bluuebunny/crossref_metadata_2025_split huggingface dataset:
Public oral health screening leads to regular dental visits: the LIFE Study
Authors: Tamada Yudai , Kusama Taro , Maeda Megumi , Murata Fumiko , Osaka Ken , Fukuda Haruhisa , Takeuchi Kenji 
Published: September 2023

ABSTRACTBackgroundAlthough periodontal disease screening has been implemented as a public oral health screening program in Japan, it remains unclear whether screening encourages regular dental visits. This study aimed to test the hypothesis that periodontal disease screening leads to subsequent regular dental visits among adults using a difference-in-differences (DID) approach.MethodsThis study used healthcare claims data of municipality residents who underwent periodontal disease screening in 2017 or 2018. For each screening recipient, four individuals of the same age and sex were extracted from those who did not undergo screening as controls. In the DID analysis, we assessed the change in the prevalence of dentist visits at least once every 180 days after screening.ResultsA total of 4,270 participants were included in the analysis. The prevalence of visiting dentists was consistent before screening among the participants who underwent screening (181–360 days before, 62.4%; 1–180 days before, 60.3%). While the prevalence was also consistent in those who did not undergo screening throughout the study period (approximately 45%), the prevalence in those who underwent screening sharply increased after undergoing the screening (1–180 days after, 81.1%) and then declined (181–360 days after, 67.8%). DID analysis indicated that the prevalence increased by 12.1% owing to screening. In addition, the age-subgroup DID estimates were higher in the younger population (aged 20–35 years, 17.4%; 40–55 years, 11.5%; 60 years, 11.0%).ConclusionPeriodontal disease screening increased subsequent dental visits, especially in younger populations.
A systematic review of (semi-)automatic quality control of T1-weighted MRI scans
Authors: Hendriks Janine , Mutsaerts Henk-Jan , Joules Richard , Peña-Nogales Óscar , Rodrigues Paulo R. , Wolz Robin , Burchell George L. , Barkhof Frederik , Schrantee Anouk 
Published: September 2023

AbstractArtifacts in magnetic resonance imaging (MRI) scans degrade image quality and thus negatively affect the outcome measures of clinical and research scanning. Considering the time-consuming and subjective nature of visual quality control (QC), multiple (semi-)automatic QC algorithms have been developed. This systematic review presents an overview of the available (semi-)automatic QC algorithms and software packages designed for raw, structural T1-weighted (T1w) MRI datasets. The objective of this review was to identify the differences among these algorithms in terms of their features of interest, performance, and benchmarks. We queried PubMed, EMBASE (Ovid), and Web of Science databases on the fifth of January 2023, and cross-checked reference lists of retrieved papers. Bias assessment was performed using PROBAST (Prediction model Risk Of Bias ASsessment Tool). A total of 18 distinct algorithms were identified, demonstrating significant variations in methods, features, datasets, and benchmarks. The algorithms were categorized into rule-based, classical machine learning-based, and deep learning-based approaches. Numerous unique features were defined, which can be roughly divided into features capturing entropy, contrast, and normative measures. Due to dataset-specific optimization, it is challenging to draw broad conclusions about comparative performance. Additionally, large variations exist in the used datasets and benchmarks, further hindering direct algorithm comparison. The findings emphasize the need for standardization and comparative studies for advancing QC in MR imaging. Efforts should focus on identifying a dataset-independent measure as well as algorithm-independent methods for assessing the relative performance of different approaches.
Racial and Ethnic Differences in the Association between Depressive Symptoms and Cognitive Outcomes in Older Adults: Findings from KHANDLE and STAR
Authors: Jimenez Marcia P , Gause Emma L. , Hayes-Larson Eleanor , Morris Emily P. , Fletcher Evan , Manly Jennifer , Gilsanz Paola , Soh Yenee , Corrada Maria , Whitmer Rachel A. , Glymour M. Maria 
Published: September 2023

ABSTRACTINTRODUCTIONDepressive symptoms are associated with higher risk of dementia but how they impact cognition in diverse populations is unclear.METHODSAsian, Black, LatinX, or White participants (n=2,227) in the Kaiser Healthy Aging and Diverse Life Experiences (age 65+) and the Study of Healthy Aging in African Americans (age 50+) underwent up to three waves of cognitive assessments over four years. Multilevel models stratified by race/ethnicity were used to examine whether depressive symptoms were associated with cognition or cognitive decline and whether associations differed by race/ethnicity.RESULTSHigher depressive symptoms were associated with lower baseline verbal episodic memory scores (−0.06, 95%CI:-0.12,-0.01; −0.15, 95%CI:-0.25,-0.04), and faster decline annually in semantic memory (−0.04, 95%CI:-0.07,-0.01; −0.10, 95%CI:-0.15,-0.05) for Black and LatinX participants. Depressive symptoms were associated with lower baseline but not decline in executive function.DISCUSSIONDepressive symptoms were associated with worse cognitive domains, with some evidence of heterogeneity across racial/ethnic groups.HighlightsWe examined whether baseline depressive symptoms were differentially associated with domain-specific cognition or cognitive decline by race/ethnicity.Depressive symptoms were associated with worse cognitive scores for all racial/ethnic groups across different domains examined.Higher depressive symptoms were associated with faster cognitive decline for semantic memory for Black and LatinX participants.The results suggest a particularly harmful association between depressive symptoms and cognition in certain racial/ethnic groups.
Differences in White Matter Structural Networks in Family Risk of Major Depressive Disorder and Suicidality: A Connectome Analysis
Authors: Kelsall Nora Clancy , Wang Yun , Gameroff Marc J , Cha Jiook , Posner Jonathan , Talati Ardesheer , Weissman Myrna M. , van Dijk Milenna Tamara 
Published: September 2023

AbstractBackgroundDepression and suicide are leading global causes of disability and death and are highly familial. Family and individual history of depression are associated with neurobiological differences including decreased white matter connectivity; however, this has only been shown for individual regions. We use graph theory models to account for the network structure of the brain with high levels of specialization and integration and examine whether they differ by family history of depression or of suicidality within a three-generation longitudinal family study with well-characterized clinical histories.MethodsClinician interviews across three generations were used to classify family risk of depression and suicidality. Then, we created weighted network models using 108 cortical and subcortical regions of interest for 96 individuals using diffusion tensor imaging derived fiber tracts. Global and local summary measures (clustering coefficient, characteristic path length, and global and local efficiencies) and network-based statistics were utilized for group comparison of family history of depression and, separately, of suicidality, adjusted for personal psychopathology.ResultsClustering coefficient (connectivity between neighboring regions) was lower in individuals at high family risk of depression and was associated with concurrent clinical symptoms. Network-based statistics showed hypoconnected subnetworks in individuals with high family risk of depression and of suicidality, after controlling for personal psychopathology. These subnetworks highlighted cortical-subcortical connections including between the superior frontal cortex, thalamus, precuneus, and putamen.ConclusionsFamily history of depression and of suicidality are associated with hypoconnectivity between subcortical and cortical regions, suggesting brain-wide impaired information processing, even in those personally unaffected.
Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiontCaballeronia insecticola
Authors: Jouan Romain , Lextrait Gaëlle , Lachat Joy , Yokota Aya , Cossard Raynald , Naquin Delphine , Timchenko Tatiana , Kikuchi Yoshitomo , Ohbayashi Tsubasa , Mergaert Peter 
Published: September 2023

AbstractCaballeronia insecticolais a bacterium belonging to theBurkholderiagenussensu lato, able to colonize multiple environments like soils and the gut of the bean bugRiptortus pedestris. To identify the essential genome of a bacterium is a first step in the understanding of its lifestyles. We constructed a saturatedHimar1mariner transposon library and revealed by transposon-sequencing (Tn-seq) that 498 protein-coding genes constitute the essential genome ofC. insecticolafor growth in free-living conditions. By comparing essential gene sets ofC. insecticolaand seven relatedBurkholderia s.l.strains, only 120 common genes were identified indicating that a large part of the essential genome is strain-specific. In order to reproduce specific nutritional conditions that are present in the gut ofR. pedestris, we grew the mutant library in minimal media supplemented with candidate gut nutrients and identified several condition-dependent fitness-defect genes by Tn-seq. To validate the robustness of the approach, insertion mutants in six fitness genes were constructed and their growth-deficiency in media supplemented with the corresponding nutrient was confirmed. The mutants were further tested for their efficiency inR. pedestrisgut colonization, confirming that gluconeogenic carbon sources, taurine and inositol, are nutrients consumed by the symbiont in the gut.
Transmissibility, infectivity, and immune resistance of the SARS-CoV-2 BA.2.86 variant
Authors: Uriu Keiya , Ito Jumpei , Kosugi Yusuke , Tanaka Yuri L , Mugita Yuka , Guo Ziyi , Hinay Alfredo A , Putri Olivia , Kim Yoonjin , Shimizu Ryo , Begum MST Monira , Jonathan Michael ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito Akatsuki , Ikeda Terumasa , Sato Kei 
Published: September 2023

AbstractIn September 2023, the SARS-CoV-2 XBB descendants, such as XBB.1.5 and EG.5.1 (originally XBB.1.9.2.5.1), are predominantly circulating worldwide. Unexpectedly, however, a lineage distinct from XBB was identified and named BA.2.86 on August 14, 2023. Notably, BA.2.86 bears more than 30 mutations in the spike (S) protein when compared to XBB and the parental BA.2, and many of them are assumed to be associated with immune evasion. Although the number of reported cases is low (68 sequences have been reported as of 7 September 2023), BA.2.86 has been detected in several continents (Europe, North America and Africa), suggesting that this variant may be spreading silently worldwide. On 17 August 2023, the WHO designated BA.2.86 as a variant under monitoring. Here we show evidence suggesting that BA.2.86 potentially has greater fitness than current circulating XBB variants including EG.5.1. The pseudovirus assay showed that the infectivity of BA.2.86 was significantly lower than that of B.1.1 and EG.5.1, suggesting that the increased fitness of BA.2.86 is not due to the increased infectivity. We then performed a neutralization assay using XBB breakthrough infection sera to address whether BA.2.86 evades the antiviral effect of the humoral immunity induced by XBB subvariants. The 50% neutralization titer of XBB BTI sera against BA.2.86 was significantly (1.6-fold) lower than those against EG.5.1. The sera obtained from individuals vaccinated with 3rd-dose monovalent, 4th-dose monovalent, BA.1 bivalent, and BA.5 bivalent mRNA vaccines exhibited very little or no antiviral effects against BA.2.86. Moreover, the three monoclonal antibodies (Bebtelovimab, Sotrovimab and Cilgavimab), which worked against the parental BA.2, did not exhibit antiviral effects against BA.2.86. These results suggest that BA.2.86 is one of the most highly immune evasive variants ever.
Early onset motor defects and electrographic seizures in a mouse model of the most common mutation in EEF1A2 related neurodevelopmental disorder, E122K
Authors: Marshall Grant F. , Fasol Melissa , Davies Faith C.J. , Le Seelleur Matthew , Alvarez Alejandra Fernandez , Bennett-Ness Cavan , Gonzalez-Sulser Alfredo , Abbott Catherine M. 
Published: September 2023

AbstractDe novoheterozygous missense mutations inEEF1A2, encoding neuromuscular translation-elongation factor eEF1A2, are associated with developmental and epileptic encephalopathies. We used CRISPR/ Cas9 to recapitulate the most common mutation, E122K, in mice. Although E122K/+ mice were not observed to have convulsive seizures, they exhibit frequent electrographic seizures and EEG abnormalities, transient early motor delays and growth defects. Both E122K homozygotes andEef1a2-null mice develop progressive motor abnormalities phenotypes, with homozygotes reaching humane endpoints by P31. Surprisingly, E122K homozygotes did not exhibit the progressive spinal neurodegeneration which drives the null phenotype. The E122K protein is relatively stable in neurons yet highly unstable in skeletal myocytes, suggesting that the E122K/E122K phenotype is instead driven by loss-of-function in muscle. Importantly, E122K homozygotes developed abnormalities far earlier than nulls, suggesting a toxic gain-of-function. This novel mouse model represents the first animal model of anEEF1A2missense mutation with face-valid phenotypes and has provided mechanistic insights needed to inform rational treatment design.
Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2
Authors: Gracias Ségolène , Chazal Maxime , Decombe Alice , Unterfinger Yves , Sogues Adrià , Pruvost Lauryne , Robert Valentine , Lacour Sandrine A. , Lemasson Manon , Sourisseau Marion , Li Zhi , Richardson Jennifer , Pellegrini Sandra , Decroly Etienne , Caval Vincent , Jouvenet Nolwenn 
Published: September 2023

AbstractThe mechanisms utilized by different flaviviruses to evade antiviral functions of interferons are varied and incompletely understood. Using virological approaches, biochemical assays and mass spectrometry analysis, we report here that the NS5 protein of tick-borne encephalitis virus (TBEV) and Louping Ill virus (LIV), two related tick-borne flaviviruses, antagonize JAK-STAT signaling through interactions with tyrosine kinase 2 (TYK2). Co-immunoprecipitation (co-IP) experiments, yeast gap-repair assays, computational protein-protein docking and functional studies identified a stretch of 10 residues of the RNA dependent RNA polymerase domain of tick-borne flavivirus NS5, but not mosquito-borne NS5, that is critical for interaction with the TYK2 kinase domain. Additional co-IP assays performed with several TYK2 orthologs revealed that the interaction was conserved across mammal species.In vitrokinase assays showed that TBEV and LIV NS5 reduced the catalytic activity of TYK2. Our results thus illustrate a novel mechanism by which viruses suppress the interferon response.TeaserInhibition of the catalytic activity of a key kinase of the JAK/STAT pathway by a viral protein
The oral pathogenPorphyromonas gingivalisresists the antimicrobial peptide LGL13K and evades the D-enantiomer by synonymous mutations inhagA
Authors: Gorr Sven-Ulrik , Chen Ruoqiong , Abrahante Juan E. , Joyce Paul B.M. 
Published: September 2023

AbstractPorphyromonas gingivalisis a keystone pathogen for periodontal disease. The bacteria are black-pigmented and require heme for growth.P. gingivalisexhibit resistance to many antimicrobial peptides, including the L-enantiomer of the antimicrobial peptide GL13K, which contributes to their success in the oral cavity.P. gingivalisW50 was resistant to LGL13K but susceptible to the stereo-isomer DGL13K. Upon prolonged exposure to DGL13K, a novel non-pigmented mutant was isolated that showed a low minimum inhibitory concentration and two-fold extended minimum duration for killing by DGL13K, consistent with tolerance to this peptide. The DGL13K tolerant bacteria exhibited synonymous mutations in thehagAgene. The mutations did not prevent mRNA expression but were predicted to alter mRNA structure. The non-pigmented bacteria were deficient in hemagglutination and hemoglobin binding, suggesting that the HagA protein was not expressed. This was supported by whole cell ELISA and gingipain activity assays, which suggested the absence of HagA but not two closely related gingipains.In vivovirulence was similar for wild-type and non-pigmented bacteria in theGalleria mellonellamodel. Loss of the hemagglutinin HagA may allow bacteria to escape from a biofilm that is under attack by antimicrobial peptides.
Precise manipulation of site and stoichiometry of capsid modification enables optimization of functional adeno-associated virus conjugates
Authors: Erickson Sarah B. , Pham Quan , Cao Xiaofu , Glicksman Jake , Kelemen Rachel E. , Shahraeini Seyed S. , Bodkin Sebastian , Kiyam Zainab , Chatterjee Abhishek 
Published: September 2023

AbstractThe ability to engineer adeno-associated virus (AAV) vectors for targeted infection of specific cell types is critically important to fully harness its potential of human gene therapy. A promising approach to achieve this objective involves chemically attaching retargeting ligands onto the virus capsid. Site-specific incorporation of a bioorthogonal noncanonical amino acid (ncAA) into the AAV capsid proteins provides a particularly attractive strategy to introduce such modifications with exquisite precision. In this study, we show that using ncAA mutagenesis, it is possible to systematically alter the attachment site of a retargeting ligand (cyclic-RGD) on the AAV capsid to create diverse conjugate architectures, and that the site of attachment heavily impacts the retargeting efficiency. We further demonstrate that the performance of these AAV conjugates is highly sensitive to the stoichiometry of capsid labeling (labels per capsid), with an intermediate labeling density (∼12 per capsid) providing optimal activity. Finally, we developed technology to precisely control the number of attachment sites per AAV capsid, by selectively incorporating a ncAA into the minor capsid proteins with high fidelity and efficiency, such that AAV-conjugates with varying stoichiometry can be synthesized in a homogeneous manner. Together, this platform provides unparalleled control over site and stoichiometry of capsid modification, which will enable the development of next-generation AAV vectors tailored with desirable attributes.
Saturated Transposon Analysis in Yeast as a One-step Method to Quantify the Fitness Effects of Gene Disruptions on a Genome-Wide Scale
Authors: Kingma Enzo , Dolsma Floor , De La Cruz Leila Margarita Iñigo , Laan Liedewij 
Published: September 2023

AbstractTransposon insertion site sequencing (TIS) is an extremely powerful tool that has greatly advanced our knowledge of functional genomics. However, studies using TIS often focus on gene essentiality and neglect possibly interesting but subtle differences in the importance of genes for fitness. As shown by other studies, expanding of the analysis of TIS data to allow a quantitative estimate of fitness has important application in genetics and evolutionary biology. Here, we present a method to estimate the fitness of gene disruption mutants on a quantitative level using data obtained from a TIS screen developed for the yeastSaccharomyces cerevisiaecalled SATAY. We show that using the average read count per transposon insertion site provides a metric for fitness that is robust across biological and technical replicate experiments. Importantly, the ability to resolve differences between gene disruption mutants with low fitness depends crucially on the inclusion of insertion sites that are not observed in the sequencing data to estimate the mean. While our method provides reproducible results between replicate SATAY datasets, the obtained fitness distribution differs substantially from those obtained using other techniques. It remains unclear whether these inconsistencies are due to biological or technical differences between the methods. Finally, we give suggestions for modifications of the SATAY procedure that could improve the resolution of the fitness estimates. Our analysis indicates that increasing the sequencing depth does very little to reduce the uncertainty in the estimates, while replacing the PCR amplification with methods that avoid or reduce the number of amplification cycles will likely be most effective in reducing noise.
Input credit scheme, farm productivity and food security nexus among smallholder rice farmers: evidence from North East Ghana
Authors: Wongnaa Camillus Abawiera , Abudu Alhassan , Abdul-Rahaman Awal , Akey Ernest Amegawovor , Prah Stephen 
Published: September 2023

PurposeThis study examined the impact of the Input Credit Scheme (ICS) by the Integrated Water Management and Agriculture Development (IWAD) on the productivity and food security of smallholder rice farmers in Ghana.Design/methodology/approachCross-sectional data from 250 rice farming households in the Mamprugu Moagduri district of the North East Region obtained from a multi-stage sampling technique were used for the study. Inverse Probability Weighted Regression Adjustment (IPWRA), Propensity Score Matching (PSM) and Kendall's coefficient of concordance were the methods of analysis employed.FindingsEmpirical results show that education, rice farming experience, dependency ratio, FBO membership, farm size and farm age were the significant factors influencing participation in the input credit scheme (ICS). Also, participants had an average rice productivity of 1,476.83 kg/ha, whereas non-participants had 1,131.81 kg/ha implying that participants increased their productivity by about 30%. In addition, the study revealed that participant households increased their household dietary diversity (HDDS) by 0.45 points amounting to about 8% diversity in their diets. High-interest rates associated with credit received, the short periods of credit repayment and the high cost of inputs provided under the scheme were the most challenging constraints associated with partaking in the ICS.Practical implicationsThe available literature on agricultural interventions have predominantly emphasized input credit as a key factor for improving cropt productivity and food security of smallholders. This study provides compelling evidence that participation in ICSs can result in substantial benefits for agricultural development, as evidenced by increased productivity leading to improved food security. The significance of these findings is highlighted by the fact that, through participation in input credit schemes, smallholder rice farmers in many developing countries see substantial improvement in their capacity to access productive resources, thereby improving their productivity, while simultaneously reducing food insecurity.Social implicationsLeveraging on the improved productivity of participants in the ICS, this study advocates that such input credit schemes should scale up to more food-insecure farming communities in Ghana.Originality/valueThe study uses a doubly robust econometric approach to evaluate the impact of ICS on smallholder rice farmers' productivity and food security in Ghana, making it the first of its kind. The findings offer a solid basis for future research and provide guidance for policymakers looking to boost agricultural development in Ghana.