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Here, we report the draft genome sequence of Nitrobacter vulgaris DSM 10236T, a nitrite-oxidizing bacterium isolated from a sewage system in Hamburg, Germany. The genome is 4.3 Mb in size with 4,585 predicted genes, including the full complement of genes necessary for growth on nitrite (narK, nxrA, nxrB, nxrC, and nxrD).

Opinion 130 deals with a Request for an Opinion asking the Judicial Commission to clarify whether the genus name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate. The Request is approved and an answer is given. The name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate because it is a later homonym of the validly published cyanobacterial name Rhodococcus Hansgirg 1884. The Judicial Commission also clarifies that it has the means to resolve such cases by conserving a name over an earlier homonym. It is concluded that the name Rhodococcus Zopf 1891 (Approved Lists 1980) is significantly more important than the name Rhodococcus Hansgirg 1884 and therefore the former is conserved over the latter. This makes the name Rhodococcus Zopf 1891 (Approved Lists 1980) legitimate.

This study aims to examine Child-Centered Play Therapy's effect on reducing behavioral problems in five- and six-year-old children living in Istanbul. The study was conducted with 20 children from socioeconomically disadvantaged families. Families applied for support to a play therapy room established in a primary school. A pre-test and post-test control group design is used. Child-Centered Play Therapy sessions were implemented in the experimental group for eight weeks as individual sessions. Data due to the children's behavior problems were collected from parents via the "Social Competence and Behavior Evaluation-30 Scale" and the family pre-interview form. Mann Whitney-U Test and Wilcoxon Test analyzed data. Results of the experimental group (ingroup analyses) show a significant difference between pre-test and post-test scores of social competence, anger aggression, and anxiety withdrawal subscales, as hypothesized. However, analyses of between groups' post-test comparisons show significant differences only in the social competence subscale. Between groups, post-test scores, comparisons of anger-aggression, and anxiety withdrawal subscales showed no significant differences. The results are discussed; additionally, observations of the researcher as a play therapist are presented.

Abstract Background As the spatial resolution of positron emission tomography (PET) scanners improves, understanding of radiotracer distributions in tissues at high resolutions is important. Hence, we propose a method for co-registration of high-resolution ex vivo specimen PET images, combined with computed tomography (CT) images, and the corresponding specimen histopathology. Methods We applied our co-registration method to breast cancer (BCa) specimens of patients who were preoperatively injected with 0.8 MBq/kg [ $$^{18}$$ 18 F]fluorodeoxyglucose ([18F]FDG). The method has two components. First, we used an image acquisition scheme that minimises and tracks tissue deformation: (1) We acquired sub-millimetre (micro)-PET-CT images of ±2 mm-thick lamellas of the fresh specimens, enclosed in tissue cassettes. (2) We acquired micro-CT images of the same lamellas after formalin fixation to visualise tissue deformation. (3) We obtained 1 hematoxylin and eosin (H&E) stained histopathology section per lamella of which we captured a digital whole slide image (WSI). Second, we developed an automatic co-registration algorithm to improve the alignment between the micro-PET-CT images and WSIs, guided by the micro-CT of the fixated lamellas. To estimate the spatial co-registration error, we calculated the distance between corresponding microcalcifications in the micro-CTs and WSIs. The co-registered images allowed to study standardised uptake values (SUVs) of different breast tissues, as identified on the WSIs by a pathologist. Results We imaged 22 BCa specimens, 13 cases of invasive carcinoma of no special type (NST), 6 of invasive lobular carcinoma (ILC), and 3 of ductal carcinoma in situ (DCIS). While the cassette framework minimised tissue deformation, the best alignment between the micro-PET-CT images and WSIs was achieved after deformable co-registration. We found an overall average co-registration error of 0.74 ± 0.17 mm between the micro-PET images and WSIs. (Pre)malignant tissue (including NST, ILC, and DCIS) generally showed higher SUVs than healthy tissue (including healthy glandular, connective, and adipose tissue). As expected, inflamed tissue and skin also showed high uptake. Conclusions We developed a method to co-register micro-PET-CT images of surgical specimens and WSIs with an accuracy comparable to the spatial resolution of the micro-PET images. While currently, we only applied this method to BCa specimens, we believe this method is applicable to a wide range of specimens and radiotracers, providing insight into distributions of (new) radiotracers in human malignancies at a sub-millimetre resolution.

In Turkey, the quest for gender equality in universities takes place under increasing anti-gender, authoritarian and neoliberal pressures. Based on interviews with academic change agents, this article explores gender equality efforts in different universities presented in the form of typology: project-led, collective and individual-led change. It suggests that change processes are context-bound, yet they face similar challenges in securing inclusivity, intersectionality and sustainability, which are better addressed by hybrid strategies. Differing from professionalised reform strategies in the global North, gender equality reform in Turkey's universities provides insights transcending binaries such as that between the university and its outside, top-down and grassroots change, and formal and informal solidarities.

Xenorhabdus species are bacterial symbionts of entomopathogenic Steinernema nematodes, in which they produce diverse secondary metabolites implicated in pathogenesis. To expand resources for natural product prospecting and exploration of host-symbiont-pathogen relationships, the genomes of Xenorhabdus cabanillasi, Xenorhabdus ehlersii, Xenorhabdus japonica, Xenorhabdus koppenhoeferii, and Xenorhabdus mauleonii were analyzed.

Abstract Aim This study explores the connection between Behçet’s disease (BD), characterized by persistent oral and genital ulcers alongside iritis, and periodontal disease. It examines the levels of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and nitric oxide (NO) in gingival crevicular fluid (GCF) and saliva. Methods Forty Behçet’s patients with gingivitis or periodontitis and 47 patients with either gingivitis or periodontitis but without BD were studied. Periodontal status was recorded with standard clinical indexes. GCF and saliva samples were obtained. NO, IL-1β and TNF-α levels were analysed. Current Behçet’s symptoms and medications usage were recorded. Results Mean salivary IL-1β was elevated (p = .045), and mean NO level was decreased in BD patients with gingivitis compared to patients without BD (p = .000). In contrast, mean NO level in crevicular fluid was higher in Behçet’s patients with periodontitis than in patients without BD (p = .009). Furthermore, among Behçet’s patients, those with vascular involvement had lower salivary NO level compared to patients without vascular involvement (p = .000). Conclusions Based on our findings, the elevated levels of IL-1β in the saliva of Behçet’s patients with gingivitis, along with the decreased NO level, indicate an altered inflammatory response in the oral cavity.

Opinion 123 places the epithet of the name Aeromonas punctata on the list of rejected epithets and clarifies the citation of authors of selected names within the genus Aeromonas. Opinion 124 denies the request to place Borreliella on the list of rejected names because the request is based on a misinterpretation of the Code, which is clarified. There are alternative ways to solve the perceived problem. Opinion 125 denies the request to place Lactobacillus fornicalis on the list of rejected names because the provided information does not yield a reason for rejection. Opinion 126 denies the request to place Prolinoborus and Prolinoborus fasciculus on the list of rejected names because a relevant type strain deposit was not examined. Opinion 127 grants the request to assign the strain deposited as ATCC 4720 as the type strain of Agrobacterium tumefaciens, thereby correcting the Approved Lists. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.

Judicial Opinion 128 addresses nomenclatural issues related to the names of classes validly published under the International Code of Nomenclature of Prokaryotes. It is confirmed that the common ending -proteobacteria of some class names is not indicative of a joint taxonomic or phylogenetic placement; that the nomenclatural type of Mollicutes Edward and Freundt 1967 (Approved Lists 1980) is Mycoplasmatales Freundt 1955 (Approved Lists 1980); and that the placement of a name on the list of rejected names does not imply that another name with the same spelling but a distinct rank is also placed on that list. The names at the rank of class Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988, Archaeobacteria Murray 1988, Bacteria Haeckel 1894 (Approved Lists 1980), Firmibacteria Murray 1988, Microtatobiotes Philip 1956 (Approved Lists 1980), Oxyphotobacteria (ex Gibbons and Murray 1978) Murray 1988, Photobacteria Gibbons and Murray 1978 (Approved Lists 1980), Proteobacteria Stackebrandt et al. 1988, Schizomycetes Nägeli 1857 (Approved Lists 1980), Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980) are placed on the list of rejected names. For three common nominative singular suffixes of genus names their genitive singular and nominative plural forms are confirmed: -bacter (-bacteris, -bacteres); -fex (-ficis, -fices); and -genes (-genis, -genes). The class names Aquificae Reysenbach 2002, Chrysiogenetes Garrity and Holt 2002, Chthonomonadetes Lee et al. 2011, Gemmatimonadetes Zhang et al. 2003, Opitutae Choo et al. 2007 and Verrucomicrobiae Hedlund et al. 1998 are orthographically corrected to Aquificia, Chrysiogenia, Chthonomonadia, Gemmatimonadia, Opitutia and Verrucomicrobiia, respectively.

In this paper the Judicial Commission provides general guidance for interpreting the International Code of Nomenclature of Prokaryotes (ICNP) and specific assistance to authors, reviewers and editors of a Request for an Opinion, or of other suggestions related to the ICNP. The role of the Judicial Commission is recapitulated, particularly with respect to the processing of such Requests. Selected kinds of nomenclature-related proposals are discussed that are unsuitable as the basis for a Request. Particular emphasis is put on Requests for placing names or epithets on the list of nomina rejicienda, and a dichotomous identification key is provided to guide potential authors of a Request that targets the name of a species or subspecies because of issues with its type strain. To this end, the criteria for the valid publication of such names under the ICNP are revisited. Aspects of other kinds of Requests are also addressed. The study is based on a comprehensive review of all Judicial Opinions issued since the publication of the Approved Lists in 1980. One goal of this paper is to assist potential authors in deciding whether their concern should be the subject of a Request, and if so, in composing it with the greatest chance of success. It is also clarified how to obtain additional help regarding nomenclature-related issues.

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.

This paper discusses service times based on vehicle class at barrier-operated toll booths. Service times were measured using four vehicle classifications: car (C), medium goods vehicle (MGV), trucks & bus (TB), and articulated truck (AT) with two payment options: electronic (ETC) and manual toll collection (MTC). Each toll booth has both payment systems and resulting in mixed toll booth utilization in terms of payment and vehicles. The collected data was utilized to estimate logistic regression, and non-parametric statistical tests were performed. Findings indicate, when vehicle size increases, so does service time for even ETC. Furthermore, logistic regression used to compute threshold service times shifting from ETC to MTC for C, MGV, TB, and AT, which were 5.92, 7.51, 10.00, and 12.80 s, respectively. The transition time for a vehicle switch from ETC to MTC based on the logistic curve is denoted by threshold service time. Below the threshold, ETC is more favorable option and affected by barrier and vehicle class. Overall, the results indicate that operators can benefit from more dynamic operational conditions facilitated by threshold service times, enabling adaptive and efficient toll booth operations. Additionally, these thresholds can serve as valuable measure of service quality for managing freeway exits.

The goal of this study was to inquire the impact of the reflective coaching (RC) on development of pre-service EFL (English as a Foreign Language) teachers' sense of efficacy and instructional skills. The reflective coaching program utilized in this study was developed and adapted by the researcher in 2016 mainly based on the theoretical views and principles of reflection, self-analysis of strengths and weaknesses and the writing of personal statements, and reflective teaching. The research approach used for this study was both quantitative and qualitative and this study is a single case study based on pre/post-test design. To achieve this goal, eight volunteer male and female (one male and seven female) undergraduate students, aged from 21 to 22, attending B.A. program in ELT, Faculty of Education, Çanakkale Onsekiz Mart University, Turkey participated in the study. For the pre/post-test design of this study, one case study group was formed. The study was conducted between February 11, 2019 and May 17, 2019. During the implementation of the RC program, the researcher also employed an overview of the instructional skills, which represented teaching behaviors desired. Results showed significant differences in favor of the implementation of RC program on development of pre-service EFL (English as a Foreign Language) teachers' sense of efficacy and instructional skills. The findings are expected to have implications for how reflective coaching can be a means to improve instructional skills and sense of efficacy and recommendations for EFL teachers and curriculum designers will also be made.

Opinion 112 denies the request to place Seliberia Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject Shewanella irciniae Lee et al. 2006 and Opinion 114 denies the request to reject the name Enterobacter siamensis Khunthongpan et al. 2014. Opinion 115 rejects the epithet of Moorella thermoautotrophica (Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate Methylothermus subterraneus Hirayama et al. 2011 as the type species of the genus Methylothermus is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name Flaviaesturariibacter is treated, as are the analogous cases of Fredinandcohnia and Hydrogeniiclostidium. The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and Hydrogeniiclostridium, respectively. Opinion 119 concludes that assigning Actinomycetales Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class Actinobacteria Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but Actinomycetales is also assigned as type of Actinomycetes Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name Amycolatopsis albidoflavus is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of Mollicutes proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.

Abstract Purpose The aim of the study was to compare the difference in survival between invasive ductal (IDC) and lobular carcinoma (ILC). Methods Data of patients (n = 1843) with a hormone receptor-positive, HER2-negative, pT1-3 IDC or ILC cancer without distant metastasis, treated at the Ghent University Hospital over the time period 2001–2015, were analyzed. Results ILC represented 13.9% of the tumors, had a higher percentage of pT3 and pN3 stages than IDC, lymphovascular space invasion (LVSI) was less present and Ki-67 was mostly low. 73.9% of ILCs were grade 2, whereas IDC had more grade 1 and grade 3 tumors. Kaplan–Meier curves and log-rank testing showed a significant worse DFS for ILC with pN ≥ 1 than for their IDC counterpart. In a multivariable Cox regression analysis the histologic tumor type, ductal or lobular, was a determinant of DFS over 120 months (IDC as reference; hazard ratio for ILC 1.77, 95% CI 1.08–2.90) just as the ER Allred score (hazard ratio 0.84, 95% CI 0.78–0.91), LVSI (hazard ratio 1.75, 95% CI 1.12–2.74) and pN3 (hazard ratio 2.29, 95% CI 1.03–5.09). Determinants of OS over ten years were age (hazard ratio 1.05, 95% CI 1.02–1.07), LVSI (hazard ratio 3.62, 95% CI 1.92–6.82) and the ER Allred score (hazard ratio 0.80, 95% CI 0.73–0.89). Conclusion The histologic tumor type, ductal or lobular, determines DFS in hormone receptor-positive, HER2-negative, pT1-3 breast cancer besides the ER Allred score, LVSI and pN3.

Both side pain and urinary system pathologies are common reasons for admission to emergency departments. Spontaneous renal pelvic rupture is also very rare. Existing renal anomalies and calculi also increase the risk of rupture. Here, we present a 50-year-old male case who developed unilateral renal pelvis rupture spontaneously without trauma.

Alzheimer's disease is a complex brain disease and is also the most common form of dementia that leads to impaired social and intellectual abilities. The disease only manifests itself with a simple forgetfulness, as the disease progresses, the patient forgets the recent events, cannot recognize his family members and close environment, and becomes in need of care in the last stage. Early detection is therefore crucial for medical intervention to prevent brain injury and prolong everyday functioning. In this study is aimed to detection of Alzheimer’s disease from EEG signals using the multitaper and ensemble learning methods. The dataset comprises of 24 healthy people and 24 Alzheimer's patients' EEG signals. 49 features were extracted by calculating the power spectral density (PSD) of the frequencies of the EEG signals between 1-49 Hz using the multitaper method. Then, the performances of AdaboostM1, Total Boost, Gentle Boost, Logit Boost, Robust Boost, and Bagging ensemble learning algorithms were compared. As a result of experiments, the Logit Boost algorithm has the highest performance. The algorithm has achieved a promising performance of 93.04% accuracy, 93.09% f1-score, 92.75% sensitivity, 93.43% precision, and 93.33% specificity.

BackgroundThe genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus.ResultsIn this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains.ConclusionsGenome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Pseudomonas is the bacterial genus of Gram-negative bacteria with the highest number of recognized species. It is divided phylogenetically into three lineages and at least 11 groups of species. The Pseudomonas putida group of species is one of the most versatile and best studied. It comprises 15 species with validly published names. As a part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, we present the genome sequences of the type strains of five species included in this group: Pseudomonas monteilii (DSM 14164T), Pseudomonas mosselii (DSM 17497T), Pseudomonas plecoglossicida (DSM 15088T), Pseudomonas taiwanensis (DSM 21245T) and Pseudomonas vranovensis (DSM 16006T). These strains represent species of environmental and also of clinical interest due to their pathogenic properties against humans and animals. Some strains of these species promote plant growth or act as plant pathogens. Their genome sizes are among the largest in the group, ranging from 5.3 to 6.3 Mbp. In addition, the genome sequences of the type strains in the Pseudomonas taxonomy were analysed via genome-wide taxonomic comparisons of ANIb, gANI and GGDC values among 130 Pseudomonas strains classified within the group. The results demonstrate that at least 36 genomic species can be delineated within the P. putida phylogenetic group of species.

Objective: Studies comparing the efficacy and safety of prophylactic regimens for central nervous system (CNS) involvement in acute lymphoblastic leukemia (ALL) are scarce in adults. This multicenter retrospective study aimed to compare the efficacy of prophylactic regimens with and without CNS irradiation on the development of CNS relapse during follow-up. Materials and Methods: This was a multicenter comparative cohort study. A total of 203 patients were included from four tertiary care centers in Turkey. Patients were divided into two groups according to whether they received CNS irradiation or not. The groups were analyzed retrospectively regarding patient and disease characteristics, with the main focus being CNS relapse. Results: While 105 patients received chemotherapy-based prophylaxis, 98 patients received additional CNS irradiation. These groups were statistically comparable in terms of demographic characteristics and risk factors for CNS involvement. In the irradiation group, patients were younger and had more stem cell transplants. In a median of 23.8 (11.1-62.4) months, there was no difference between the two groups regarding CNS relapse-free survival (log-rank p=0.787). Conclusion: Craniospinal irradiation may not be indispensable for every adult patient with ALL, similarly to pediatric patients. It is crucial to avoid the long-term toxicities of radiation, especially in patients with long life expectancy. Craniospinal irradiation may be reserved for therapeutic use in cases of CNS relapse and prophylaxis for some high-risk patients.

Purpose: The measurements’ reference points associated with foramen magnum (FM) and cranium were examined in this retrospective study. Also, the relation between FM and cranium harmony were calculated both on dry skull and in healthy subjects performed on computed tomography (CT). Materials and Methods: The present study was carried out on 185 healthy adult subjects (90 females; 95 males) aged between 18–67 years and 15 dried skull of unknown gender of an Anatolian population. The shapes of the FM were classified as two semicircle, oval, round, egg, tetragonal, pentagonal, hexagonal and irregular shapes. The anteroposterior length and transverse width of the FM and cranium were measured on both photos and CT. Results: The means and standard deviations of the measurements were given for three groups. To control the accuracy of FM width (FMW) and length (FML) results, a formula was used for three groups including dried skull and CT measurements of females and males, seperately (FMW=Cranial width (CW)/4.26 for group 1, CW/4.66 for group 2 and CW/4.66 for group 3; and FML=Cranial length (CL)/4.51 for group 1, CL/4.33 for group 2 and CL/4.16 for group 3). The oval type FM was predominant (26.67%) in dried skull and (23.33%) in females and (28.42%) in males. Conclusion: The present study presents noteworthy data about FM and cranium harmony of the adult Turkish population and dry skulls that will show a harmony between cranium and foramen magnum in clinical practice. There was no tetragonal and hexagonal FM types in dried skulls and tetragonal type FM was the least seen type in females and males.

Abstract Background Up to 60% of breast cancer patients treated with chemotherapy is confronted with cognitive problems, which can have a significant impact on daily activities and quality of life (QoL). We investigated whether exercise training improves cognition in chemotherapy-exposed breast cancer patients 2–4 years after diagnosis. Methods Chemotherapy-exposed breast cancer patients, with both self-reported cognitive problems and lower than expected performance on neuropsychological tests, were randomized to an exercise or control group. The 6-month exercise intervention consisted of supervised aerobic and strength training (2 h/week), and Nordic/power walking (2 h/week). Our primary outcome was memory functioning (Hopkins Verbal Learning Test-Revised; HVLT-R). Secondary outcomes included online neuropsychological tests (Amsterdam Cognition Scan; ACS), self-reported cognition (MD Anderson Symptom Inventory for multiple myeloma; MDASI-MM), physical fitness (relative maximum oxygen uptake; VO2peak), fatigue (Multidimensional Fatigue Inventory), QoL (European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire; EORTC QLQ C-30), depression (Patient Health Questionnaire-9, Hospital Anxiety and Depression Scale; HADS), and anxiety (HADS). HVLT-R total recall was analyzed with a Fisher exact test for clinically relevant improvement (≥ 5 words). Other outcomes were analyzed using multiple regression analyses adjusted for baseline and stratification factors. Results We randomized 181 patients to the exercise (n = 91) or control group (n = 90). Two-third of the patients attended ≥ 80% of the exercise sessions, and physical fitness significantly improved compared to control patients (B VO2peak 1.4 ml/min/kg, 95%CI:0.6;2.2). No difference in favor of the intervention group was seen on the primary outcome. Significant beneficial intervention effects were found for self-reported cognitive functioning [MDASI-MM severity (B-0.7, 95% CI − 1.2; − 0.1)], fatigue, QoL, and depression. A hypothesis-driven analysis in highly fatigued patients showed positive exercise effects on tested cognitive functioning [ACS Reaction Time (B-26.8, 95% CI − 52.9; − 0.6) and ACS Wordlist Learning (B4.4, 95% CI 0.5; 8.3)]. Conclusions A 6-month exercise intervention improved self-reported cognitive functioning, physical fitness, fatigue, QoL, and depression in chemotherapy-exposed breast cancer patients with cognitive problems. Tested cognitive functioning was not affected. However, subgroup analysis indicated a positive effect of exercise on tested cognitive functioning in highly fatigued patients. Trial Registration Netherlands Trial Registry: Trial NL5924 (NTR6104). Registered 24 October 2016, https://www.trialregister.nl/trial/5924 .