UNASSIGNED: The aim of the study was to evaluate the modulating effects of five commonly used sweetener (glucose, inulin, isomaltulose, tagatose, trehalose) containing mouth rinses on the oral microbiome.
UNASSIGNED: A single-centre, double-blind, parallel randomized clinical trial was performed with healthy, 18-55-year-old volunteers (N = 65), who rinsed thrice-daily for two weeks with a 10% solution of one of the allocated sweeteners. Microbiota composition of supragingival dental plaque and the tongue dorsum coating was analysed by 16S RNA gene amplicon sequencing of the V4 hypervariable region (Illumina MiSeq). As secondary outcomes, dental plaque red fluorescence and salivary pH were measured.
UNASSIGNED: Dental plaque microbiota changed significantly for two groups: inulin (F = 2.0239, p = 0.0006 PERMANOVA, Aitchison distance) and isomaltulose (F = 0.67, p = 0.0305). For the tongue microbiota, significant changes were observed for isomaltulose (F = 0.8382, p = 0.0452) and trehalose (F = 1.0119, p = 0.0098). In plaque, 13 species changed significantly for the inulin group, while for tongue coating, three species changed for the trehalose group (ALDEx2, p < 0.1). No significant changes were observed for the secondary outcomes.
UNASSIGNED: The effects on the oral microbiota were sweetener dependant with the most pronounced effect on plaque microbiota. Inulin exhibited the strongest microbial modulating potential of the sweeteners tested. Further full-scale clinical studies are required.

N4-methylcytosine (4mC) is a modified form of cytosine found in DNA, contributing to epigenetic regulation. It exists in various genomes, including the Rosaceae family encompassing significant fruit crops like apples, cherries, and roses. Previous investigations have examined the distribution and functional implications of 4mC sites within the Rosaceae genome, focusing on their potential roles in gene expression regulation, environmental adaptation, and evolution. This research aims to improve the accuracy of predicting 4mC sites within the genome of Fragaria vesca, a Rosaceae plant species. Building upon the original 4mc-w2vec method, which combines word embedding processing and a convolutional neural network (CNN), we have incorporated additional feature encoding techniques and leveraged pre-trained natural language processing (NLP) models with different deep learning architectures including different forms of CNN, recurrent neural networks (RNN) and long short-term memory (LSTM). Our assessments have shown that the best model is derived from a CNN model using fastText encoding. This model demonstrates enhanced performance, achieving a sensitivity of 0.909, specificity of 0.77, and accuracy of 0.879 on an independent dataset. Furthermore, our model surpasses previously published works on the same dataset, thus showcasing its superior predictive capabilities.

In order to study the integration of reticuloendotheliosis virus (REV) in pigeonpox virus (PPV), we collected suspected pigeonpox disease material, amplified the 4b core protein gene of PPV, the gp90 gene of REV, and the integrated sequence fragments from the end of the ORF201 segment of PPV to the beginning of the LTR of REV, and sequenced these genes. The results showed that a 4b core protein fragment of 332 bp was amplified and identified as pigeonpox virus, which was named SX/TY/LTR 01/2023. Sequence analysis showed that the pigeonpox virus isolate belonged to genotype A2, which was the closest to the domestic CVL strain, with a identity of 99.4%. A band of 1191 bp was amplified from the gp90 gene of REV, named SX/TY/PPV-REV01/2023, and sequence analysis indicated that REV belonged to genotype III. The sequence analysis showed that REV belonged to genotype III, and belonged to the same large branch as the domestic isolates JSRD0701 and LNR0801, with 99.3% identity. The integrated sequence fragment was amplified to a band of 637 bp, which determined that the REV sequence was integrated in the PPV rather than a mixed infection of the two viruses. This indicates that REV was integrated in this isolation of PPV, suggesting that pigeon farms need to prevent reticuloendotheliosis at the same time when preventing pigeonpox.

Working life is associated with lifestyle, screening uptake, and occupational health risks that may explain differences in cancer onset. To better understand the association between working life and cancer risk, we need to account for the entire employment history. We investigated whether lifetime employment trajectories are associated with cancer risk. We used data from 6,809 women and 5,716 men, average age 70 years, from the Survey of Health, Ageing, and Retirement in Europe. Employment history from age 16 to 65 was collected retrospectively using a life calendar and trajectories were constructed using sequence analysis. Associations between employment trajectories and self-reported cancer were assessed using logistic regression. We identified eight employment trajectories for women and two for men. Among women, the risk of cancer was higher in the trajectories \"Mainly full-time to home/family\", \"Full-time or home/family to part-time\", \"Mainly full-time\", and \"Other\" compared with the \"Mainly home/family\" trajectory. Among men, the risk of cancer was lower in the \"Mainly self-employment\" trajectory compared with \"Mainly full-time\". We could show how employment trajectories were associated with cancer risk, underlining the potential of sequence analysis for life course epidemiology. More research is needed to understand these associations and determine if causal relationships exist.

UNASSIGNED: In occult hepatitis C virus infection (OCI), hepatitis C virus ribonucleic acid (HCV RNA) is detectable in peripheral blood mononuclear cells (PBMCs) but is not evident in serum or plasma. Understanding of OCI in patients with seronegative anti-HCV antibodies is limited.
UNASSIGNED: In this study, six HCV isolates from haemodialysis (HD) patients with seronegative OCI were identified by molecular assays and phylogenetic analysis. The virus infectivity was assessed ex vivo using a primary naïve PBMC culture system. HCV isolates obtained from the PBMCs of 10 patients with chronic HCV infection (CCI) were characterised concurrently and used as positive controls in the cell culture.
UNASSIGNED: Sequence analysis of the 5\' untranslated region (UTR) and non-structural 5B (NS5B) region revealed that HCV genotype 3 was the most prevalent virus type in both the OCI and CCI groups. One of the occult HCV isolates was identified as a mixed type. The mean viral load (log10 RNA copies/106 cells) in the PBMC samples of the OCI group (M = 3.4, SD = 0.7) was lower than that of the CCI group (M = 4.6, SD = 1.7). Upon culture, de novo OCI-HCV replicates were detected in five out of six naïve PBMC cultures. Analysis of the replicates showed a single guanine addition in the domain III of 5\'-UTR but the overall molecular structure was retained.
UNASSIGNED: Seronegative OCI is an active form of infection that replicates at a low level in PBMCs. Seronegative OCI may share the same route of transmission as CCI. The retained viral competency may have an implication for its persistence.

Ancient genomics has revolutionized our understanding of human evolution and migration history in recent years. Here, we present a protocol to prepare samples for ancient genomics research. We describe steps for releasing DNA from human remains, DNA library construction, hybridization capture, quantification, and sequencing. We then detail procedures for mapping sequence reads and population genetics analysis. This protocol also outlines challenges in extracting ancient DNA samples and authenticating ancient DNA to uncover the genetic history and diversity of ancient populations. For complete details on the use and execution of this protocol, please refer to Tao et al.1.

Smiliogastrinae are recognized for their high nutritional and ornamental value. In this study, we employed high-throughput sequencing technology to acquire the complete mitochondrial genome sequences of Dawkinsia filamentosa and Pethia nigrofasciata. The gene composition and arrangement order in these species were similar to those of typical vertebrates, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region. The mitochondrial genomes of D. filamentosa and P. nigrofasciata measure 16,598 and 16,948 bp, respectively. Both D. filamentosa and P. nigrofasciata exhibit a significant preference for AT bases and an anti-G bias. Notably, the AT and GC skew values of the ND6 gene fluctuated markedly, suggesting that the selection and mutation pressures on this gene may differ from those affecting other genes. Phylogenetic analysis, based on the complete mitochondrial genomes of 23 Cyprinidae fishes, revealed that D. filamentosa is closely related to the sister group comprising Dawkinsia denisonii and Sahyadria chalakkudiensis. Similarly, P. nigrofasciata forms a sister group with Pethia ticto and Pethia stoliczkana.

Late-onset Alzheimer\'s disease (LOAD) has a strong genetic component. Participants in Long-Life Family Study (LLFS) exhibit delayed onset of dementia, offering a unique opportunity to investigate LOAD genetics.
We conducted a whole genome sequence analysis of 3475 LLFS members. Genetic associations were examined in six independent studies (N = 14,260) with a wide range of LOAD risk. Association analysis in a sub-sample of the LLFS cohort (N = 1739) evaluated the association of LOAD variants with beta amyloid (Aβ) levels.
We identified several single nucleotide polymorphisms (SNPs) in tight linkage disequilibrium within the MTUS2 gene associated with LOAD (rs73154407, p = 7.6 × 10-9). Association of MTUS2 variants with LOAD was observed in the five independent studies and was significantly stronger within high levels of Aβ42/40 ratio compared to lower amyloid.
MTUS2 encodes a microtubule associated protein implicated in the development and function of the nervous system, making it a plausible candidate to investigate LOAD biology.
Long-Life Family Study (LLFS) families may harbor late onset Alzheimer\'s dementia (LOAD) variants. LLFS whole genome sequence analysis identified MTUS2 gene variants associated with LOAD. The observed LLFS variants generalized to cohorts with wide range of LOAD risk. The association of MTUS2 with LOAD was stronger within high levels of beta amyloid. Our results provide evidence for MTUS2 gene as a novel LOAD candidate locus.

This study, conducted on a Swedish population cohort, explores how internalized (depressive and functional somatic) and externalized (smoking, drinking, truancy, vandalism, delinquency) mental health symptoms, as well as close interpersonal relations (family climate and school connectedness) reported during adolescence, influence the work-life course up to late midlife.
We examined repeated measurements of labour market status from age 16 to 56 using sequence analyses. We identified five different labour market attachment (LMA16-56) trajectories, namely \'strong,\' \'early intermediate,\' \'early weak,\' \'late weak,\' and \'constantly weak.\' Multinomial logistic regressions were employed to relate each of the nine determinants to the identified trajectories.
When compared to the risk of \'strong\' LMA16-56, adversity in all conditions, except for vandalism, entailed a higher risk of the \'constantly weak\' trajectory. Moreover, all conditions, except for functional somatic symptoms, entailed a higher risk of the \'late weak\' LMA16-56. The risk of the \'early intermediate\' LMA16-56 was non-significant across all the conditions.
This study contributes to existing knowledge through its novel exploration of labour market attachment and the revelation of the significance of proximal interpersonal relationships in attachment outcomes. Additionally, the study reaffirms the importance of externalizing behaviour, while suggesting that internalized symptoms in adolescence might have a less influential, though not negligible, role. These results underscore the importance of addressing acting out behaviour and nurturing human relationships during compulsory basic education, when the entire age group is still within reach. This approach aims not only to reduce frictions in the school-to-work transition but also to prevent midlife labour market attachment problems that may arise with delayed intervention.

BACKGROUND: This study aimed to describe sequences of vocational rehabilitation services among individuals with approved vocational rehabilitation in Germany and to identify typical service sequences.
METHODS: We used administrative data on vocational rehabilitation services and questionnaire data on health and work ability to describe frequencies and sequences of vocational rehabilitation services financed by the Federal German Pension Insurance. Through sequence analysis, we were able to map the service sequences. We did cluster analyses to identify typical different service sequences.
RESULTS: Our sample included 1,652 individuals with 2,584 services. Integration services and two-year vocational retraining were the most common services. We could identify three different service clusters around integration services: shorter ones, followed by employer benefits and without employer benefits. We found two different clusters around two-year vocational retraining: shorter and longer clusters. Two-year vocational retraining was more often initiated by preparatory services and followed by employer benefits than integration services. Longer services in both clusters were associated with better baseline data for physical health, work ability, risk of future work disability, and younger age than shorter services. People in two-year-vocational retraining reported at baseline better general health, better work ability, low risk of future work disability, and less mental illness compared to people in integration services.
CONCLUSIONS: Multiple services, that is, sequences of services, were more likely to occur among individuals with more complex services like two-year vocational retraining. Utilization of complex services and longer services was influenced by health, age, risk of future work disability, and education.
BACKGROUND: German Clinical Trials Register DRKS00009910, registration 25/01/2016.