraceptives are among the most commonly used contraceptive methods. However, Italian women underused reliable hormonal contraceptives as compared with other European women. There is a need to streamline access to oral contraception, with expected benefits on emotional well-being of women and potential savings for health system in Italy. Indeed, women can only access to oral contraceptives through mandatory medical prescription. This is one of the most important barrier experienced by women. We hereby provide an expert opinion on the potential reclassification, extending pharmacy services to include responsible and appropriate use of POP, as an opportunity also in Italy to increase the use of safe and effective contraceptive methods. [ABSTRACT FROM AUTHOR]

The present study used genome-based approaches to investigate the taxonomic relationship between Kitasatospora cineracea DSM 44780T and Kitasatospora niigatensis DSM 44781T, two species that were previously described by Tajima et al. (Int J Syst Evol Microbiol 51:1765–1771, 2001). The digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI), and average nucleotide identity (ANI) values between the genomes of the two type strains were 90.3, 98.7, and 99.1%, respectively. These values exceeded the established thresholds of 70% (dDDH) and 95–96% (ANI and AAI) for bacterial species delineation, suggesting that K. cineracea and K. niigatensis should share the same taxonomic position. Furthermore, our analysis using the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and the Maximum Likelihood core-genes tree inferred using FastTree2 consistently demonstrated that K. cineracea DSM 44780T and K. niigatensis DSM 44781T are closely related, as indicated by the clustering of these strains in the core-genes phylogenomic tree. Based on these findings, we propose that K. niigatensis should be considered a later heterotypic synonym of K. cineracea. [ABSTRACT FROM AUTHOR]

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Background: Stable coronary artery disease (CAD) presents with intermediate lesions that complicate treatment decisions. Visual assessment of coronary angiography may not accurately reflect the hemodynamic significance of these lesions. Instantaneous Wave- Free Ratio (IFR) is a new physiological index providing objective information on lesion functional significance. This study aimed to detect magnitude and direction of reclassification of intermediate lesions treatment after hemodynamic assessment by IFR in patients with stable CAD. Methods: This prospective observational study was carried out on 50 patients with stable coronary artery disease admitted to a single center. Patient received coronary angiography for a consultant's visual evaluation in order to identify the first treatment protocol. Hemodynamic assessment using IFR was performed for intermediate lesions to reclassify the treatment strategy. Results: The mean age of the patients was 64.2 ± 12.11 years, with 76% males and 24% females. The majority of patients had hypertension (74%), followed by diabetes mellitus (46%), hyperlipidemia (64%), smoking history (62%), and chronic kidney disease (22%). Based on the IFR assessment, 80% of patients were reclassified to receive medical treatment, while 20% underwent PCI. Conclusion: Our study results show that IFR is a reliable and accurate tool for guiding revascularization decisions in CAD patients. The majority of patients in our study, 80%, were safely reclassified to medical treatment based on IFR results. In the remaining 20% of patients, IFR results showed significant lesions that required PCI. [ABSTRACT FROM AUTHOR]

Xaa-Pro dipeptidase (XPD, EC 3.4.13.9; also known as prolidase) catalyzes the hydrolysis of the iminopeptide bond in the trans-Xaa-Pro dipeptides (Xaa represents any amino acid except proline), which makes it find wide applications in food, medical and environmental protection fields. In the present study, a novel Xaa-Pro dipeptidase from Aspergillus phoenicis ATCC 14332 (ApXPD) was heterologously expressed and biochemically characterized. Reclassification based on phylogenetic analysis and the version 12.5 MEROPS database showed that this enzyme was the only fungal XPD in the unassigned subfamily that shared the highest sequence identity with Xanthomonas campestris prolidase but not with that from the more related fungal species A. niudulans. As compared with other prolidases, ApXPD also contained a long N-terminal tail (residues 1–63) and an additional region (PAPARLREKL) and used a different arginine residue for dipeptide selectivity. After heterologous expression and partial purification, recombinant ApXPD was highly active and stable over the alkaline range from 8.5 to 10.0, with maximum activity at pH 9.0 and more than 80% activity retained after 1 h incubation at pHs of 8.5–10.0 (55 °C). It also had an apparent optimum temperature of 55 °C and remained stable at 20–30 °C. Moreover, this enzyme was a cobalt-dependent prolidase that only cleaved dipeptides Lys-Pro, Gly-Pro, and Ala-Pro rather than other dipeptides, tripeptides, and tetrapeptides. All these distinct features make A. phoenicis ATCC 14332 XPD unique among currently known prolidases, thus defining a novel Xaa-Pro dipeptidase subfamily. [ABSTRACT FROM AUTHOR]

The taxonomic status of 43 Psychrobacter species was examined based upon the genome sequences of their type strains. Three groups of type strains were found to be conspecific, Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628–635, 2004. 10.1078/0723202042369956) and Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291–1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450–1455, 2015. 10.1099/ijs.0.000118) and Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835–846, 2000. 10.1099/00207713-50-2-835); and Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44–53, 2001. 10.1078/0723-2020-00006), Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291–1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628–635, 2004. 10.1078/0723202042369956). For all three groups, the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values are > 97.69% and > 80.2%, respectively. This conclusion is supported by similarities in morphology, growth properties, and fatty acid compositions. Based on this evidence, we propose the reclassification of Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628–635, 2004. 10.1078/0723202042369956) as a later heterotypic synonym of Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291–1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450–1455, 2015. 10.1099/ijs.0.000118) as a later heterotypic synonym of Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835–846, 2000. 10.1099/00207713-50-2-835), and Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291–1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628–635, 2004. 10.1078/0723202042369956) as later heterotypic synonyms of Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44–53, 2001. 10.1078/0723-2020-00006). [ABSTRACT FROM AUTHOR]

Abstract Background Differentiating between type 1 diabetes (T1D) and type 2 diabetes (T2D) can be difficult in adults. The aim of this study was to determine the frequency of diagnostic reclassification from T2D to T1D, the characteristics of the patients and the impact on the management of the disease. Methods Observational and descriptive study including patients diagnosed with T1D in Asturias (Spain) between 2011 and 2020 who had been considered as T2D for at least 12 months. Results A total of 205 patients were included, representing 45.3% of those diagnosed with T1D over 30 years of age. Median time of evolution as T2D was 7,8 years. The age was 59.1 ± 12.9 years. BMI was > 25 kg/m2 in 46.8% of patients. HbA1c was 9.1 ± 2.1%, 77 ± 22 mmol/mol, and 56.5% were using insulin. Pancreatic antibodies were present in 95.5%, the most frequent being GAD, 82.6%. At 6 months, basal insulin use increased from 46.9 to 86.3%, and HbA1c decreased, 9.2 ± 2.0%vs7.7 ± 1.2%, 77 ± 22vs60 ± 13 mmol/mol; p

Oral contraceptives are among the most commonly used contraceptive methods. However, Italian women underused reliable hormonal contraceptives as compared with other European women. There is a need to streamline access to oral contraception, with expected benefits on emotional well-being of women and potential savings for health system in Italy. Indeed, women can only access to oral contraceptives through mandatory medical prescription. This is one of the most important barrier experienced by women. We hereby provide an expert opinion on the potential reclassification, extending pharmacy services to include responsible and appropriate use of POP, as an opportunity also in Italy to increase the use of safe and effective contraceptive methods.

An evidence-based consensus meeting was held with urologists, a pharmacist and a cardiologist to perform a structured benefit-risk analysis of reclassifying tadalafil, a phosphodiesterase type 5 (PDE5) inhibitor for treatment of erectile dysfunction (ED), to be available without prescription in Germany. As per the Brass process endorsed by regulatory authorities, an evidence-based Brass value tree was developed, which identified the incremental benefits and risks that should be considered above the safety and efficacy evidence required for prescription medicines. During the Group Delphi consensus meeting, the expert panel rated the likelihood and clinical impact of each benefit and risk on a scale of 0 (none) to 3 (high). Overall attribute scores were calculated from the product of the mean likelihood and mean clinical impact scores giving a possible score of 0–9. The overall benefit attribute scores ranged from 2.8 to 5.4. The overall risk attribute scores ranged from 0.2 to 2.2 though most were 1.0 or less (3 or more is generally considered to be of concern). On balance, the independent meeting scored the benefits of reclassification of tadalafil higher than the risks and considered the risk mitigation strategies of the packaging label and patient information leaflet (PIL) sufficient. [ABSTRACT FROM AUTHOR]

The present study was carried out to clarify the taxonomic position of Bacillus massiliigorillae and Bacillus sinesaloumensis. The 16S rRNA gene sequences extracted from the Bacillus sinesaloumensis Marseille-P3516T (FTOX00000000) and Bacillus massiliigorillae G2T (CAVL000000000) genomes showed 98.5 and 99.1% similarity with the type strains of Ferdinandcohnia humi and Peribacillus endoradicis, respectively. The amino acid identity (AAI) values of Bacillus sinesaloumensis Marseille-P3516T were higher with Ferdinandcohnia members, while Bacillus massiliigorillae G2T with Peribacillus members. In phylogenomic and phylogenetic trees, Bacillus sinesaloumensis Marseille-P3516T and Bacillus massiliigorillae G2T clade with members of the genera Ferdinandcohnia and Peribacillus, respectively. Based on the above results, we propose to transfer Bacillus massiliigorillae to the genus Peribacillus as Peribacillus massiliigorillae comb. nov., and Bacillus sinesaloumensis to the genus Ferdinandcohnia as Ferdinandcohnia sinesaloumensis comb. nov. [ABSTRACT FROM AUTHOR]

Scarab beetles (Scarabaeidae) are a diverse and ecologically important group of angiosperm‐associated insects. As conventionally understood, scarab beetles comprise two major lineages: dung beetles and the phytophagous Pleurosticti. However, previous phylogenetic analyses have not been able to convincingly answer the question whether or not the two lineages form a monophyletic group. Here, we report our results from phylogenetic analyses of more than 4000 genes mined from transcriptomes of more than 50 species of Scarabaeidae and other Scarabaeoidea. Our results provide convincing support for the monophyly of Scarabaeidae, confirming the debated sister group relationship of dung beetles and phytophagous pleurostict scarabs. Supermatrix‐based maximum likelihood and multispecies coalescent phylogenetic analyses strongly imply the subfamily Melolonthinae as currently understood being paraphyletic. We consequently suggest various changes in the systematics of Melolonthinae: Sericinae Kirby, 1837 stat. rest. and sensu n. to include the tribes Ablaberini, Diphucephalini and Sericini, and Sericoidinae Erichson, 1847 stat. rest. and sensu n. to include the tribes Automoliini, Heteronychini, Liparetrini, Maechidiini, Phyllotocini, Scitalini, and Sericoidini. Both subfamilies appear to consistently form a monophyletic sister group to all remaining subfamilies so far included within pleurostict scarabs except Orphninae. Our results represent a major step towards understanding the diversification history of one of the largest angiosperm‐associated radiations of beetles. [ABSTRACT FROM AUTHOR]

Background: Differentiating between type 1 diabetes (T1D) and type 2 diabetes (T2D) can be difficult in adults. The aim of this study was to determine the frequency of diagnostic reclassification from T2D to T1D, the characteristics of the patients and the impact on the management of the disease. Methods: Observational and descriptive study including patients diagnosed with T1D in Asturias (Spain) between 2011 and 2020 who had been considered as T2D for at least 12 months. Results: A total of 205 patients were included, representing 45.3% of those diagnosed with T1D over 30 years of age. Median time of evolution as T2D was 7,8 years. The age was 59.1 ± 12.9 years. BMI was > 25 kg/m2 in 46.8% of patients. HbA1c was 9.1 ± 2.1%, 77 ± 22 mmol/mol, and 56.5% were using insulin. Pancreatic antibodies were present in 95.5%, the most frequent being GAD, 82.6%. At 6 months, basal insulin use increased from 46.9 to 86.3%, and HbA1c decreased, 9.2 ± 2.0%vs7.7 ± 1.2%, 77 ± 22vs60 ± 13 mmol/mol; p < 0.0001. Conclusions: Diagnosis as T2D in patients with T1D in adults is common. Age, BMI, insulin use and other clinical features are not definitely discriminatory. GAD is the antibody of choice in case of diagnostic suspect. Reclassification has important implications for metabolic control. [ABSTRACT FROM AUTHOR]

The purple sulfur bacterium Thiocapsa roseopersicina BBS is interesting from both fundamental and practical points of view. It possesses a thermostable HydSL hydrogenase, which is involved in the reaction of reversible hydrogen activation and a unique reaction of sulfur reduction to hydrogen sulfide. It is a very promising enzyme for enzymatic hydrogenase electrodes. There are speculations that HydSL hydrogenase of purple bacteria is closely related to sulfur metabolism, but confirmation is required. For that, the full genome sequence is necessary. Here, we sequenced and assembled the complete genome of this bacterium. The analysis of the obtained whole genome, through an integrative approach that comprised estimating the Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (DDH) parameters, allowed for validation of the systematic position of T. roseopersicina as T. bogorovii BBS. For the first time, we have assembled the whole genome of this typical strain of a new bacterial species and carried out its functional description against another purple sulfur bacterium: Allochromatium vinosum DSM 180T. We refined the automatic annotation of the whole genome of the bacteria T. bogorovii BBS and localized the genomic positions of several studied genes, including those involved in sulfur metabolism and genes encoding the enzymes required for the TCA and glyoxylate cycles and other central metabolic pathways. Eleven additional genes coding proteins involved in pigment biosynthesis was found.

An evidence-based consensus meeting was held with urologists, a pharmacist and a cardiologist to perform a structured benefit-risk analysis of reclassifying tadalafil, a phosphodiesterase type 5 (PDE5) inhibitor for treatment of erectile dysfunction (ED), to be available without prescription in Germany. As per the Brass process endorsed by regulatory authorities, an evidence-based Brass value tree was developed, which identified the incremental benefits and risks that should be considered above the safety and efficacy evidence required for prescription medicines. During the Group Delphi consensus meeting, the expert panel rated the likelihood and clinical impact of each benefit and risk on a scale of 0 (none) to 3 (high). Overall attribute scores were calculated from the product of the mean likelihood and mean clinical impact scores giving a possible score of 0–9. The overall benefit attribute scores ranged from 2.8 to 5.4. The overall risk attribute scores ranged from 0.2 to 2.2 though most were 1.0 or less (3 or more is generally considered to be of concern). On balance, the independent meeting scored the benefits of reclassification of tadalafil higher than the risks and considered the risk mitigation strategies of the packaging label and patient information leaflet (PIL) sufficient.

The Black-throated Laughingthrush (Pterorhinus chinensis) is a bird belonging to the order Passeriformes and the family Leiothrichidae, and is found in Cambodia, China, Laos, Myanmar, Thailand and Vietnam. Pterorhinus chinensis was once classified as belonging to the genus Garrulax. However, recent research has reclassified it in the genus Pterorhinus. In this study, we sequenced and characterized the complete mitogenome of P. chinensis. The complete mitochondrial genome of P. chinensis is 17,827 bp in length. It consists of 13 PCGs, 22 tRNAs, two rRNAs, and two control regions. All genes are coded on the H-strand, except for one PCG (nad6) and eight tRNAs. All PCGs are initiated with ATG and stopped by five types of stop codons. Our comparative analyses show irregular gene rearrangement between trnT and trnP genes with another similar control region emerging between trnE and trnF genes compared with the ancestral mitochondrial gene order, called "duplicate CR gene order". The phylogenetic position of P. chinensis and phylogenetic relationships among members of Leiotrichidae are assessed based on complete mitogenomes. Phylogenetic relationships based on Bayesian inference and maximum likelihood methods showed that Garrulax and (Pterorhinus + Ianthocincla) formed a clade. Leiothrix and Liocichla also formed a clade. Our study provides support for the transfer of P. chinensis from Garrulax to Pterorhinus. Our results provide mitochondrial genome data to further understand the mitochondrial genome characteristics and taxonomic status of Leiothrichidae. [ABSTRACT FROM AUTHOR]

Streptomyces sp. N11-50 was isolated from deep-sea water and found to produce diketopiperazine (DKP) compounds such as albonoursin and cyclo(Phe-Leu). This study aimed to reveal the potential to synthesize diverse nonribosomal peptide and polyketide compounds as the other secondary metabolites different from DKP after clarifying the taxonomic position. Strain N11-50 was identified as Streptomyces albus, as it showed 100% 16S rRNA gene sequence similarities and 95.5% DNA–DNA relatedness to S. albus NBRC 13014T. We annotated the nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters in the genome. Consequently, five NRPS, one hybrid PKS/NRPS, five type-I PKS and one type-II PKS gene clusters were observed, of which we predicted the products through bioinformatic analysis. These gene clusters were well conserved in already whole-genome sequence (WGS)-published strains belonging to S. albus. On the other hand, our taxonogenomic analysis revealed that three WGS-published S. albus strains were not S. albus. Two of the three should be classified as Streptomyces albidoflavus, and the remaining one was likely a new genomospecies. After reclassifying these appropriately, we demonstrated species-specific profiles of the NRPS and PKS gene clusters with little strain-level diversities. [ABSTRACT FROM AUTHOR]

This study provides empirical evidence related to the application of fixed asset accounting at the level of ministries or institutions' work units, with the research location at a university in Indonesia. Through this research, it can be proven that recording the value of fixed assets in the Statement of Financial Position sourced from the conversion of the value of capital expenditures in the LRA tends to cause problems if the codification of expenditure accounts does not contain the separation of recording the components of building support. The research in this study used a descriptive method by tracing historical/documentation data. The data studied comes from the documentation of planning/budgeting, budget realization, and financial reporting in 2015, especially those related to capital expenditure and fixed asset recording. The documentation starts from DIPA, RKA-KL, SPM, Contract Documents, Supervisory Consultant Reports, Contractor Reports for Construction Development Work, Financial Reports from SAIBA applications, and data from SIMAK-BMN. Data processing was carried out using descriptive statistical methods with the help of the Microsoft Excel application program. The results of this study indicate that after separating the recognition of building support components, the value of additional fixed assets in the agency in 2015 changed significantly. This research concludes that reclassification is needed after the value of capital expenditure is converted into the value of fixed assets to comply with PSAP 07, and maintenance expenditure can be budgeted. [ABSTRACT FROM AUTHOR]

Introduction: The use of Asian-specific Body Mass Index (aBMI) cutoffs may be more appropriate than general World Health Organization BMI (gBMI) cutoffs in determining recommended gestational weight gain (GWG) for Asian women. Since aBMI cutoffs are lower than gBMI, more Asian women will be reclassified into higher aBMI categories from gBMI. The prevalence of reclassification and its impact on GWG are not known. Methods: We utilized the electronic health records of 8886 Kaiser Permanente Hawaii members aged ≥ 18 with a singleton live birth. Prepregnancy BMI was first classified using gBMI criteria, then aBMI criteria. BMI categories were "underweight", "normal", "overweight" and "obese"; GWG was classified into lower ("lGWG"), met ("mGWG"), and exceed ("eGWG") GWG per WHO recommendations. Self-reported race/ethnicity include Asian, Asian + Pacific Islander, and Asian + white. Multiple logistic regression was used to estimate adjusted odds of reclassification. The Cochran-Mantel–Haenszel test was used to evaluate associations between race/ethnicity and GWG. Results: > 40% of women in each racial/ethnic group were reclassified. Asian + Pacific Islander women had significantly higher odds of being reclassified (p <.0001). In the normal gBMI and aBMI category, Asian + Pacific Islander women had the largest eGWG group. In the overweight gBMI category, Asian + Pacific Islander women had the largest eGWG group; in the overweight aBMI category, Asian + white women had the largest eGWG group. Discussion: A sizable percent of women were reclassified into higher BMI categories when aBMI was applied. Mixed-race Asian women were more likely to exceed GWG recommendations than Asian women. [ABSTRACT FROM AUTHOR]

Reclassification is a crucial outcome for English learner (EL) students' academic progress. Though ELs spend a large portion of their academic time with general education teachers, we know little about the role general education teachers play in developing ELs' English language proficiency. Drawing from a longitudinal administrative dataset from Tennessee, this study uses discrete-time survival analysis to estimate the relationship between ELs' likelihood of reclassification and characteristics of their general education English language arts (ELA) teachers in Grades 3–8. The study finds that several measures of teacher effectiveness consistently predict EL reclassification. Sensitivity and robustness checks substantiate these relationships. Findings have important policy implications for the identification and assignment of ELs to effective general education ELA teachers. [ABSTRACT FROM AUTHOR]

Objectives This study applied the 2022 criteria for granulomatosis with polyangiitis (GPA) proposed by the ACR and EULAR (the 2022 ACR/EULAR criteria) to Korean patients with previously diagnosed GPA to investigate the number of patients who could be reclassified as having GPA. Methods Sixty-five patients with GPA, who met the 2012 revised International Chapel Hill Consensus Conference Nomenclature of Vasculitides and the 2007 European Medicines Agency algorithm for GPA, were included in this study. They were reclassified based on the 2022 ACR/EULAR criteria. Results Of the 65 patients, 48 patients (73.8%) were reclassified as having GPA. A patient could not be reclassified as having GPA if the patient did not have a total score of 5 despite granulomas on biopsy or clear GPA surrogate markers. Among the 17 patients unclassified as having GPA, 16 patients were reclassified as having MPA and one as having unclassifiable vasculitis, and furthermore, 94.1% of them harboured MPO-ANCA (or perinuclear (P)-ANCA). Conclusion The concordance rate between the 2022 ACR/EULAR criteria for GPA and the previous criteria in patients with previously diagnosed GPA was 73.8%. Although the 2022 ACR/EULAR criteria are the product of the most advanced methodologic process, it should be noted that there were some consequences of distorting the CHCC definition, and further discussion is required, especially with respect to the weightage of the items. [ABSTRACT FROM AUTHOR]

The current genus Rhodopirellula consists of marine bacteria which belong to the family Pirellulaceae of the phylum Planctomycetota. Members of the genus Rhodopirellula are aerobic, mesophiles and chemoheterotrophs. The here conducted analysis built on 16S rRNA gene sequence and multi-locus sequence analysis based phylogenomic trees suggested that the genus is subdivided into four clades. Existing Rhodopirellula species were studied extensively based on phenotypic, genomic and chemotaxonomic parameters. The heterogeneity was further confirmed by overall genome-related indices (OGRI) including digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), and percentage of conserved proteins (POCP). AAI and POCP values between the clades of the genus Rhodopirellula were 62.2–69.6% and 49.5–62.5%, respectively. Comparative genomic approaches like pan-genome analysis and conserved signature indels (CSIs) also support the division of the clades. The genomic incoherence of the members of the genus is further supported by variations in phenotypic characteristics. Thus, with the here applied integrated comparative genomic and polyphasic approaches, we propose the reclassification of the genus Rhodopirellula to three new genera: Aporhodopirellula gen. nov., Allorhodopirellula gen. nov., and Neorhodopirellula gen. nov. [ABSTRACT FROM AUTHOR]

Background: Breast cancer is one of the three most common cancers worldwide and is the most common malignancy in women. Treatment approaches for breast cancer are diverse and varied. Clinicians must balance risks and benefits when deciding treatments, and models have been developed to support this decision-making. Genomic risk scores (GRSs) may offer greater clinical value than standard clinicopathological models, but there is limited evidence as to whether these models perform better than the current clinical standard of care. Methods: PREDICT and GRSs were adapted using data from the original papers. Univariable Cox proportional hazards models were produced with breast cancer-specific survival (BCSS) as the outcome. Independent predictors of BCSS were used to build multivariable models with PREDICT. Signatures which provided independent prognostic information in multivariable models were incorporated into the PREDICT algorithm and assessed for calibration, discrimination and reclassification. Results: EndoPredict, MammaPrint and Prosigna demonstrated prognostic power independent of PREDICT in multivariable models for ER-positive patients; no score predicted BCSS in ER-negative patients. Incorporating these models into PREDICT had only a modest impact upon calibration (with absolute improvements of 0.2–0.8%), discrimination (with no statistically significant c-index improvements) and reclassification (with 4–10% of patients being reclassified). Conclusion: Addition of GRSs to PREDICT had limited impact on model fit or treatment received. This analysis does not support widespread adoption of current GRSs based on our implementations of commercial products. [ABSTRACT FROM AUTHOR]

Two Gram-stain-positive, motile, endospore-forming, facultatively anaerobic strains, designated MEBiC13591T and MEBiC13594T, were isolated from tidal flat sediment of the Incheon City on the west coast of Korea. Growth of both novel strains was observed at pH 5–9 (optimum, pH 7–7.5), and in 0–8% NaCl (optimum, 2% for MEBiC13591T and 3% for MEBiC13594T). Strains MEBiC13591T and MEBiC13594T grew optimally at 50 °C, (37.5–56.1 °C) and 44 °C (20.7–50.7 °C), respectively. The main cellular fatty acids of strain MEBiC13591T were iso-C15: 0, anteiso-C15: 0, iso-C16: 0, iso-C17: 0 and anteiso-C17: 0, while those for strain MEBiC13594T were C14: 0, iso-C14: 0, iso-C15: 0, anteiso-C15: 0 and C16: 0. In both taxa, the major isoprenoid was MK-7. The genomic DNA G + C contents were 34.1 and 37.0 mol% for MEBiC13591T and MEBiC13594T, respectively. A 16S rRNA gene sequence analysis revealed that the novel strains showed high similarity with members of the genera Aeribacillus (95.0%) and Caldibacillus (93.5–94.5%); however, showed lower than 90% with Caldibacillus debilis TfT. Phylogenetic and Phylogenomic analysis revealed that two novel strains comprised distinct phyletic line with members formerly assigned to Caldibacillus. Based on genomic indices, such as AAI and ANI, members formerly affiliated with Caldibacillus and Bacillus as well as the novel strains should be classified into five independent genera. Based on the phenotypic, genomic and biochemical data, strains MEBiC13591T and MEBiC13594T represent two novel species in the novel genus, for which the names Fervidibacillus albus gen. nov., sp. nov. (MEBiC13591T [= KCCM 43317T = KCTC 43181T = JCM 33662T = MCCC 1K04565T]), and Fervidibacillus halotolerans sp. nov. (MEBiC13594T [= KCTC 43182T = JCM 34001T]) are proposed. Three additional genera Caldifermentibacillus, Palidibacillus, and Perspicuibacillus are also proposed by reclassification of the several species with valid names that formerly affiliated with the genera Caldibacillus. [ABSTRACT FROM AUTHOR]

Three novel facultatively methylotrophic bacteria, strains 3CT, 1A, 8P, were isolated from activated sludges. The isolates were aerobic, Gram-stain-negative, non-motile, non-spore forming rods multiplying by binary fission. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethylethanolamine, phosphatidylmonomethylethanolamine, and diphosphatidylglycerol. The major fatty acids of cells were С18:1ω7c, C19:0ω8c cyclo and C16:0. Levels of 16S rRNA gene similarity indicates that the closely relatives are representatives of the genera Starkeya, Ancylobacter, Angulomicrobium and Methylorhabdus (96.4–99.4%). Genomic comparisons of 3CT and its closest relatives, S. novella DSM 506T and S. koreensis Jip08T, shared 87.3 and 86.8% nucleotide identity and 28.3 and 26.8% digital DNA–DNA hybridization values, respectively. The average amino acid identities between the strain 3CT and representatives of Starkeya, Ancylobacter and Angulomicrobium were in the range of 75.6–84.3%, which combines these strains into a single genus and gives rise to their reclassification. Based on polyphasic analyses, the strains 3CT, 1A, 8P represents a novel species of the genus Ancylobacter, for which the name Ancylobacter moscoviensis sp. nov. is proposed. The type strain is 3CT (= VKM B-3218T = KCTC 62336T). Furthermore, we also suggested the reclassification of Starkeya novella as Ancylobacter novellus comb. nov., Starkeya koreensis as Ancylobacter koreensis comb. nov., Angulomicrobium tetraedrale as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme as Ancylobacter amanitiformis comb. nov. and Methylorhabdus multivorans as Ancylobacter multivorans comb. nov. with the emended description of the genus Ancylobacter. [ABSTRACT FROM AUTHOR]

Aim. To assess the significance of troponin I (hs-cTnI) for cardio­vascular risk stratification in a population of Russian working-age men and women of.Material and methods. The data of 13976 men and women aged 25-64 from the ESSE-RF1 and ESSE-RF2 multicenter studies were analyzed. The examination included following points: standard questionnaire, measurements of height, weight, waist circumference, body mass index, blood pressure, pulse rate, biochemical tests. The level of hs-cTnI in blood serum samples stored at -70оC in the Biobank of the National Medical Research Center for Therapy and Preventive Medicine was determined by chemiluminescent immunoassay analysis. Individual cardiovascular risk was calculated using the SCORE scale: values 12 pg/ml; women 10 pg/ml. We analyzed following hard endpoints: cardiovascular death or non-fatal myocardial infarction, and composite endpoint: the same and stroke.Results. The prospective analysis of the relationship between troponin levels and endpoints and composite endpoints showed that in participants without prior CVD, hs-cTnI levels >12 pg/ml in men and >10 pg/ml in women are associated with an increased risk of endpoints and composite endpoints by 3,39 (1,91-6,03) and 2,69 (1,6-4,52) times (p