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We present a full genome sequence for the thermophilic denitrifier Geobacillus thermodenitrificans subsp. calidus DSM 22629T (3,408,575 bp, 48.94% GC). This genome includes 3,615 predicted genes, including those needed to reduce nitrate to nitrogen gas. This organism and genome sequence provide valuable resources for future phylogenetic, genomic, and biotechnological research.

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.

Endocrine disruptors, particularly phthalates like Dimethyl phthalate (DMP) and Diisobutyl phthalate (DiBP), are prevalent environmental contaminants posing significant health risks. This study investigates the combined neurotoxic effects of DMP and DiBP on SH-SY5Y neuroblastoma cells by analyzing cytotoxicity, oxidative stress, and apoptosis. Using MTT and Neutral Red Uptake assays, we determined the IC50 values for DMP and DiBP as 11.35 mM and 1.307 mM, respectively. Flow cytometry revealed increased Reactive Oxygen Species (ROS) levels, indicating oxidative stress, while apoptosis assays showed enhanced cell death with combined phthalate exposure. The results demonstrate a synergistic effect, exacerbating cytotoxic and oxidative damage beyond individual exposures. This study highlights the compounded risk of phthalate mixtures, urging comprehensive risk assessments and regulatory policies to mitigate human health risks from combined chemical exposures.

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.

Jaywalking significantly increases accident risks compared to marked crosswalks. Overpasses are often installed to address this, but violations continue. This study examines pedestrian behavior at overpass locations, focusing on 438 individuals recorded on video. Factors like parked vehicles, gender, age, group size, mobile phone distraction, carrying items, the number of waiting pedestrians upon arrival, waiting times, and traffic volume were analyzed. Since jaywalking is more frequent during off-peak hours when traffic is not congested, observations were made at random intervals during these times. A binary logit model was used to identify the factors influencing jaywalking. The study found that points of interest near overpasses significantly affect pedestrian behavior. Additionally, parked vehicles near the overpass reduce crossing distance, encouraging jaywalking. Policy recommendations include implementing parking restrictions and strategically locating overpasses to align with pedestrian movement patterns and nearby points of interest.

The present study aims to evaluate the relationship between smartphone addiction and depression in primary care. Three hundred fifty-two people who participated in our research, designed as a cross-sectional study, filled out the Short Version of the Smartphone Addiction scale and Beck’s Depression Inventory. Among the participants, 28.9% were found to have smartphone addiction and 52.3% were found to have depressive symptoms. The mean score of participants in the Smartphone Addiction Scale was 24.32 ± 11.24 points (n = 352). The mean score in Beck’s Depression Inventory was 10.80 ± 7.94 points. A positive significant relationship was found between depression frequency and social media usage duration (1–2 hours/ day) and length of social media usage (≥5 hours/day). A weak but positive and significant correlation was found between Smartphone Addiction Scale and Beck’s Depression Inventory (r = 0.147; p = .006). In the regression analysis, it was determined that having an income between 1000 and 1999 TL, having a computer at home, having other addictions other than smoking, and being addicted to a smartphone increase the risk of depression development. The relationship between smartphone addiction and depression should be given attention. The factors influencing smartphone addiction should be considered. Especially the social media and smartphone usage should be limited.

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.

Mevcut literatüre odaklanarak alandaki ilerlemeyi, yönünü ve güncel eğilimleri tespit etmeye çalışan araştırmalar öz yansıtıcı çalışmalar olarak adlandırılmaktadır. İletişim alanına yönelen öz yansıtıcı bir çalışma olarak bu araştırmada Türkiye’de yayınlanan ve ESCI indeksinde taranan Connectist: Istanbul University Journal of Communication Sciences, İlef Dergisi ve Türkiye İletişim Araştırmaları Dergisi ele alınarak 2020-2022 yılları arasında yayınlanan araştırma makaleleri önce bibliyometrik analiz, ardından içerik analizi tekniği ile iki aşamada incelemiştir. Böylece 2023 Şubat-Nisan tarihleri arasında gerçekleşen bu araştırmada Türkiye’nin iletişim alanında önde gelen dergileri üzerinden alanın güncel bir görünümü elde edilmeye çalışılmıştır. Bu kapsamda toplam 210 makale araştırmanın örneklemi olarak belirlenmiştir. İletişim alanında yapılan çalışmalar göz önüne alındığında, ilgili dergilerdeki araştırma makalelerine yönelik karşılaştırmalı olarak gerçekleşen bibliyometrik analiz ve içerik analizine rastlanmaması araştırmanın özgünlüğünü ifade eder. Gerçekleştirilen analizler neticesinde; (1) sosyal medya ve COVID-19 anahtar kelimelerinin ön plana çıktığı; blockchain, yapay zekâ, pandemi iletişimi, dezenformasyon, sürdürülebilirlik, sürdürülebilir iletişim, sivil toplum ile kullanımlar ve doyumlar anahtar kelimelerinin dikkat çektiği, (2) çoğunlukla dijital medyaya odaklanıldığı, (3) fon kullanan makale sayısının oldukça az olduğu, (4) makalelerin çoğunlukla Türkiye menşeli olduğu ve Türkçe yazıldığı, (5) büyük çoğunluğun İletişim Çalışmaları alanına ait olduğu, (6) makalelerin neredeyse tamama yakınının tek bir araştırmadan oluştuğu, (7) nitel araştırma yöntemi ile içerik analizi araştırma tekniğinin ve (8) örneklem bağlamında ise ikincil verilerin ve amaçlı örnekleme yönteminin daha sık tercih edildiği bulgulanmıştır.

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.

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.

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.

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.

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.