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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]

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]

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]

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]

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]

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]

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]

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]

The current classification of diabetes, based on hyperglycaemia, islet-directed antibodies and some insufficiently defined clinical features, does not reflect differences in aetiological mechanisms and in the clinical course of people with diabetes. This review discusses evidence from recent studies addressing the complexity of diabetes by proposing novel subgroups (subtypes) of diabetes. The most widely replicated and validated approach identified, in addition to severe autoimmune diabetes, four subgroups designated severe insulin-deficient diabetes, severe insulin-resistant diabetes, mild obesity-related diabetes and mild age-related diabetes subgroups. These subgroups display distinct patterns of clinical features, disease progression and onset of comorbidities and complications, with severe insulin-resistant diabetes showing the highest risk for cardiovascular, kidney and fatty liver diseases. While it has been suggested that people in these subgroups would benefit from stratified treatments, RCTs are required to assess the clinical utility of any reclassification effort. Several methodological and practical issues also need further study: the statistical approach used to define subgroups and derive recommendations for diabetes care; the stability of subgroups over time; the optimal dataset (e.g. phenotypic vs genotypic) for reclassification; the transethnic generalisability of findings; and the applicability in clinical routine care. Despite these open questions, the concept of a new classification of diabetes has already allowed researchers to gain more insight into the colourful picture of diabetes and has stimulated progress in this field so that precision diabetology may become reality in the future. [ABSTRACT FROM AUTHOR]

The taxonomic position of Bacillus alkalicola was evaluated using phylogenetic and genome-based comparisons. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic (based on concatenation of protein-marker genes) trees, Bacillus alkalicola clade with the members of the genus Evansella. The amino acid identity (AAI) values suggested to reclassify Bacillus alkalicola as a member of the genus Evansella. The average nucleotide identity (ANI) value between Bacillus alkalicola and the members of the genus Evansella was lower than the threshold values for bacterial species delineation. Based on the results, we propose to transfer Bacillus alkalicola to the genus Evansella as Evansella alkalicola comb. nov. The type strain is Zby6T (=CGMCC 1.10368T=JCM 17098T=NBRC 107743T). [ABSTRACT FROM AUTHOR]

The genus Streptococcus, a member of family Streptococcaceae, is known for its wide range of industrial, clinical and human relevance. Among the species of genus Streptococcus two members, namely Streptococcus koreensis and Streptococcus ilei, were isolated from subgingival dental plaque and human small intestinal fluid, respectively. The 16S rRNA gene sequence similarity of the type strains of these members shows a similarity of 99.87%. In this study, we performed a systematic study to clarify the taxonomic assignment of these two species. Genome similarity assessment based on whole-genome sequence information such as average nucleotide identity using orthoANI and fastANI, digital DNA–DNA hybridization value between S. koreensis and S. ilei were 96.31, 96.60, 86.4 and 97.63, respectively. All these genome similarity values clearly exceeded the species delineation cutoffs. Phylogenetic assessment using 16S rRNA gene and whole-genome information using PhyloPhlAn, which uses around 400 conserved genes across bacterial phyla, provides additional evidence for these members forming a monophyletic clade in the phylogenetic tree. Pan genome analysis suggests a very large core genome (n = 1374) and the presence of no unique gene between the genomes of S. koreensis and S. ilei. Additionally, we found highly syntenic genomes of type strains of these two species. Based on these evidences, we propose S. ilei should be reclassified as a later heterotypic synonym of S. koreensis. [ABSTRACT FROM AUTHOR]

Among the species of genus Streptococcus two members namely Streptococcus ratti and Streptococcus ursoris were isolated from oral cavity of rat and bear, respectively. Type strain of these members shows a 16S rRNA gene sequence similarity of 98.9%. Based on systematic phylo-taxonogenomics investigations, we could deduce the taxonomic assignment of the members of these species. Genome similarity assessment among the type strain of these members using average nucleotide identity (orthoANI and fastANI), digital DNA–DNA hybridization and average amino acid identity (AAI) were 98.5, 98.3, 88, and 98.3% respectively. All these values exceed the species delineation cutoffs suggesting a unified species. Phylogenetic tree obtained using 16S rRNA gene sequence also indicates the monophyletic nature of the member strains. Such monophyletic taxonomic positioning of the strains was further complemented with the whole genome-based phylogenomic tree. Based on these evidences, we propose S. ursoris should be reclassified as a later heterotypic synonym of S. ratti. [ABSTRACT FROM AUTHOR]

Purpose: To date, two haemogregarines have been described from the white-spotted wall gecko, Tarentola annularis in Egypt. These species are Haemogregarina annularis and Haemogregarina tarentannulari. Although these two species initially were described as different species parasitizing T. annularis, both forms look identical due to their similar morphology and morphometric characteristics from the same host species. Here we will clarify, using traditional morphological description of the blood and tissue stages, combined with molecular analysis, the identity of the haemoparasites infecting T. annularis in Egypt. Methods: Thin blood smears were screened from 50 gecko, Tarentola annularis and merognic stages were identified in the lung of the infected geckos. Parasite DNA was extracted and PCR was carried out to amplify parasite 18S rDNA. Results: Morphological criteria of parasite stages, mature gamont stages and mergonic stages were similar to the two previously reported Haemogregarina species. In the phylogenetic tree, the present haemogregarine fell within a clade comprising most of Hepatozoon species infecting reptiles. Conclusion: Our morphological comparison supported that the two previously described Haemogregarina species were the same and allowed us to consider Haemogregarina tarentannulari as a junior synonym of Haemogregarina annularis. Our phylogenetic analysis gave us the opportunity to reassign Haemogregarina annularis to the genus Hepatozoon and being identified as Hepatozoon annularis n. comb. [ABSTRACT FROM AUTHOR]

Hyperglycaemia first detected during pregnancy is either gestational diabetes mellitus (GDM) or previous undiagnosed diabetes. We aimed to study if there were a first trimester fasting glycaemia (FTG) and a glycated haemoglobin (HbA1c) cut-off values associated with type 2 diabetes mellitus (T2DM) or abnormal glucose homeostasis (AGH) at the post-partum oral glucose tolerance test (OGTT) reclassification. We retrospectively studied a group of pregnant women from the Portuguese National Registry of GDM. Receiver-operating characteristic (ROC) curves were used to determine the best FTG and HbA1c cut-offs to predict T2DM and AGH. We studied 4068 women. The area under the ROC curves (AUC) for the association with T2DM was 0.85 (0.80–0.90) for FTG and 0.85 (0.80–0.91) for HbA1c. The best FTG cut-off for association with T2DM was 99 mg/dL: sensitivity 77.4%, specificity 74.3%, positive predictive value (PPV) 4.8%, and negative predictive value (NPV) 99.5%. The best HbA1c cut-off for association with T2DM was 5.4%: sensitivity 79.0%, specificity 80.1%, PPV 5.7%, and NPV 99.6%. The AUC for the association of FTG and HbA1c with AGH were 0.73 (0.70–0.76) and 0.71 (0.67–0.74), respectively. The best FTG cut-off for predicting AGH was 99 mg/dL: sensitivity 59.4%, specificity 76.2%, PPV 17.0%, and NPV 95.8%. The best HbA1c cut-off was 5.4%: sensitivity 48.7%, specificity 81.5%, PPV 17.8%, and NPV 95.1%. We suggest an FTG of 99 mg/dL and an HbA1c of 5.4% as the best cut-offs below which T2DM is unlikely to be present. Almost all patients with FTG < 99 mg/dL and HbA1c < 5.4% did not reclassify as T2DM. These early pregnancy cut-offs might alert the physician for the possibility of a previous undiagnosed diabetes and alert them to the importance of testing for it after delivery. [ABSTRACT FROM AUTHOR]

Purpose: This study aimed to evaluate the effectiveness of apparent diffusion coefficient (ADC) parameters in distinguishing between Prostate Cancer Research International Active Surveillance (PRIAS) non-reclassification and reclassification groups during active surveillance (AS) of prostate cancer. Methods: We included 55 patients who fulfilled the PRIAS criteria and underwent ≥ 2 magnetic resonance imaging (MRI) including diffusion-weighted imaging with an interval of ≤ 3 years between baseline and second MRI. A mono-exponential fitting model was used to automatically create ADC maps with minimum b-values of 0 and maximum of 2000 s/mm2. For detectable lesions on ADC maps, the lesions were manually segmented on each slice of the ADC maps. For undetectable lesions, the corresponding normal-appearing zone of the lobe on each slice of ADC maps was segmented. The ADC data for each slice were summed to obtain the 25th, 50th, and 75th percentile ADC values of the histogram at baseline and second MRI. These ADC parameters at baseline and second MRI, and the changes of ADC parameters from baseline to second MRI were compared between PRIAS non-reclassification and reclassification groups. Results: The PRIAS reclassification group had significantly lower 25th, 50th, and 75th percentile ADC values at second MRI compared to the non-reclassification group. The non-reclassification group had significantly lower changes in ADC values in these percentiles compared to the reclassification group. Conclusion: The ADC parameters at second MRI and the changes from baseline to second MRI may be effective distinguishing factors between PRIAS non-reclassification and reclassification groups. [ABSTRACT FROM AUTHOR]

While genomic medicine is becoming an important part of patient care with an ever-increasing diagnostic yield, recontacting patients after reclassification of variants of uncertain clinical significance (VUSs) remains a major challenge. Although periodical reinterpretation of VUSs is highly desired, recontacting former patients with new classifications is commonly not fulfilled in practice. We draw on semi-structured interviews with 20 Israeli healthcare professionals and stakeholders involved in communicating the results of genome-wide sequencing to patients. Findings show agreement that an individual health care professional cannot address the task of recontacting patients after re-classification, and that responsibility should be shared among the medical specialties, laboratory scientists, as well as patients. In the absence of established guidelines, many respondents suggested that the patient should be informed about reclassification during a follow-up contact but they disagreed who should be responsible for informing the patient. HCPs agreed that the solution to this challenge involves a centralized automated database that is accessible, continuously updated, and facilitates retrospective as well as prospective flagging of reclassification for patients who can benefit from this information. National and international policies providing concrete guidelines on the optimal way to recontact patients with new valuable genomic information are needed. [ABSTRACT FROM AUTHOR]

In the present study, the taxonomic positions of Evansella polygoni, Evansella clarkii, Bacillus shivajii and Bacillus tamaricis were evaluated using phylogenetic and genome-based comparisons. In phylogenetic (based on 16S rRNA sequencing) and phylogenomic (based on concatenation of protein-marker genes) trees, Bacillus shivajii and Bacillus tamaricis were placed between genera Evansella and Alteribacter. The amino acid identity (AAI) values suggested that Bacillus shivajii and Bacillus tamaricis were members of the genus Evansella. The average nucleotide identity (ANI) value between Evansella polygoni and Evansella clarkii was higher than the threshold values for bacterial species delineation, indicating that they belong to the same species. Based on the results, we propose to reclassify Evansella polygoni as a later heterotypic synonym of Evansella clarkii and transfer Bacillus shivajii and Bacillus tamaricis to the genus Evansella as Evansella shivajii comb. nov. and Evansella tamaricis comb. nov. [ABSTRACT FROM AUTHOR]

In the framework of generalized linear models for binary responses, we develop parametric methods that yield estimators for regression coefficients less compromised by an inadequate posited link function. The improved inference are obtained without correcting a misspecified model, and thus are referred to as wrong-model inference. A byproduct of the proposed methods is a simple test for link misspecification in this class of models. Impressive bias reduction in estimators for the regression coefficients from the proposed methods and promising power of the proposed test to detect link misspecification are demonstrated in simulation studies. We also apply these methods to a classic data example frequently analyzed in the existing literature concerning this class of models. [ABSTRACT FROM AUTHOR]

Background: The consent of community pharmacists is an important factor for the successful implementation of Rx-to-OTC switches but is not part of the official reclassification procedure in Germany. Objective: The aim was to identify potential switch candidates and indications in addition to a basic assessment of new switches in Germany. Setting: The survey was distributed via the online survey tool of the pharmaceutical journal "Deutsche Apotheker Zeitung" within the period from 20 September to 8 October 2017. Methods: The survey comprised 17 questions. Besides some basic parameters, the questionnaire included a list of proposals for new switch candidates, a vote on the general support as well as economic and health professional expectations regarding further switches. Main outcome measure: The highest consent scores were obtained for second-generation antihistamines for treatment of hay fever such as desloratadine, fexofenadine and levocetirizine. Results: Nine hundred forty pharmacy employees participated in the survey. Beside second-generation antihistamines, there are further preferred switches for nasal glucocorticoids, proton pump inhibitors, ocular antibiotics and emergency kits for acute dyspnoea. Conclusion: Pharmacists strongly welcome further switches. This leads to high acceptance rates, especially for a switch of desloratadine, as this was the most named active ingredient possible for a switch within the survey. Impact of findings on practice statements: The outcome of this survey can support pharmaceutical companies in decision-making about which active substances they should submit a switch application for. Additionally, this helps fulfil patient needs, because pharmacists know best what is beneficial for patient self-care. In addition, all other actors involved in this process can see what is required and can rethink their position regarding further switches. [ABSTRACT FROM AUTHOR]

Purpose: Active surveillance (AS) strategies for patients with low- and early intermediate-risk prostate cancer are still not consistently defined. Within a controlled randomized trial, active surveillance was compared to other treatment options for patients with prostate cancer. Aim of this analysis was to report on termination rates of patients treated with AS including different grade groups. Methods: A randomized trial comparing radical prostatectomy, active surveillance, external beam radiotherapy and brachytherapy was performed from 2013 to 2016 and included 345 patients with low- and early intermediate-risk prostate cancer (ISUP grade groups 1 and 2). The trial was prematurely stopped due to slow accrual. A total of 130 patients were treated with active surveillance. Among them, 42 patients were diagnosed with intermediate-risk PCA. Reference pathology and AS quality control were performed throughout. Results: After a median follow-up time of 18.8 months, 73 out of the 130 patients (56%) terminated active surveillance. Of these, 56 (77%) patients were histologically reclassified at the time of rebiopsy, including 35% and 60% of the grade group 1 and 2 patients, respectively. No patients who underwent radical prostatectomy at the time of reclassification had radical prostatectomy specimens ≥ grade group 3. Conclusion: In this prospectively analyzed subcohort of patients with AS and conventional staging within a randomized trial, the 2-year histological reclassification rates were higher than those previously reported. Active surveillance may not be based on conventional staging alone, and patients with grade group 2 cancers may be recommended for active surveillance in carefully controlled trials only. [ABSTRACT FROM AUTHOR]

The genus Halioglobus is one of the environmentally relevant members of the family Halieaceae, class Gammaproteobacteria. At present, the genus is composed of three validly published species. However, in the recent study of the family Halieaceae, the species Halioglobus pacificus was observed to branch outside of the main clade formed by the members of Halioglobus, suggesting its distinct taxonomic placement within the family. In the present study, the taxonomic placement of H. pacificus was reassessed using comparative genomics. Phylogenomic analysis revealed the paraphyletic relationship of H. pacificus with the type species of the genus Halioglobus, and further demonstrated its genus-level placement. This phylogenetic relationship was reinforced by the average nucleotide and amino acid identity values shared by H. pacificus with the members of the family Halieaceae. Moreover, the results of the pan-genome analysis, together with the phenotype data, further supported the exclusion of H. pacificus from the genus Halioglobus. Based on these findings, the species H. pacificus is thereby assigned to a new genus Parahalioglobus gen. nov. as Parahalioglobus pacificus comb. nov., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Background: The accurate interpretation of BRCA1/2 variants becomes increasingly important in breast cancer and other related cancers including ovarian cancer, prostate cancer, pancreatic cancer and so forth. In the past decades, especially before year 2015, limitations of techniques and lack of databases and guidelines have led to possible misinterpretation of the clinical significance of sequence variants of BRCA1/2. A published study reported reclassification of some BRCA1/2 variants previously classified as variants of uncertain significance (VUS) to likely pathogenic in breast or ovarian cancer patients from Korea. However, little is known about the situation in Chinese population. Methods: We retrospectively retrieved 109 publications studying about BRCA1/2 variants of Chinese population from the year 1999 to year 2019 (March). After excluding publications of meta-analysis and publications with missing data, 72 publications were eventually retained for subsequent analysis. In total, 1,351 BRCA variants (673 BRCA1 variants and 678 BRCA2 variants) derived from 42,430 Chinese cancer patients were standardized and reinterpreted using ACMG/AMP 2015 guidelines and China Expert Consensus on BRCA variant interpretation by genetic counselors. Results: Among the 1,351 BRCA variants, the majority of interpretation (91.7%, 1,239/1,351) remained the same as previously published. However, there were 112 (8.3%, 112/1,351) variants (64 BRCA1, 48 BRCA2) reclassified with different categories. Conclusions: Our results demonstrated that clinical significance of not only VUS, but also pathogenic/likely pathogenic variants varied from time to time in the Chinese population. Precise reinterpretation of BRCA1/2 variants is of crucial importance to genetic counseling or clinical decision-making for risk individuals or patients. [ABSTRACT FROM AUTHOR]

Purpose: Ultrasound examinations of atherosclerotic carotid plaques can be used to calculate risk markers associated with plaque vulnerability. Recent studies demonstrate significant inter-frame variability in risk markers. Here, we investigate risk marker variability in symptomatic plaques and its impact on reclassification of plaque vulnerability, as well as its association with the shape of the temporal variation over the cardiac cycle.Methods: 56 patients with symptomatic carotid stenosis were included in this study. 88 plaques were identified and the plaque risk markers size (area), echogenicity (gray scale median, GSM) and heterogeneity (coarseness) were measured in all frames of ultrasound B-mode image sequences. Inter-frame variability was quantified using the coefficient of variation (CV).Results: Inter-frame variabilities of the risk markers were area CV 5-8%; GSM CV 4-7%; coarseness CV 8-15% and was in general significantly lower in large as compared to smaller plaques. The variability in GSM risk marker caused a reclassification of vulnerability in 30 to 38% of the plaques. Temporal variations in GSM with a heart rate periodic or drift/trending pattern were found in smaller plaques (< 26 mm2), whereas random pattern was found in larger plaques. In addition, hypoechoic plaques (GSM < 25) were associated with cyclic variation pattern, independent of their size.Conclusions: Risk marker variability causes substantial reclassification of plaque vulnerability in symptomatic patients. Inter-frame variation and its temporal pattern should be considered in the design of future studies related to risk markers. [ABSTRACT FROM AUTHOR]

Phylogenetic analysis of the 16S rRNA gene sequences showed that the type species of the genus Methylarcula, Methylarculamarina h1T was closely related to Paracoccus saliphilus DSM 18447T with high sequence similarity (97.8%). The genome of Methylarcula marina h1T was sequenced and its average nucleotide identity (ANI) and in silico DNA–DNA hybridization with Paracoccus type strains were 72.6–88.2% and 19.1–36.3%, respectively. Genome comparison showed significant similarity between the genes of methylo-trophy of Methylarcula marina h1T and Paracoccus saliphilus DSM 18447T. Genome analysis of M. marina strain h1T revealed the presence of the genes involved in oxidation of methanol, formaldehyde, and methylamine, as well as of the genes of the N-methylglutamate and icl− serine pathways, but not the genes of functional ribulose bisphosphate carboxylase. According to the phenotypic, chemotaxonomic, and genome-encoded traits of Methylarcula marina h1T, it should be transferred to the genus Paracoccus as a novel species, for which the name Paracoccus methylarcula nom. nov. (type strain h1T = VKM B-2159T = CCUG 72982T) is proposed. [ABSTRACT FROM AUTHOR]

To determine the potential of a non-invasive acoustic device (CADScor®System) to reclassify patients with intermediate pre-test probability (PTP) and clinically suspected stable coronary artery disease (CAD) into a low probability group thereby ruling out significant CAD. Audio recordings and clinical data from three studies were collected in a single database. In all studies, patients with a coronary CT angiography indicating CAD were referred to coronary angiography. Audio recordings of heart sounds were processed to construct a CAD-score. PTP was calculated using the updated Diamond-Forrester score and patients were classified according to the current ESC guidelines for stable CAD: low < 15%, intermediate 15-85% and high > 85% PTP. Intermediate PTP patients were re-classified to low probability if the CAD-score was ≤ 20. Of 2245 patients, 212 (9.4%) had significant CAD confirmed by coronary angiography ( ≥ 50% diameter stenosis). The average CAD-score was higher in patients with significant CAD (38.4 ± 13.9) compared to the remaining patients (25.1 ± 13.8; p < 0.001). The reclassification increased the proportion of low PTP patients from 13.6% to 41.8%, reducing the proportion of intermediate PTP patients from 83.4% to 55.2%. Before reclassification 7 (3.1%) low PTP patients had CAD, whereas post-reclassification this number increased to 28 (4.0%) (p = 0.52). The net reclassification index was 0.209. Utilization of a low-cost acoustic device in patients with intermediate PTP could potentially reduce the number of patients referred for further testing, without a significant increase in the false negative rate, and thus improve the cost-effectiveness for patients with suspected stable CAD. [ABSTRACT FROM AUTHOR]

Background: Although BRCA1 or BRCA2 (BRCA1/2) genetic testing plays an important role in determining treatment modalities in patients with hereditary breast and ovarian cancer, sequence variants with unknown clinical significance or variant of uncertain significance (VUS) have limited use in medical decision-making. With vast quantities of gene-related data being updated, the clinical significance of VUS may change over time. We reinterpreted the sequence variant previously reported as BRCA1/2 VUS results in patients with breast or ovarian cancer and assessed whether the clinical significance of VUS was changed. Methods: We retrospectively reviewed medical records of 423 breast or ovarian cancer patients who underwent BRCA1/2 genetic testing from 2010 to 2017. The VUSs in BRCA1/2 were reanalyzed using the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology standards and guidelines (ACMG/AMP 2015 guidelines) and the VUS was reclassified into five categories: "pathogenic", "likely pathogenic", "VUS", "likely benign", and "benign". Results: A total of 75 patients (48 sequence types of VUS) were identified as carrying either one or more VUS in BRCA1/2. Among the 75 patients, two patients (2.7%) were reclassified as "likely pathogenic", 30 patients (40.0%) were reclassified as either "benign" or "likely benign", and the remaining 43 patients (57.3%) were still classified as VUS category. Conclusions: Since the clinical significance of VUS in BRCA1/2 may vary from time to time, reinterpretation of the VUS results could contribute to clinical decision-making. [ABSTRACT FROM AUTHOR]

A taxonomic study was carried out on strain SA5d-4T, which was isolated from a marine limpet (Patelloida saccharina lanx [Reeve, 1855]) collected from intertidal rocks in Xiamen, China. Strain SA5d-4T was aerobic, Gram-positive, lacked flagellum, non-motile, filamentous, formed a slightly-yellowish colony, and non-sporulating. The strain grew optimally at 28 °C, at pH values 7.0–8.0, and in the presence of 1–2% (w/v) sodium chloride. The major cellular fatty acids identified were iso-C15:0, iso-C17:0ω10c, and iso-C17:0. The dominated respiratory quinone was menaquinone-7. The major phospholipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The genomic DNA G + C content was 35.3 mol%, calculated from a draft genome sequence. Phylogenetic analysis based on the full-length 16S rRNA gene sequence showed that strain SA5d-4T belongs to a new genus within the family Bacillaceae, and this gene shares 95.6% similarity with that from Bacillus taeanensis BH030017T, 95.2% with Bacillus algicola KMM 3737T, 95.1% with Bacillus alkalinitrilicus ANL-iso4T, 94.9% with Bacillus hwajinpoensis SW-72T, and 94.6% with Anaerobacillus alkalidiazotrophicus MS6T. Whole genome phylogenetic analyses indicated that strain SA5d-4T formed a monophyletic branch with B. taeanensis BH030017T. The average nucleotide identity between strain SA5d-4T and B. taeanensis BH030017T was 69.6%. Based on polyphasic taxonomic characteristics, strain SA5d-4T represents a novel species of a new genus, for which the name Lottiidibacillus patelloidae gen. nov., sp. nov., is proposed with the type strain SA5d-4T (= MCCC 1A11654T = KCTC 33831T). Based on phylogenetic analyses, B. taeanensis should be transferred to a new genus, named Maribacillus, as Maribacillus taeanensis comb. nov., with type strain BH030017T (= KCTC 3918T = DSM 16466T). [ABSTRACT FROM AUTHOR]

Almost by definition, radical innovations create a need to revise existing classification systems. In this paper, we argue that classification system changes and patent reclassification are common and reveal interesting information about technological evolution. To support our argument, we present three sets of findings regarding classification volatility in the U.S. patent classification system. First, we study the evolution of the number of distinct classes. Reconstructed time series based on the current classification scheme are very different from historical data. This suggests that using the current classification to analyze the past produces a distorted view of the evolution of the system. Second, we study the relative sizes of classes. The size distribution is exponential so classes are of quite different sizes, but the largest classes are not necessarily the oldest. To explain this pattern with a simple stochastic growth model, we introduce the assumption that classes have a regular chance to be split. Third, we study reclassification. The share of patents that are in a different class now than they were at birth can be quite high. Reclassification mostly occurs across classes belonging to the same 1-digit NBER category, but not always. We also document that reclassified patents tend to be more cited than non-reclassified ones, even after controlling for grant year and class of origin. [ABSTRACT FROM AUTHOR]

Patients' understanding of a genetic variant of unknown clinical significance (VUS) is likely to influence beliefs about risk implications, consequent medical decisions, and other actions such as involvement in research. We interviewed 26 self-selected participants with a clinically identified VUS before they enrolled into a VUS reclassification study. Semi-structured interviews addressed topics including motivation to get genetic test, experience with the VUS result, affective responses to receiving VUS, and perceived effect of VUS and reclassification on medical care. We found that family and personal history of disease were the most prevalent motivators for getting a genetic test. Participants demonstrated mixed understanding of VUS. Most expressed negative effect on learning of their VUS result and uncertainty about its impact on clinical management. Most expected reclassification efforts to benefit their family members but not themselves. Some expressed distrust of their providers following a VUS result. Participation in the VUS reclassification study appeared to be motivated by four factors for patients with VUS—negative effect about VUS, uncertainty about its impact on clinical management, concern for family members' well-being, and to advance science. Perhaps the direct acknowledgement and appraisal of uncertainty as a means of coping was missing in some pre-test counseling experienced by our participants and thus they were not psychologically prepared for atypical VUS results. The finding of VUS-induced provider distrust suggests a need for careful consideration of appropriate pre- and post-test counseling about VUS. [ABSTRACT FROM AUTHOR]

In the context of the United States K-12 school system, reclassification processes of emergent bilinguals are laden with high-stakes assessments. Largely absent in reclassification scholarship is the consideration of how reclassification policies uniquely affect those learners with identified disabilities. Applying an intersectionality lens that foregrounds political and structural critique, we conducted an interpretive policy analysis of reclassification policies in two states, New Mexico and California. In the analysis, we examined the coalescence of federal and state policies governing reclassification procedures along with assessment designs and practices as they impact the educational realities of emergent bilinguals with disabilities. The analysis illuminated how existing policies and practices marginalize emergent bilinguals with disabilities by making reclassification improbable for students with intersecting disability and second language acquisition needs. We argue that the unlikelihood of being reclassified as Fluent-English Proficient has profound educational consequences for emergent bilinguals, who over time may become disproportionately represented in both special education as well as the long-term English learner population in schools. [ABSTRACT FROM AUTHOR]

The aim of this study was to determine the number of cases of papillary thyroid carcinoma (PTC) which could be reclassified as non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) in our institute over a 10-year period, document their clinical status and assess the number of slides that had to be reviewed per case to exclude NIFTP. The histopathology reports for thyroid resections for all papillary carcinoma over a 10-year period (2007-2016) were reviewed. Five hundred forty-five histopathology reports were reviewed, and 71 cases were identified as potential cases of NIFTP. Forty-nine (69%) cases had been referred from external departments and the slides were not available for review. Of the remaining 22 (31% of 71) cases, 5 were reclassified as NIFTP. The 17 cases that were not reclassified as NIFTP required review of 114 of 356 slides (median 5.5 slides per case) was required to exclude NIFTP. For the 5 NIFTP cases, 58 slides were reviewed (median 12 slides per case). We found that review of the histology reports alone was adequate for exclusion in most cases, e.g. classic PTC or EVPTC cases with documented lymphovascular invasion or capsular invasion. As a single exclusion criterion is required for exclusion from reclassification as NIFTP, this can be achieved efficiently. Two of the five patients received radioactive iodine [RAI] as per standard treatment at time of diagnosis, on the basis of tumour size. None have recurrent or metastatic disease with mean follow-up of 5.8 years. [ABSTRACT FROM AUTHOR]

Background In 2014, New Zealand reclassified sildenafil (for erectile dysfunction) to allow supply by specially trained pharmacists under strict criteria. Objective The study aimed to determine pharmacists' experiences and perspectives on the training for, and supply of sildenafil under this model. Setting New Zealand community pharmacy. Method This qualitative study captured data with a semi-structured interview used with purposively-sampled participants. A maximum variation sample was used to select a wide range of pharmacists working in various pharmacies, including pharmacists who were trained to provide sildenafil and those not trained to supply sildenafil. Consenting pharmacists were interviewed, with interviews audio-recorded and transcribed. Analysis used a framework approach. Main outcome measures Topics explored included: satisfaction and experience of the training; suitability and usability of the screening tools; experiences of the supply process and why some pharmacists chose not to become trained. Results Thirty-five pharmacists were interviewed. Training was seen as uncomplicated and the screening tools provided confidence that key consultation areas were covered. Most consultations reportedly took 15-20 min, some up to 60 min. Pharmacists reported being comfortable with the consultations. Many men requesting supply fell outside of the parameters, resulting in medical referral. This new model of supply was seen as a positive for pharmacists and their patients. Unaccredited pharmacists reported a perceived lack of interest from men, or ability to provide the service as reasons for not seeking accreditation. Conclusion New Zealand's model of pharmacist supply of sildenafil appears workable with some areas for improvement identified. [ABSTRACT FROM AUTHOR]

Purpose: A breast cancer risk prediction rule previously developed by Rosner and Colditz has reasonable predictive ability. We developed a re-fitted version of this model, based on more than twice as many cases now including women up to age 85, and further extended it to a model that distinguished risk factor prediction of tumors with different estrogen/progesterone receptor status. Methods: We compared the calibration and discriminatory ability of the original, the re-fitted, and the type-specific models. Evaluation used data from the Nurses' Health Study during the period 1980-2008, when 4384 incident invasive breast cancers occurred over 1.5 million person-years. Model development used two-thirds of study subjects and validation used one-third. Results: Predicted risks in the validation sample from the original and re-fitted models were highly correlated ( ρ = 0.93), but several parameters, notably those related to use of menopausal hormone therapy and age, had different estimates. The re-fitted model was well-calibrated and had an overall C-statistic of 0.65. The extended, type-specific model identified several risk factors with varying associations with occurrence of tumors of different receptor status. However, this extended model relative to the prediction of any breast cancer did not meaningfully reclassify women who developed breast cancer to higher risk categories, nor women remaining cancer free to lower risk categories. Conclusions: The re-fitted Rosner-Colditz model has applicability to risk prediction in women up to age 85, and its discrimination is not improved by consideration of varying associations across tumor subtypes. [ABSTRACT FROM AUTHOR]

Background In 2012, in a first for the developed world, New Zealand reclassified trimethoprim to allow specially trained pharmacists to supply the medicine without a prescription to women with cystitis fitting specific criteria. Objective This study explored pharmacists' views of the training and screening tool, impact on practice, and the pharmacists' perceptions of views of patients and doctors. Methods Structured interviews were conducted with 28 New Zealand pharmacists trained to supply trimethoprim. These pharmacists were selected to represent geographical spread as well as urban, suburban and rural. The key areas for investigation were: satisfaction about training, appropriateness of training, opinions on the screening tool, impact on clinical practice and perception of others. Audio recorded interviews were thematically analyzed. Results Of 40 pharmacies invited, 28 pharmacists agreed to participate. Most pharmacists were positive about being able to supply trimethoprim, the training and increased clinical focus of their practice. The content of the training was considered appropriate, as was the screening tool, which was well utilised during consultations. Minor suggestions on the training and consultation materials were provided. Some pharmacists reported that referral to the doctor without supply in a minority of trimethoprim consultations, frustrated some women. Frequency of supplies varied considerably by pharmacists from none supplied to weekly supplies. Some pharmacists questioned the exclusion to supply for women who had taken antibiotics in the last six months. Many women had reportedly appreciated the easier access in the pharmacy compared with doctor access, especially at weekends, but sometimes misunderstood the role of the pharmacist in the supply. While pharmacists reported that some doctors had been negative about pharmacist-supply, others were informing women about the service from the pharmacist. Conclusion Pharmacist supply of trimethoprim using mandated training and a screening tool or algorithm for supply is workable and well-accepted by pharmacists. Minor changes have been recommended. Further research is needed to understand perspectives of other stakeholders (women, doctors and practice nurses) and outcomes for patients. [ABSTRACT FROM AUTHOR]

With the use of whole genome sequencing, the taxonomic status of Lactobacillus fermentum 90 TC-4 strain from Russian collections were studied. Complex analysis of phenotypical and genetic properties was conducted using phenotypic and molecular genetic methods. The main characteristics of the genome and biochemical activity profile of the strain were determined. A comparative analysis of the mass spectrum of ribosomal proteins of the strain, its biochemical properties, a fragment of 16S rRNA gene sequencing, and the entire genome revealed that the present strain belongs to the species L. fermentum, confirming its taxonomic status in accordance with modern taxonomy. [ABSTRACT FROM AUTHOR]

Introduction: A substantial interobserver variation in the differential diagnosis of hyperplastic polyps (HPs) and sessile or traditional serrated adenomas (SSAs/TSAs) has been described. Methods: The aim of this study is to determine the magnitude of reclassification of HPs and associated factors after pathological reassessment of specimens from screening and surveillance colonoscopies, and to estimate its consequences for follow-up recommendations. Results: Among 1694 screening and surveillance colonoscopies, a total of 536 polyps were initially diagnosed as HPs and remained unchanged in 88.5 % ( n = 474), whereas 7.6 ( n = 41) and 1.1 % ( n = 6) were reclassified as SSA and TSA, respectively. Compared to definite HPs, SSAs were found more frequently in men than in women (82.9 vs. 61.2 %, p < 0.05), and in individuals ≥65.0 years (51.2 vs. 31.6 %, p = 0.05). Also, more SSAs were >5 mm in size (36.6 vs. 6.3 %, p < 0.05) and were localized in the proximal colon (31.7 vs. 11.8 %, p < 0.05). In a mixed model analysis, age ≥65.0 years (OR 4.13, 95 % CI 1.22-14.2), snare polypectomy (OR 23.6, 95 % CI 4.86-115), and coincident advanced adenomas (OR 7.56, 95 % CI 1.31-43.5) were significantly ( p < 0.05) associated with reclassification to SSAs. Only 0.53 % of patients had received false recommendations for follow-up visits based on the incorrect HP diagnosis. A c.1799T>A, p.V600E BRAF mutation was detected in 21.9 % ( n = 9) of reclassified SSAs. Conclusion: Considering these factors may be helpful in serrated lesions that are difficult to allocate. Incorrect recommendations regarding control colonoscopy intervals due to misdiagnosed HPs can explain only a small fraction of interval colorectal cancers. [ABSTRACT FROM AUTHOR]

Purpose: To define clinical and pathological factors predicting reclassification at the time of 1-year repeat biopsy (re-Bx) based on a Japanese cohort forming part of the Prostate Research International: Active Surveillance (PRIAS) study. Patients and methods: The inclusion criteria for the PRIAS study are as follows: clinical stage T1c/T2, PSA ≤ 10 ng/ml, PSA density (PSAD) < 0.2 ng/ml per milliliter, one or two positive biopsy cores, and Gleason score (GS) ≤ 6 at initial diagnostic biopsy. Baseline clinical characteristics and prostate-specific antigen doubling time (PSADT) at the time of re-Bx were analyzed via multivariate logistic regression with respect to reclassification and 'no cancer' status on the 1-year re-Bx. Results: A total of 386 patients were enrolled in PRIAS-JAPAN by the end of 2013. Of these, 216 underwent re-Bx at 1 year. A total of 73 patients (33.8 %) were reclassified, whereas 74 (34.3 %) had no cancer. Older age, a higher PSAD, a higher positive core rate, and a shorter PSADT were significant predictors of reclassification. The positive core rate was the predictor common to reclassification, no cancer, and high GS, upon re-Bx. Conclusions: An interim analysis of a Japanese AS cohort participating in PRIAS revealed that the positive core rate was strongly associated with reclassification at the 1-year re-Bx. However, although amendment of the PRIAS inclusion criteria to incorporate a positive core might reduce any concern about underestimation, this would also reduce the number of patients undergoing AS. [ABSTRACT FROM AUTHOR]

A taxonomic study was carried out on strain 22II-S11g, which was isolated from the surface seawater of the Atlantic Ocean. The bacterium was found to be Gram-negative, rod shaped without flagellum, oxidase positive and weakly catalase positive. Growth was observed at NaCl concentrations of 0.5-9 % and at temperatures of 10-41 °C. The isolate was incapable of gelatin hydrolysis and unable to reduce nitrate to nitrite, degrade aesculin and Tween 80. On the basis of 16S rRNA gene sequence similarity, strain 22II-S11g was found to be most closely related to Oceanicola batsensis HTCC2597 (97.26 %), followed by Oceanicola nitratireducens JLT1210 (96.39 %), whilst other species of genus Oceanicola shared 94.00-96.34 % sequence similarity. However, it showed low similarity to Oceanicola granulosus HTCC2516 (94.79 %), the type species of the genus Oceanicola. Phylogenetic analysis showed that strain 22II-S11g formed a clade with six species currently classified in the genus Oceanicola, but strain O. granulosus HTCC2516 and strain O. litoreus M-M22 clustered with two other genera respectively. The ANI values between strain 22II-S11g and two type strains ( O. batsensis HTCC2597 and O. granulosus HTCC2516) are 91.86 and 91.81 % respectively. The digital DNA-DNA hybridization estimate values between strain 22II-S11g and two type strains ( O. batsensis HTCC2597 and O. granulosus HTCC2516) are 23.4 ± 2.4 and 20.0 ± 2.3 %, respectively. The principal fatty acids were identified as summed feature 8 (C ω7 c/ ω6 c), C, C ω7 c11-methyl and C 3OH. The G+C content determined from the draft genome sequence is 64.1 mol%. The respiratory quinone was determined to be Q-10 (100 %). Phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, phosphatidylcholine, a phospholipid and three lipids were identified in the polar lipids. The combined genotypic and phenotypic data also show that strain 22II-S11g should not be assigned to the genus Oceanicola; consequently strain 22II-S11g is concluded to represent a novel species of a novel genus in the family Rhodobacteraceae, for which the name Pseudooceanicola atlanticus gen. nov., sp. nov. is proposed (type strain 22II-S11g = KCTC 42004 = LMG 27424 = MCCC 1A09160). Six misclassified species should be transferred to the novel genus Pseudooceanicola as follows: O. batsensis should be transferred to the genus Pseudooceanicola as Pseudooceanicola batsensis comb. nov. (type strain HTCC2597 = ATCC BAA-863 = DSM 15984 = KCTC 12145); Oceanicola marinus should be transferred to the genus Pseudooceanicola as Pseudooceanicola marinus comb. nov. (type strain AZO-C = LMG 23705 = BCRC 17591); O. nitratireducens should be transferred to the genus Pseudooceanicola as Pseudooceanicola nitratireducens comb. nov. (type strain JLT1210 = LMG 24663 = CGMCC 1.7292); Oceanicola nanhaiensis should be transferred to the genus Pseudooceanicola as Pseudooceanicola nanhaiensis comb. nov. (type strain SS011B1-20 = LMG 23508 = CGMCC 1.6293); Oceanicola antarcticus should be transferred to the genus Pseudooceanicola as Pseudooceanicola antarcticus comb. nov. (type strain Ar-45 = CGMCC 1.12662 = LMG 27868); and Oceanicola flagellatus should be transferred to the genus Pseudooceanicola as Pseudooceanicola flagellatus comb. nov. (type strain DY470 = CGMCC 1.12664 = LMG 27871). [ABSTRACT FROM AUTHOR]

The Net Reclassification Improvement (NRI) has become a popular metric for evaluating improvement in disease prediction models through the past years. The concept is relatively straightforward but usage and interpretation has been different across studies. While no thresholds exist for evaluating the degree of improvement, many studies have relied solely on the significance of the NRI estimate. However, recent studies recommend that statistical testing with the NRI should be avoided. We propose using confidence ellipses around the estimated values of event and non-event NRIs which might provide the best measure of variability around the point estimates. Our developments are illustrated using practical examples from EPIC-Potsdam study. [ABSTRACT FROM AUTHOR]

There are occasional marked discordances in BMD T-scores at the lumbar spine (LS) and femoral neck (FN). We investigated whether such discordances could contribute independently to fracture prediction using FRAX. We studied 21,158 women, average age 63 years, from 10 prospective cohorts with baseline FRAX variables as well as FN and LS BMD. Incident fractures were collected by self-report and/or radiographic reports. Extended Poisson regression examined the relationship between differences in LS and FN T-scores (ΔLS-FN) and fracture risk, adjusted for age, time since baseline and other factors including FRAX 10-year probability for major osteoporotic fracture calculated using FN BMD. To examine the effect of an adjustment for ΔLS-FN on reclassification, women were separated into risk categories by their FRAX major fracture probability. High risk was classified using two approaches: being above the National Osteoporosis Guideline Group intervention threshold or, separately, being in the highest third of each cohort. The absolute ΔLS-FN was greater than 2 SD for 2.5 % of women and between 1 and 2 SD for 21 %. ΔLS-FN was associated with a significant risk of fracture adjusted for baseline FRAX (HR per SD change = 1.09; 95 % CI = 1.04-1.15). In reclassification analyses, only 2.3-3.2 % of the women moved to a higher or lower risk category when using FRAX with ΔLS-FN compared with FN-derived FRAX alone. Adjustment of estimated fracture risk for a large LS/FN discrepancy (>2SD) impacts to a large extent on only a relatively small number of individuals. More moderate (1-2SD) discordances in FN and LS T-scores have a small impact on FRAX probabilities. This might still improve clinical decision-making, particularly in women with probabilities close to an intervention threshold. [ABSTRACT FROM AUTHOR]

Little is known about the curricular experiences schools provide English learner students (ELs) to meet the dual goals of attaining English language proficiency (ELP) and grade-level achievement. I introduce the concept of Curricular Streams to provide a more nuanced comparative analysis of four urban middle schools, focusing on: (a) the extent to which they provided English language development (ELD) instruction and access to the core and full curriculum; and (b) the relative emphasis on ELP versus core academic content, remediation versus acceleration, and isolation versus integration of ELs with non-EL peers. I situate the Curricular Streams within the schools' broader cultures and practices. The results reveal local definitions of EL status and wide variation in EL Curricular Streams: One school emphasized ELP and remediation over access to the core. Another integrated ELs more quickly into mainstream courses, yet its remediation emphasis limited access to the core. The third provided more access, but isolated ELs. The fourth provided more access to the core, accelerated ELD, and eschewed interventions. The evidence suggests that schools are groping for solutions and it raises questions about the efficacy of EL state policy that relies on local control for interpretation. I provide implications for research, policy, and practice and hypotheses about the characteristics of Curricular Streams and school cultures that might increase ELs' opportunity to learn and achieve the dual goals. [ABSTRACT FROM AUTHOR]

A Gram-negative, aerobic, non-flagellated and rod-shaped or ovoid bacterial strain, designated DSSK2-3, was isolated from the junction between the ocean and a freshwater spring at Jeju island, South Korea. Strain DSSK2-3 was found to grow optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences revealed that strain DSSK2-3 joins the cluster comprising the type strains of Pacificibacter maritimus and Roseovarius marinus, with which it exhibited the highest sequence similarity values of 96.04 and 95.75 %, respectively. Sequence similarities to the type strains of other recognized species were <95.74 %. Strain DSSK2-3 was found to contain Q-10 as the predominant ubiquinone and C ω7 c as the major fatty acid. The polar lipid profile of strain DSSK2-3 was found to contain phosphatidylglycerol, an unidentified lipid and an unidentified aminolipid as major components, which distinguished the strain from those of phylogenetically related taxa. The DNA G+C content of strain DSSK2-3 was determined to be 60.8 mol%. On the basis of the phylogenetic data and the chemotaxonomic and other phenotypic properties, strain DSSK2-3 is considered to represent a new genus and species within the class Alphaproteobacteria, for which the name Aquimixticola soesokkakensis gen. nov., sp. nov. is proposed. The type strain of A. soesokkakensis is DSSK2-3 (=KCTC 42137 = CECT 8620). In this study, it is also proposed that R. marinus should be reclassified as a member of the genus Pacificibacter and the description of the genus Pacificibacter is emended. [ABSTRACT FROM AUTHOR]

Multigene phylogenies have been instrumental in revising the classification of ascosporic (teleomorph) yeasts in a natural system based on lines of descent. Although many taxonomic changes have already been implemented for teleomorph taxa, this is not yet the case for the large genus Candida and smaller anascosporic (anamorph) genera. In view of the recently introduced requirement that a fungal species or higher taxon be assigned only a single valid name under the new International Code of Nomenclature for algae, fungi, and plants (Melbourne Code), the current species of Candida and other anamorph yeast genera must undergo revision to make genus membership consistent with phylogenetic affinities. A review of existing data and analyses shows that certain Candida species may be assigned to teleomorph genera with high confidence using multigene phylogenies. Candida species that form well-circumscribed phylogenetic clades without any teleomorph member justify the creation of new genera. However, a considerable number of Candida species sit at the end of isolated and often long branches, and hence cannot be assigned to larger species groups. They should be maintained in Candida sensu lato until studied by multigene analyses in datasets with comprehensive taxon sampling. The principle of name stability has to be honoured to the largest extent compatible with a natural classification of Candida species. [ABSTRACT FROM AUTHOR]

SFAS No. 115 requires firms to recognize available-for-sale (AFS) securities at fair value with accumulated unrealized gains and losses (AUGL) recorded in accumulated other comprehensive income. Firms reclassify AUGL to net income when they realize gains and losses. We refer to the amount reclassified each period by 'RECLASS.' As of 1998, SFAS No. 130 requires firms to present RECLASS prominently in their financial statements. We investigate the incremental explanatory power of RECLASS for banks' market values and market-adjusted returns. In the market value analysis, we control for AUGL, other components of book value of equity, net income before extraordinary items and RECLASS (NIBEX), and other components of comprehensive income. In the returns analysis, we control for ΔAUGL, ΔNIBEX, and extraordinary items. We find high positive coefficients on RECLASS in both analyses, consistent with investors pricing RECLASS as a relatively permanent component of net income. Exploring possible explanations for these pricing implications, we find no evidence that they are attributable to RECLASS remedying unreliable fair value measurement of AUGL. We provide three distinct analyses indicating that RECLASS's pricing implications are explained in significant part by it helping investors predict banks' future performance. Our results illustrate that an important type of amortized cost accounting information, realized gains and losses, remains highly useful to investors despite the overall fair-value-accounting framework for AFS securities. [ABSTRACT FROM AUTHOR]

The incidence of type 2 diabetes can be reduced substantially by implementing preventive measures in high-risk individuals, but this requires prior knowledge of disease risk in the individual. Various diabetes risk models have been designed, and these have all included a similar combination of factors, such as age, sex, obesity, hypertension, lifestyle factors, family history of diabetes and metabolic traits. The accuracy of prediction models is often assessed by the area under the receiver operating characteristic curve (AROC) as a measure of discrimination, but AROCs should be complemented by measures of calibration and reclassification to estimate the incremental value of novel biomarkers. This review discusses the potential of novel biomarkers to improve model accuracy. The range of molecules that serve as potential predictors of type 2 diabetes includes genetic variants, RNA transcripts, peptides and proteins, lipids and small metabolites. Some of these biomarkers lead to a statistically significant increase of model accuracy, but their incremental value currently seems too small for routine clinical use. However, only a fraction of potentially relevant biomarkers have been assessed with regard to their predictive value. Moreover, serial measurements of biomarkers may help determine individual risk. In conclusion, current risk models provide valuable tools of risk estimation, but perform suboptimally in the prediction of individual diabetes risk. Novel biomarkers still fail to have a clinically applicable impact. However, more efficient use of biomarker data and technological advances in their measurement in clinical settings may allow the development of more accurate predictive models in the future. [ABSTRACT FROM AUTHOR]

Objective: To investigate the value of the calcium score (CaSc) plus clinical evaluation to restrict referral for CT coronary angiography (CTCA) by reducing the number of patients with an intermediate probability of coronary artery disease (CAD). Methods: We retrospectively included 1,975 symptomatic stable patients who underwent clinical evaluation and CaSc calculation and CTCA or invasive coronary coronary angiography (ICA). The outcome was obstructive CAD (≥50 % diameter narrowing) assessed by ICA or CTCA in the absence of ICA. We investigated two models: (1) clinical evaluation consisting of chest pain typicality, gender, age, risk factors and ECG and (2) clinical evaluation with CaSc. Discrimination of the two models was compared. The stepwise reclassification of patients with an intermediate probability of CAD (10-90 %) after clinical evaluation followed by clinical evaluation with CaSc was assessed by clinical net reclassification improvement (NRI). Results: Discrimination of CAD was significantly improved by adding CaSc to the clinical evaluation (AUC: 0.80 vs. 0.89, P < 0.001). CaSc and CTCA could be avoided in 9 % using model 1 and an additional 29 % of CTCAs could be avoided using model 2. Clinical NRI was 57 %. Conclusion: CaSc plus clinical evaluation may be useful in restricting further referral for CTCA by 38 % in symptomatic stable patients with suspected CAD. Key Points: • CT calcium scores ( CaSc) could proiritise referrals for CT coronary angiography ( CTCA) • CaSc provides an incremental discriminatory value of CAD compared with clinical evaluation • Risk stratification is better when clinical evaluation is combined with CaSc • Appropriate use of clinical evaluation and CaSc helps avoid unnecessary CTCA referrals [ABSTRACT FROM AUTHOR]

Several states, including Arizona, have enacted English-only legislation, within the past decade, impacting the schooling of students who are identified as English language learner (ELLS). As a result, ELLS in Arizona are assigned to a prescriptive program-apart from their fluent English-speaking peers-for 4 h a day, during a time 'not normally to exceed 1 year.' The ultimate goal is to reclassify ELLs to fluent English proficient (FEP) status, exit them from the program and integrate students into 'mainstream' classrooms, where no additional support services are offered. Since language policies are dictating the instructional policy decisions regarding assessment and reclassification of ELLS, the authors argue that it is necessary to critically examine how English-only policies-especially the discourse of policy making-contribute to the shift in the definition of reclassification, its process and ultimately, the consequences for students. Thus, the paper unpacks the shifts in reclassification policy and process; our critical discourse analysis of the legislators' meetings, based on the work of van Leeuwen (Discourse Commun 1(1):91-112, ), show that although Arizona's ELL Task Force set out to develop an educational policy to prepare ELLS linguistically and academically within one school year, the timeframe (or time limit) took precedence to the academic preparedness of newly reclassified students-a population that is academically vulnerable. [ABSTRACT FROM AUTHOR]

Making a prognosis is to predict the course of a disease and estimate the probability (or risk) of the appearance of a given outcome in relationship to clinical or non-clinical characteristics. Prognostic assessment is usually modelled by multivariable mathematic equations (prognostic models). In this article we describe what a prognostic model is, how to build a good one, why and how it is important to evaluate its generalizability and accuracy by means of discrimination, calibration and reclassification. [ABSTRACT FROM AUTHOR]

Support vector machines (SVMs) have good accuracy and generalization properties, but they tend to be slow to classify new examples. In contrast to previous work that aims to reduce the time required to fully classify all examples, we present a method that provides the best-possible classification given a specific amount of computational time. We construct two SVMs: a “full” SVM that is optimized for high accuracy, and an approximation SVM (via reduced-set or subset methods) that provides extremely fast, but less accurate, classifications. We apply the approximate SVM to the full data set, estimate the posterior probability that each classification is correct, and then use the full SVM to reclassify items in order of their likelihood of misclassification. Our experimental results show that this method rapidly achieves high accuracy, by selectively devoting resources (reclassification) only where needed. It also provides the first such progressive SVM solution that can be applied to multiclass problems. [ABSTRACT FROM AUTHOR]