bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time course of the triglyceride glucose index accumulation with the risk of cardiovascular disease and all-cause mortality
Authors: Tian Xue , Chen Shuohua , Zhang Yijun , Zhang Xiaoli , Xu Qin , Wang Penglian , Wu Shouling , Wang Anxin , Luo Yanxia 
Published: September 2022

Abstract
Background
Future risk of cardiovascular disease (CVD) and mortality is associated with cumulative amount TyG index (cumTyG) exposure, while whether time course of TyG accumulation modulates the risk remains unclear. This study sought to examine the associations of cumTyG index accumulation time course with the risk of CVD and all-cause mortality.

Methods
We enrolled 51,734 participants free of CVD and underwent three examinations at year 2006, 2008, and 2010. CumTyG from baseline to the third examination was calculated. Time course of cumTyG accumulation was calculated as the slope of TyG versus time from 2006 to 2010, or as splinting the overall TyG index accumulation into early (cumTyG06 − 08) and late accumulation (cumTyG08 − 10). Participants were categorized by the combination of cumTyG < or ≥ median (34.44 × years) and a negative or positive TyG slope.

Results
During a median follow-up of 9.04 years, we identified 3,602 incident CVD cases and 3,165 deaths. The risk of CVD and all-cause mortality increased with decreased TyG slope, the corresponding adjusted hazard ratio (aHR) with 95% confidence interval (CI) was 1.11 (1.04–1.19) and 1.18 (1.10–1.26) for patients with a negative TyG slope, respectively. Consistently, a later accumulation of TyG index was not associated with the risk of CVD and all-cause mortality after adjustment for an early accumulation. When considering the combination of cumTyG index and time course, participants with a cumTyG ≥ median and a negative TyG slope had elevated risk of CVD (aHR, 1.37; 95% CI, 1.24–1.51) and all-cause mortality (aHR, 1.28; 95% CI, 1.15–1.43). Additionally, the association was more prominent in young adults.

Conclusion
Early TyG index accumulation resulted in a greater risk of CVD and all-cause mortality than later TyG later accumulation with the same overall cumulative exposure, emphasizing the importance of optimal TyG index control earlier in life.
Risk prediction models for incident type 2 diabetes in Chinese people with intermediate hyperglycemia: a systematic literature review and external validation study
Authors: Xu Shishi , Coleman Ruth L. , Wan Qin , Gu Yeqing , Meng Ge , Song Kun , Shi Zumin , Xie Qian , Tuomilehto Jaakko , Holman Rury R. , Niu Kaijun , Tong Nanwei 
Published: September 2022

Abstract
Background
People with intermediate hyperglycemia (IH), including impaired fasting glucose and/or impaired glucose tolerance, are at higher risk of developing type 2 diabetes (T2D) than those with normoglycemia. We aimed to evaluate the performance of published T2D risk prediction models in Chinese people with IH to inform them about the choice of primary diabetes prevention measures.

Methods
A systematic literature search was conducted to identify Asian-derived T2D risk prediction models, which were eligible if they were built on a prospective cohort of Asian adults without diabetes at baseline and utilized routinely-available variables to predict future risk of T2D. These Asian-derived and five prespecified non-Asian derived T2D risk prediction models were divided into BASIC (clinical variables only) and EXTENDED (plus laboratory variables) versions, with validation performed on them in three prospective Chinese IH cohorts: ACE (n = 3241), Luzhou (n = 1333), and TCLSIH (n = 1702). Model performance was assessed in terms of discrimination (C-statistic) and calibration (Hosmer–Lemeshow test).

Results
Forty-four Asian and five non-Asian studies comprising 21 BASIC and 46 EXTENDED T2D risk prediction models for validation were identified. The majority were at high (n = 43, 87.8%) or unclear (n = 3, 6.1%) risk of bias, while only three studies (6.1%) were scored at low risk of bias. BASIC models showed poor-to-moderate discrimination with C-statistics 0.52–0.60, 0.50–0.59, and 0.50–0.64 in the ACE, Luzhou, and TCLSIH cohorts respectively. EXTENDED models showed poor-to-acceptable discrimination with C-statistics 0.54–0.73, 0.52–0.67, and 0.59–0.78 respectively. Fifteen BASIC and 40 EXTENDED models showed poor calibration (P < 0.05), overpredicting or underestimating the observed diabetes risk. Most recalibrated models showed improved calibration but modestly-to-severely overestimated diabetes risk in the three cohorts. The NAVIGATOR model showed the best discrimination in the three cohorts but had poor calibration (P < 0.05).

Conclusions
In Chinese people with IH, previously published BASIC models to predict T2D did not exhibit good discrimination or calibration. Several EXTENDED models performed better, but a robust Chinese T2D risk prediction tool in people with IH remains a major unmet need.
Glucose consumption rate-dependent transcriptome profiling of Escherichia coli provides insight on performance as microbial factories
Authors: Fragoso-Jiménez Juan Carlos , Gutierrez-Rios Rosa María , Flores Noemí , Martinez Alfredo , Lara Alvaro R. , Delvigne Frank , Gosset Guillermo 
Published: September 2022

AbstractBackgroundThe modification of glucose import capacity is an engineering strategy that has been shown to improve the characteristics ofEscherichia colias a microbial factory. A reduction in glucose import capacity can have a positive effect on production strain performance, however, this is not always the case. In this study,E. coliW3110 and a group of four isogenic derivative strains, harboring single or multiple deletions of genes encoding phosphoenolpyruvate:sugar phosphotransferase system (PTS)-dependent transporters as well as non-PTS transporters were characterized by determining their transcriptomic response to reduced glucose import capacity.ResultsThese strains were grown in bioreactors with M9 mineral salts medium containing 20 g/L of glucose, where they displayed specific growth rates ranging from 0.67 to 0.27 h−1, and specific glucose consumption rates (qs) ranging from 1.78 to 0.37 g/g h. RNA-seq analysis revealed a transcriptional response consistent with carbon source limitation among all the mutant strains, involving functions related to transport and metabolism of alternate carbon sources and characterized by a decrease in genes encoding glycolytic enzymes and an increase in gluconeogenic functions. A total of 107 and 185 genes displayed positive and negative correlations withqs, respectively. Functions displaying positive correlation included energy generation, amino acid biosynthesis, and sugar import.ConclusionChanges in gene expression ofE. colistrains with impaired glucose import capacity could be correlated withqsvalues and this allowed an inference of the physiological state of each mutant. In strains with lowerqsvalues, a gene expression pattern is consistent with energy limitation and entry into the stationary phase. This physiological state could explain why these strains display a lower capacity to produce recombinant protein, even when they show very low rates of acetate production. The comparison of the transcriptomes of the engineered strains employed as microbial factories is an effective approach for identifying favorable phenotypes with the potential to improve the synthesis of biotechnological products.
Emerging role of non-coding RNAs in the regulation of Sonic Hedgehog signaling pathway
Authors: Ghafouri-Fard Soudeh , Khoshbakht Tayyebeh , Hussen Bashdar Mahmud , Taheri Mohammad , Samsami Majid 
Published: September 2022

AbstractSonic Hedgehog (Shh) signaling cascade is one of the complex signaling pathways that control the accurately organized developmental processes in multicellular organisms. This pathway has fundamental roles in the tumor formation and induction of resistance to conventional therapies. Numerous non-coding RNAs (ncRNAs) have been found to interact with Shh pathway to induce several pathogenic processes, including malignant and non-malignant disorders. Many of the Shh-interacting ncRNAs are oncogenes whose expressions have been increased in diverse malignancies. A number of Shh-targeting miRNAs such as miR-26a, miR-1471, miR-129-5p, miR-361-3p, miR-26b-5p and miR-361-3p have been found to be down-regulated in tumor tissues. In addition to malignant conditions, Shh-interacting ncRNAs can affect tissue regeneration and development of neurodegenerative disorders. XIST, LOC101930370, lncRNA-Hh, circBCBM1, SNHG6, LINC‐PINT, TUG1 and LINC01426 are among long non-coding RNAs/circular RNAs that interact with Shh pathway. Moreover, miR-424, miR-26a, miR-1471, miR-125a, miR-210, miR-130a-5p, miR-199b, miR-155, let-7, miR-30c, miR-326, miR-26b-5p, miR-9, miR-132, miR-146a and miR-425-5p are among Shh-interacting miRNAs. The current review summarizes the interactions between ncRNAs and Shh in these contexts.
Beta amyloid deposition and cognitive decline in Parkinson’s disease: a study of the PPMI cohort
Authors: Mihaescu Alexander S. , Valli Mikaeel , Uribe Carme , Diez-Cirarda Maria , Masellis Mario , Graff-Guerrero Ariel , Strafella Antonio P. 
Published: September 2022

AbstractThe accumulation of beta amyloid in the brain has a complex and poorly understood impact on the progression of Parkinson’s disease pathology and much controversy remains regarding its role, specifically in cognitive decline symptoms. Some studies have found increased beta amyloid burden is associated with worsening cognitive impairment in Parkinson’s disease, especially in cases where dementia occurs, while other studies failed to replicate this finding. To better understand this relationship, we examined a cohort of 25 idiopathic Parkinson’s disease patients and 30 healthy controls from the Parkinson’s Progression Marker Initiative database. These participants underwent [18F]Florbetaben positron emission tomography scans to quantify beta amyloid deposition in 20 cortical regions. We then analyzed this beta amyloid data alongside the longitudinal Montreal Cognitive Assessment scores across 3 years to see how participant’s baseline beta amyloid levels affected their cognitive scores prospectively. The first analysis we performed with these data was a hierarchical cluster analysis to help identify brain regions that shared similarity. We found that beta amyloid clusters differently in Parkinson’s disease patients compared to healthy controls. In the Parkinson’s disease group, increased beta amyloid burden in cluster 2 was associated with worse cognitive ability, compared to deposition in clusters 1 or 3. We also performed a stepwise linear regression where we found an adjusted R2 of 0.495 (49.5%) in a model explaining the Parkinson’s disease group’s Montreal Cognitive Assessment score 1-year post-scan, encompassing the left gyrus rectus, the left anterior cingulate cortex, and the right parietal cortex. Taken together, these results suggest regional beta amyloid deposition alone has a moderate effect on predicting future cognitive decline in Parkinson’s disease patients. The patchwork effect of beta amyloid deposition on cognitive ability may be part of what separates cognitive impairment from cognitive sparing in Parkinson’s disease. Thus, we suggest it would be more useful to measure beta amyloid burden in specific brain regions rather than using a whole-brain global beta amyloid composite score and use this information as a tool for determining which Parkinson’s disease patients are most at risk for future cognitive decline.
Combined alteration of lamin and nuclear morphology influences the localization of the tumor-associated factor AKTIP
Authors: La Torre Mattia , Merigliano Chiara , Maccaroni Klizia , Chojnowski Alexandre , Goh Wah Ing , Giubettini Maria , Vernì Fiammetta , Capanni Cristina , Rhodes Daniela , Wright Graham , Burke Brian , Soddu Silvia , Burla Romina , Saggio Isabella 
Published: September 2022

AbstractBackgroundLamins, key nuclear lamina components, have been proposed as candidate risk biomarkers in different types of cancer but their accuracy is still debated. AKTIP is a telomeric protein with the property of being enriched at the nuclear lamina. AKTIP has similarity with the tumor susceptibility gene TSG101. AKTIP deficiency generates genome instability and, in p53−/−mice, the reduction of the mouse counterpart of AKTIP induces the exacerbation of lymphomas. Here, we asked whether the distribution of AKTIP is altered in cancer cells and whether this is associated with alterations of lamins.MethodsWe performed super-resolution imaging, quantification of lamin expression and nuclear morphology on HeLa, MCF7, and A549 tumor cells, and on non-transformed fibroblasts from healthy donor and HGPS (LMNA c.1824C > T p.Gly608Gly) and EDMD2 (LMNA c.775 T > G) patients. As proof of principle model combining a defined lamin alteration with a tumor cell setting, we produced HeLa cells exogenously expressing the HGPS lamin mutant progerin that alters nuclear morphology.ResultsIn HeLa cells, AKTIP locates at less than 0.5 µm from the nuclear rim and co-localizes with lamin A/C. As compared to HeLa, there is a reduced co-localization of AKTIP with lamin A/C in both MCF7 and A549. Additionally, MCF7 display lower amounts of AKTIP at the rim. The analyses in non-transformed fibroblasts show that AKTIP mislocalizes in HGPS cells but not in EDMD2. The integrated analysis of lamin expression, nuclear morphology, and AKTIP topology shows that positioning of AKTIP is influenced not only by lamin expression, but also by nuclear morphology. This conclusion is validated by progerin-expressing HeLa cells in which nuclei are morphologically altered and AKTIP is mislocalized.ConclusionsOur data show that the combined alteration of lamin and nuclear morphology influences the localization of the tumor-associated factor AKTIP. The results also point to the fact that lamin alterations per se are not predictive of AKTIP mislocalization, in both non-transformed and tumor cells. In more general terms, this study supports the thesis that a combined analytical approach should be preferred to predict lamin-associated changes in tumor cells. This paves the way of next translational evaluation to validate the use of this combined analytical approach as risk biomarker.
Immune-mediated diseases are associated with a higher incidence of dementia: a prospective cohort study of 375,894 individuals
Authors: Zhang Ya-Ru , Yang Liu , Wang Hui-Fu , Wu Bang-Sheng , Huang Shu-Yi , Cheng Wei , Feng Jian-Feng , Yu Jin-Tai 
Published: September 2022

Abstract
Background
Immune system dysregulation plays a vital role in the pathogenesis of neurodegenerative diseases, even considered to be as important as classical pathological protein aggregation assumption. However, the associations of immune-mediated diseases with incident dementia are unclear and need to be clarified in prospective studies with a large population and long follow-up time.

Methods
We investigated the relationship between any or individual immune-mediated diseases and incident dementia based on a prospective cohort UK Biobank. The risk for dementia was assessed with multivariable hazard ratio (HR) and 95% confidence interval (CI) after adjusting for various potential confounders using time-varying Cox proportional hazards regression. We also performed the subgroup Cox analysis stratified by time since immune-mediated diseases and gender. Causal mediation analyses with 1000 bootstrapped iterations were conducted to explore the mediation effects of peripheral immune cells on the associations of immune-mediated diseases with dementia.

Results
A total of 375,894 participants were included in the study, among which 5291 developed dementia during a median follow-up of 9.08 years. Immune-mediated diseases were associated with an increased risk of dementia (HR, 1.10; 95% CI, 1.00–1.21), and the risk was highest between 1 and 2 years after immune-mediated diseases onset (HR, 2.74; 95% CI, 1.86–4.04). Females who suffered from immune-mediated diseases were more prone to AD, while males were more susceptible to VD. Four of the individual immune-mediated diseases including type I diabetes mellitus (HR, 2.49; 95% CI, 1.97–3.15), rheumatic fever or rheumatic heart diseases (HR, 1.36; 95% CI, 1.05–1.77), multiple sclerosis (HR, 2.87; 95% CI, 1.92–4.30), and necrotizing vasculopathies (HR, 1.71; 95%CI, 1.03–2.85) were significantly related to higher dementia incidence. The relationship between immune-mediated diseases and dementia was partially mediated by peripheral immune cells including neutrophils and lymphocytes.

Conclusions
In this large cohort study, immune-mediated diseases were proven to be significantly associated with an increased risk of incident dementia, especially for type I diabetes mellitus which was observed to be related to the higher incidence of all types of dementia. Our findings could provide new sights on dementia pathogenesis and intervention from the perspective of systemic immunology and immune-mediated diseases.
Improved CTAB method for RNA extraction of thick waxy leaf tissues from sago palm (Metroxylon sagu Rottb.)
Authors: Yan Wei-Jie , Pendi Fifi Hafizzah , Hussain Hasnain 
Published: September 2022

AbstractBackgroundThere is a growing interest in transcriptomics studies parallel to the advancement of transcriptome databases and bioinformatics, which provided the opportunity to study responses to growths, stimuli and stresses. There is an increase in demand for excellent RNA extraction techniques. General RNA extraction protocols can be used in RNA extraction, but the quality and quantity vary in different types of tissues from different organisms. Hence, a specific RNA extraction method for each organism’s tissue type is required to obtain the desired RNA quality and quantity.ResultsThe improved CTAB RNA extraction method is superior to the PCI method and MRIP method for thick waxy leaves that were applied for mature sago palm (Metroxylon saguRottb.) leaf tissue and produce total RNA extract with good purity (OD 260/280 ≥ 1.8, OD 260/230 ≥ 2.0) and integrity (RIN ~ 7). RNA sequencing was conducted with the extracted samples and showed good assembly results (Q20 ≥ 97, Q30 ≥ 91%, assembly mean length ≥ 700 bp).ConclusionThe improved CTAB RNA extraction method enables rapid, cost-effective, and relatively simple RNA extraction from waxy, fibrous and high-in-polyphenol sago palm (M. saguRottb.) leaf tissue with next-generation RNA sequencing recommended quality.Graphical Abstract
Integrating arts with STEM and leading with STEAM to increase science learning with equity for emerging bilingual learners in the United States
Authors: Hughes Bradley S. , Corrigan Michael W. , Grove Douglas , Andersen Sage B. , Wong Joseph T. 
Published: September 2022

AbstractBackgroundTo inform STEM education for benefiting emerging bilingual (EB) and English fluent (EF) students, the present study evaluated the order effects of integrating science and arts within a large-scale, ongoing effort investigating the efficacies of Next Generation Science Standards (NGSS)-aligned Science Technology, Engineering, and Math (STEM) methodologies to provide more equitable opportunities to students to learn science through Arts integration (STEAM). The experiment examines the curriculum integrating order of implementing combinations of STEM and STEAM approaches in fifth grade life and physical science instruction, comparing (STEM → STEAM) vs (STEAM → STEM).ResultsTtests and a three-way between-groups analysis of covariance examined the impact of instructional order, language fluency, and teachers’ implementation fidelity. Findings indicate similar results in life and physical sciences, in which the STEAM first approach produced significantly higher science learning gains for both EF and EB students, revealing some higher learning gains for EF students, but with greater STEAM first order effect advantages for EB students overall. While EF students show higher learning gain scores in the high fidelity classrooms, the advantage of the STEAM first order is greater for EB students in all classroom fidelity levels and even within low to moderate implementation fidelity classrooms, as may commonly occur, such that the integration order of STEAM before STEM strategy is particularly advantageous to EB learners.ConclusionsThe integration pattern of leading with STEAM and following with STEM offers an important opportunity to learn for EB students, and increases equity in opportunities to learn among EB and EF learners of science. Both EB and EF students benefit similarly and significantly in high fidelity implementation classrooms. However, the gains for EF students are not significant in low fidelity implementation classrooms, while in such low fidelity implementation classrooms, the EB students still benefited significantly despite the poor implementation. These results suggest that a strong compensating STEAM first order effect advantage is possibly involved in the implementation system for the EB population of learners. Teaching science through the arts with STEAM lessons is an effective approach that can be significantly improved through introducing STEM units with the STEAM first order effect advantage.
Machine learning-based calibration of the GOCE satellite platform magnetometers
Authors: Styp-Rekowski Kevin , Michaelis Ingo , Stolle Claudia , Baerenzung Julien , Korte Monika , Kao Odej 
Published: September 2022

AbstractAdditional datasets from space-based observations of the Earth’s magnetic field are of high value to space physics and geomagnetism. The use of platform magnetometers from non-dedicated satellites has recently successfully provided additional spatial and temporal coverage of the magnetic field. The Gravity and steady-state Ocean Circulation Explorer (GOCE) mission was launched in March 2009 and ended in November 2013 with the purpose of measuring the Earth’s gravity field. It also carried three platform magnetometers onboard. Careful calibration of the platform magnetometers can remove artificial disturbances caused by other satellite payload systems, improving the quality of the measurements. In this work, a machine learning-based approach is presented that uses neural networks to achieve a calibration that can incorporate a variety of collected information about the satellite system. The evaluation has shown that the approach is able to significantly reduce the calibration residual with a mean absolute residual of about 6.47nT for low- and mid-latitudes. In addition, the calibrated platform magnetometer data can be used for reconstructing the lithospheric field, due to the low altitude of the mission, and also observing other magnetic phenomena such as geomagnetic storms. Furthermore, the inclusion of the calibrated platform magnetometer data also allows improvement of geomagnetic field models. The calibrated dataset is published alongside this work.
Graphical Abstract