bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the ability to extract MLVA profiles ofVibrio choleraeisolates from WGS data generated with Oxford Nanopore Technologies
Authors: Ambroise Jérôme , Bearzatto Bertrand , Durant Jean-Francois , Irenge Leonid M. , Gala Jean-Luc 
Published: February 2023

AbstractMultiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used by laboratory-based surveillance networks to subtype pathogens causing foodborne and water-borne disease outbreaks. TheMLVATypeshiny application was previously designed to extract MLVA profiles ofVibrio choleraeisolates from WGS data, and provide backward compatibility with traditional MLVA typing methods. The previous development and validation work was done on short (pair-end 300 and 150 nt long) reads from Illumina MiSeq and Hiseq sequencing. In the initial phase of this work, theMLVATypeapplication was validated on long reads generated by Oxford Nanopore Technologies (ONT) sequencing platforms. The MLVA profiles ofV. choleraeisolates (n=9) from the Democratic Republic of the Congo were produced using theMLVATypeapplication on WGS data. The WGS-derived MLVA profiles were extracted from canu (v.2.2) assemblies obtained through MinION and GridION sequencing by ONT. The results were compared to those obtained from SPAdes assemblies (v3.13.0; k-mer 175) generated from short-read (pair-end 300-bp) data obtained by MiSeq sequencing, Illumina, taken as a reference. For each isolate, the MLVA profiles were concordant for all three sequencing methods, demonstrating that theMLVATypeapplication can accurately predict the MLVA profiles from assembled genomes generated with long-reads ONT sequencers.In the final phase of this study, we conducted phylogenomic analysis on data generated by both sequencing technologies, highlighting the superior resolution of Illumina short-read sequencing compared to the ONT-based approach. However, there was a remarkable concordance between isolate clusters identified using ONT-based MLVA profiles and those derived from the short-read-based phylogenomic analysis. This striking agreement enabled us to identify specific benefits and drawbacks of both technologies.
Reducing Cross-Cultural Comparability Bias Obtained with Measurement Invariance Analysis by Means of Anchoring Vignettes in Heterogeneous Refugee Samples
Authors: Menold Natalja , Biddle Louise , von Hermanni Hagen , Kadel Jasmin , Bozorgmehr Kayvan 
Published: February 2023

AbstractBackgroundConfigural, metric, and scalar measurement invariance have been indicators of bias-free statistical cross-group comparisons, although they are difficult to verify in the data. Low comparability of translated questionnaires or the different use of response formats by respondents might lead to rejection of measurement invariance and point to comparability bias in studies that use different languages. Anchoring vignettes have been proposed as a method to control for the different use of response formats by respondents (RC-DIF) as implemented by means of rating scales. We evaluate the question whether the comparability bias obtained by means of measurement invariance analysis can be reduced by means of anchoring vignettes or by considering socio- demographic heterogeneity as an alternative approach.MethodsWe use the Health System Responsiveness (HSR) questionnaire in English and Arabic in a refugee population. We collected survey data in English (n = 183) and Arabic (n=121) in a random sample of refugees in the third largest German federal state. We conducted multiple-sample Confirmatory Factor Analyses (MGCFA) to analyse measurement invariance and compared the results when 1) using rescaled data on the basis of anchoring vignettes (non-parametric approach), 2) including information on DIF from the analyses with anchoring vignettes as covariates (parametric approach) and 3) including socio-demographic covariates.ResultsFor the HSR, every level of measurement invariance between Arabic and English questionnaires was rejected. Implementing rescaling on the basis of anchoring vignettes provided superior results over the initial MGCFA analysis, since configural, metric and scalar invariance could not be rejected. When using solely socio-demographic covariates, scalar measurement invariance could not be rejected, but configural and metric invariance had to be rejected.ConclusionsSurveys may consider anchoring vignettes as a method to obtain more satisfactory results of measurement invariance analyses; however, socio-demographic information cannot be included in the models as a standalone method. More research on the efficient implementation of anchoring vignettes and further development of methods to incorporate them when modelling measurement invariance is needed.
Identification of High Likelihood of Dementia in Population-Based Surveys using Unsupervised Clustering: a Longitudinal Analysis
Authors: Gharbi-Meliani Amin , Husson François , Vandendriessche Henri , Bayen Eleonore , Yaffe Kristine , Bachoud-Lévi Anne-Catherine , de Langavant Laurent Cleret 
Published: February 2023

SUMMARYBackgroundDementia is defined by cognitive decline that affects functional status. Longitudinal ageing surveys often lack a clinical diagnosis of dementia though measure cognitive and function over time. We used unsupervised machine learning and longitudinal data to identify transition to probable dementia.MethodsMultiple Factor Analysis was applied to longitudinal function and cognitive data of 15,278 baseline participants (aged 50 years and more) from the Survey of Health, Ageing, and Retirement in Europe (SHARE) (waves 1, 2 and 4–7, between 2004 and 2017). Hierarchical Clustering on Principal Components discriminated three clusters at each wave. We estimated probable or “Likely Dementia” prevalence by sex and age, and assessed whether dementia risk factors increased the risk of being assigned probable dementia status using multistate models. Next, we compared the “Likely Dementia” cluster with self-reported dementia status and replicated our findings in the English Longitudinal Study of Ageing (ELSA) cohort (waves 1–9, between 2002 and 2019, 7,840 participants at baseline).FindingsOur algorithm identified a higher number of probable dementia cases compared with self-reported cases and showed good discriminative power across all waves (AUC ranged from 0.754 [0.722–0.787] to 0.830 [0.800–0.861]). “Likely Dementia” status was more prevalent in older people, displayed a 2:1 female/male ratio and was associated with nine factors that increased risk of transition to dementia: low education, hearing loss, hypertension, drinking, smoking, depression, social isolation, physical inactivity, diabetes, and obesity. Results were replicated in ELSA cohort with good accuracy.InterpretationMachine learning clustering can be used to study dementia determinants and outcomes in longitudinal population ageing surveys in which dementia clinical diagnosis is lacking.FundingFrench Institute for Public Health Research (IReSP), French National Institute for Health and Medical Research (Inserm), NeurATRIS Grant (ANR-11-INBS-0011), and Front-Cog University Research School (ANR-17-EUR-0017).
Paediatric traumatic brain injury as a risk factor for psychosis and psychotic symptoms: a systematic review and meta-analysis
Authors: Yau King-Chi , Revill Grace , Blackman Graham , Shaikh Madiha , Bell Vaughan 
Published: February 2023

AbstractBackgroundPsychosis is one of the most disabling psychiatric disorders. Paediatric traumatic brain injury (pTBI) has been cited as a developmental risk factor for psychosis, however this association has never been assessed meta-analytically.MethodsA systematic review and meta-analysis of the association between pTBI and subsequent psychotic disorders/symptoms was performed. The study was pre-registered (CRD42022360772) adopting a random-effects model to estimate meta-analytic odds ratio (OR) and 95% confidence interval (CI) using the Paule–Mandel estimator. Subgroup (study location, study design, psychotic disorder vs subthreshold symptoms, assessment type, and adult vs adolescent onset) and meta-regression (quality of evidence) analyses were also performed. The robustness of findings was assessed through sensitivity analyses. The meta-analysis is available online as a computational notebook with an open dataset.ResultsWe identified 10 relevant studies and eight were included in the meta-analysis. Based on a pooled sample size of 479,686, the pooled OR for the association between pTBI and psychosis outcomes was 1.80 (95% CI [1.11, 2.95]). There were no subgroup effects and no outliers. Both psychotic disorder and subthreshold symptoms were associated with pTBI. The overall association remained robust after removal of low-quality studies, however the OR reduced to 1.43 (95% CI [1.04, 1.98]). A leave-one-out sensitivity analysis showed the association was robust to removal of all but one study which changed the estimate to marginally non-significant.ConclusionsWe report cautious meta-analytic evidence for a positive association between pTBI and future psychosis. New evidence will be key in determining long-term reliability of this finding.
Chromatin accessibility associated with aquaculture relevant traits in tilapia
Authors: Mehta Tarang K. , Man Angela , Ciezarek Adam , Ranson Keith , Penman David , Di-Palma Federica , Haerty Wilfried 
Published: February 2023

AbstractThe Nile tilapia (Oreochromis niloticus) accounts for ∼9% of global freshwater finfish production however, extreme cold weather and decreasing freshwater resources has created the need to develop resilient strains. By determining the genetic bases of aquaculture relevant traits, we can genotype and breed desirable traits into farmed strains. We developed and optimised ATAC-seq fromO. niloticusgill tissues to identify regulatory regions accounting for gene expression associated with gill adaptations. We find that SNPs from 27 tilapia species are enriched in noncoding regions, with 95% of accessible gene promoter regions being SNP-containing. Regulatory variants of TF binding sites are likely driving gene expression differences associated with tilapia gill adaptations, and differentially segregate in freshwater and euryhaline tilapia species. The generation of novel open chromatin data integrated with gene expression and genetic variants revealed candidate genes, genetic relationships, and loci associated with aquaculture relevant traits like salinity and osmotic stress acclimation.
TRGdb: a universal resource for exploration of taxonomically restricted genes in bacteria
Authors: Zielezinski Andrzej , Dobrychlop Wojciech , Karlowski Wojciech M. 
Published: February 2023

AbstractThe TRGdb database is a resource dedicated to taxonomically restricted genes (TRGs) in bacteria. It provides a comprehensive collection of genes that are specific to different genera and species, according to the latest release of bacterial taxonomy. The user interface allows for easy browsing and searching as well as sequence similarity exploration. The website also provides information on each TRG protein sequence, including its level of disorder, complexity, and tendency to aggregate. TRGdb is a valuable resource for gaining a deeper understanding of the TRGs-associated, unique features and characteristics of bacterial organisms. The TRGdb resource is freely accessible throughwww.combio.pl/trgdb.
UV-B-induced dynamics of constitutive heterochromatin inArabidopsis thaliana
Authors: Johann to Berens Philippe , Golebiewska Kinga , Peter Jackson , Molinier Jean 
Published: February 2023

AbstractSunlight regulates transcriptional programs and triggers the shaping of the genome throughout plant development. Among the different sunlight wavelengths that reach the surface of the Earth, UV-B (280-315 nm) controls the expression of hundreds of genes for the photomorphogenic responses and also induces the formation of photodamage that interfere with genome integrity and transcriptional programs. The combination of cytogenetics and deep-learning-based analyses allowed determining the location of UV-B-induced photoproducts and quantifying the effects of UV-B irradiation on constitutive heterochromatin content in different Arabidopsis natural variants acclimated to various UV-B regimes. We identified that UV-B-induced photolesions are enriched within chromocenters. Furthermore, we uncovered that UV-B irradiation promotes constitutive heterochromatin dynamics that differs among the Arabidopsis ecotypes having divergent heterochromatin contents. Finally, we identified that the proper restoration of the chromocenter shape, upon DNA repair, relies on the UV-B photoreceptor, UV RESISTANCE LOCUS 8 (UVR8). These findings shed the light on the effect of UV-B exposure and perception in heterochromatin dynamics and structure inArabidopsis thaliana.Statements and DeclarationsAll authors certify that they have no affiliations with or involvement in any organization or entity with any financial interest or non-financial interest in the subject matter or materials discussed in this manuscript.
Cotranscriptional demethylation induces global loss of H3K4me2 from active genes inArabidopsis
Authors: Mori Shusei , Oya Satoyo , Takahashi Mayumi , Takashima Kazuya , Inagaki Soichi , Kakutani Tetsuji 
Published: February 2023

AbstractBased on studies of animals and yeasts, methylation of histone H3 lysine 4 (H3K4me1/2/3, for mono-, di-, and tri-methylation, respectively) is regarded as the key epigenetic modification of transcriptionally active genes. In plants, however, H3K4me2 correlates negatively with transcription, and the regulatory mechanisms of this counterintuitive H3K4me2 distribution in plants remain largely unexplored. A previous genetic screen for factors regulating plant regeneration identified Arabidopsis LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3), which is a major H3K4me2 demethylase. Here, we show that LDL3-mediated H3K4me2 demethylation depends on the transcription elongation factor Paf1C and phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII). In addition, LDL3 binds to phosphorylated RNAPII. These results suggest that LDL3 is recruited to transcribed genes by binding to elongating RNAPII and demethylates H3K4me2 cotranscriptionally. Importantly, the negative correlation between H3K4me2 and transcription is disrupted in theldl3mutant, demonstrating the genome-wide impacts of the transcription-driven LDL3 pathway to control H3K4me2 in plants. Our findings implicate H3K4me2 in plants as chromatin memory for transcriptionally repressive states, which ensures robust gene control.
Effects of hepatic mitochondrial pyruvate carrier deficiency on de novo lipogenesis and glycerol-mediated gluconeogenesis in mice
Authors: Yiew Nicole K.H. , Deja Stanislaw , Ferguson Daniel , Cho Kevin , Jarasvaraparn Chaowapong , Jacome-Sosa Miriam , Lutkewitte Andrew J. , Mukherjee Sandip , Fu Xiaorong , Singer Jason M. , Patti Gary J. , Burgess Shawn C. , Finck Brian N. 
Published: February 2023

SUMMARYThe liver coordinates the systemic response to nutrient deprivation and availability by producing glucose from gluconeogenesis during fasting and synthesizing lipids viade novolipogenesis (DNL) when carbohydrates are abundant. Mitochondrial pyruvate metabolism is thought to play important roles in both gluconeogenesis and DNL. We examined the effects of hepatocyte-specific mitochondrial pyruvate carrier (MPC) deletion on the fasting-refeeding response. Rates of DNL during refeeding were impaired by liver MPC deletion, but this did not reduce intrahepatic lipid content. During fasting, glycerol is converted to glucose by two pathways; a direct cytosolic pathway essentially reversing glycolysis and an indirect mitochondrial pathway requiring the MPC. MPC deletion reduced the incorporation of13C-glycerol into TCA cycle metabolites but not into newly synthesized glucose. However, suppression of glycerol metabolism did not affect glucose concentrations in fasted hepatocyte-specific MPC-deficient mice. Thus, glucose production by kidney and intestine may compensate for MPC deficiency in hepatocytes.
A novel order-level lineage of ammonia-oxidizingThaumarchaeotais widespread in marine and terrestrial environments
Authors: Zheng Yue , Wang Baozhan , Gao Ping , Yang Yiyan , Su Xiaoquan , Ning Daliang , Tao Qing , Zhao Feng , Wang Dazhi , Zhang Yao , Li Meng , Winkler Mari-K.H. , Ingalls Anitra E. , Zhou Jizhong , Zhang Chuanlun , Stahl David A. , Jiang Jiandong , Martens-Habbena Willm , Qin Wei 
Published: February 2023

AbstractAmmonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant groups of Archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those of marine and soil AOA. We here report a novel AOA orderCandidatusNitrosomirales that forms a deeply branching basal sister lineage to the thermophilicCa.Nitrosocaldales. Metagenomic and 16S rRNA gene read mapping demonstrates the dominant presence ofNitrosomiralesAOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Notably, terrestrialNitrosomiralesAOA show the genetic capacity of using formate as an alternative source of reductant and appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including the genes encoding urease, nitrite reductase, and V-type ATPase. Potential metabolic versatility and acquired functions may facilitate their radiation into a variety of subsurface, marine, and soil environments. Molecular thermometer-based evolutionary analysis suggests thatNitrosomiralesoriginated from thermophilic environments and transitioned into temperate habitats in parallel withNitrososphaeralesandNitrosopumilales. We also provide evidence that terrestrial-marine habitat transitions occurred within each one of the four AOA orders, which reveals a more complex evolutionary trajectory of major AOA lineages than previously proposed. Together, these findings establish a robust taxonomic and evolutionary framework of AOA and provide new insights into the ecology and evolution of this globally abundant functional guild.
Mental health symptoms in Latin America during the first year of COVID-19 pandemic: a meta-analysis of prevalence and potential moderator variables
Authors: Torrente F. , Ailán D. , Del Cerro E. , Del Negro J. , Gorodetzky B. , Slonimschik D. , Cetkovich-Bakmas M. , López P. 
Published: February 2023

AbstractThis meta-analysis examines the impacts of the COVID-19 pandemic on mental health in Latin America during its first year, using data from 71 studies with 231,441 participants. To address knowledge gaps in the existent literature we considered the type of study design, country of origin, effects of lockdown, and several potential moderating factors. We found prevalence rates of 31% for depression symptoms and 36% for anxiety symptoms. These estimates were higher than those observed in studies from the northern hemisphere. Longitudinal studies showed that depressive symptoms persisted over time, and lockdowns were associated with mildly increased anxiety levels. Female gender was associated with higher rates of depressive symptoms. Our analyses revealed high statistical heterogeneity, and moderating factors such as pandemic duration, COVID-19 cases and deaths, and lockdown stringency did not explain observed mental health symptoms. Methodological limitations include an overreliance on cross-sectional studies and a lack of pre-pandemic parameters that may lead to an overestimation of mental health symptom rates. Overall, this study provides valuable insights into mental health symptoms in Latin America during the first year of the COVID-19 pandemic, highlighting the need for improved epidemiological research and mental health support in the region.
A long-term ketogenic diet in young and aged rats has dissociable effects on prelimbic cortex and CA3 ensemble activity
Authors: Hernandez Abbi R. , Barrett Maya E. , Lubke Katelyn N. , Maurer Andrew P. , Burke Sara N. 
Published: February 2023

AbstractAge-related cognitive decline has been linked to distinct patterns of cellular dysfunction in the prelimbic cortex (PL) and the CA3 subregion of the hippocampus. Because higher cognitive functions require both structures, selectively targeting a neurobiological change in one region, at the expense of the other, is not likely to restore normal behavior in older animals. One change with age that both the PL and CA3 share, however, is a reduced ability to utilize glucose, which can produce aberrant neural activity patterns. The current study used a ketogenic diet (KD) intervention, which reduces the brain’s reliance on glucose, and has been shown to improve cognition, as a metabolic treatment for restoring neural ensemble dynamics in aged rats. Expression of the immediate-early genesArcandHomer1a were used to quantify the neural ensembles that were active in the home cage prior to behavior, during a working memory/biconditional association task, and a continuous spatial alternation task. Aged rats on the control diet had increased activity in CA3 and less ensemble overlap in PL between different task conditions than did the young animals. In the PL, the KD was associated with increased activation of neurons in the superficial cortical layers. The KD did not lead to any significant changes in CA3 activity. These observations suggest that the KD does not restore neuron activation patterns in aged animals, but rather the availability of ketone bodies in the frontal cortices may permit the engagement of compensatory mechanisms that produce better cognitive outcomes.Significance StatementThis study extends understanding of how a ketogenic diet (KD) intervention may improve cognitive function in older adults. Young and aged rats were given 3 months of a KD or a calorie-match control diet and then expression of the immediate-early genesArcandHomer1a were measured to examine neural ensemble dynamics during cognitive testing. The KD diet was associated with increased activation of neurons in the superficial layers of the PL, but there were no changes in CA3. These observations are significant because they suggest that compensatory mechanisms for improving cognition are engaged in the presence of elevated ketone bodies. This metabolic shift away from glycolysis can meet the energetic needs of the frontal cortices when glucose utilization is compromised.
Predicted loss of function alleles in Bassoon (BSN) are associated with obesity
Authors: Zhu Na , LeDuc Charles A. , Fennoy Ilene , Laferrère Blandine , Doege Claudia A. , Shen Yufeng , Chung Wendy K. , Leibel Rudolph L. 
Published: February 2023

AbstractBassoon (BSN) is a component of a hetero-dimeric presynaptic cytomatrix protein that orchestrates neurotransmitter release with Piccolo (PCLO) from glutamatergic neurons throughout the brain. Heterozygous missense variants inBSNhave previously been associated with neurodegenerative disorders in humans. We performed an exome-wide association analysis of ultra-rare variants in about 140,000 unrelated individuals from the UK Biobank to search for new genes associated with obesity. We found that rare heterozygous predicted loss of function (pLoF) variants inBSNare associated with higher BMI with log10-p value of 11.78 in the UK biobank cohort. The association was replicated in the All of Us whole genome sequencing data. Additionally, we have identified two individuals (one of whom has ade novovariant) with a heterozygous pLoF variant in a cohort of early onset or extreme obesity at Columbia University. Like the individuals identified in the UKBB and All of us Cohorts, these individuals have no history of neurobehavioral or cognitive disability. Heterozygosity for pLoFBSNvariants constitutes a new etiology for obesity.