Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproduction, DNA methylation and biological age.

STUDY QUESTION Are reproductive characteristics associated with genome-wide DNA methylation and epigenetic age? SUMMARY ANSWER Our data suggest that increasing parity is associated with differences in blood DNA methylation and small increases in epigenetic age. WHAT IS KNOWN ALREADY A study of 397 young Filipino women (ages 20-22) observed increasing epigenetic age with an increasing number of pregnancies. STUDY DESIGN, SIZE, DURATION We used data from 2356 non-Hispanic white women (ages 35-74) enrolled in the Sister Study cohort. PARTICIPANTS/MATERIALS, SETTING, METHODS Data on reproductive history were ascertained via questionnaire. Of the 2356 women, 1897 (81%) reported at least one live birth. Among parous women, 487 (26%) women reported ever experiencing a pregnancy complication. Three epigenetic clocks (i.e. Hannum, Horvath and Levine) and genome-wide methylation were measured in DNA from whole blood using Illumina's HumanMethylation450 BeadChip. We estimated association β-values and 95% CIs using linear regression. MAIN RESULTS AND THE ROLE OF CHANCE All three epigenetic clocks showed weak associations between number of births and epigenetic age (per live birth; Hannum: β = 0.16, 95% CI = 0.02, 0.29, P = 0.03; Horvath: β = 0.12, 95% CI = -0.04, 0.27, P = 0.14; Levine: β = 0.27, 95% CI = 0.08, 0.45, P = 0.01); however, additional adjustment for current BMI attenuated the associations. Among parous women, a history of abnormal glucose tolerance during pregnancy was associated with increased epigenetic age by the Hannum clock (β = 0.96; 95% CI = 0.10, 1.81; P = 0.03) and Levine clocks (β = 1.69; 95% CI = 0.54, 2.84; P < 0.01). In epigenome-wide analysis, increasing parity was associated with methylation differences at 17 CpG sites (Bonferroni corrected P≤ 1.0 × 10-7). LIMITATIONS, REASONS FOR CAUTION We relied on retrospective recall to ascertain reproductive history and pregnancy complications. WIDER IMPLICATIONS OF THE FINDINGS Our findings suggest that parity is associated with small increases in epigenetic age and with DNA methylation at multiple sites in the genome. STUDY FUNDING/COMPETING INTEREST(S) This research was supported by the Intramural Research program of the NIH, National Institute of Environmental Health Sciences (Z01-ES049033, Z01-ES049032 and Z01-ES044055). None of the authors have a conflict of interest. TRIAL REGISTRATION NUMBER Not applicable.
Discovery and structure–activity relationship of plastoquinone analogs as anticancer agents against chronic myelogenous leukemia cells

Two series of amino‐1,4‐benzoquinones (AQ1–18) based on the structural analogs of plastoquinones were synthesized and the structure–activity relationship against chronic myelogenous leukemia activity was examined. All of the synthesized compounds were tested for their cytotoxic effects on different leukemic cell lines. Of interest, AQ15 exhibited a better selectivity than the reference drug imatinib on cancer cells. Owing to this, AQ15 was selected for a further apoptosis/necrosis evaluation where AQ15‐treated K562 cells demonstrated similar apoptotic effects like imatinib‐treated cells at their IC50 values. The inhibitory effects of AQ15 and the other three compounds with various activities against eight tyrosine kinases, including ABL1, were investigated. AQ15 showed weak activity against ABL1, and a correlation was observed between the anti‐K562 and anti‐ABL1 activities. The binding mode of AQ15 into the ATP binding pocket of ABL1 kinase was predicted in silico, showing the formation of some key interactions. In addition, AQ15 was shown to suppress the downstream signaling of BCR‐ABL in K562 cells. Finally, AQ15 obviously cleaved DNA in the presence of an iron(II) complex system, indicating that this can be the major mechanism of its antiproliferative action, whereas the mild inhibition of ABL kinase is just in‐part mechanism of its overall outstanding cellular activity.
Differential Susceptibility and Innate Immune Response of Aedes aegypti and Aedes albopictus to the Haitian Strain of the Mayaro Virus

Mayaro (MAYV) is an emerging arthropod-borne virus belonging to the Alphavirus genus of the Togaviridae family. Although forest-dwelling Haemagogus mosquitoes have been considered as its main vector, the virus has also been detected in circulating Aedes ssp mosquitoes. Here we assess the susceptibility of Aedes aegypti and Aedes albopictus to infection with MAYV and their innate immune response at an early stage of infection. Aedes albopictus was more susceptible to infection with MAYV than Ae. aegypti. Analysis of transcript levels of twenty immunity-related genes by real-time PCR in the midgut of both mosquitoes infected with MAYV revealed increased expression of several immune genes, including CLIP-domain serine proteases, the anti-microbial peptides defensin A, E, cecropin E, and the virus inducible gene. The regulation of certain genes appeared to be Aedes species-dependent. Infection of Ae. aegypti with MAYV resulted in increased levels of myeloid differentiation2-related lipid recognition protein (ML26A) transcripts, as compared to Ae. albopictus. Increased expression levels of thio-ester-containing protein 22 (TEP22) and Niemann–Pick type C1 (NPC1) gene transcripts were observed in infected Ae. albopictus, but not Ae. aegypti. The differences in these gene expression levels during MAYV infection could explain the variation in susceptibility observed in both mosquito species.
Bactericidal Activity of Lactic Acid against Clinical, Carbapenem-Hydrolyzing, Multi-Drug-Resistant Klebsiella pneumoniae Planktonic and Biofilm-Forming Cells

Carbapenem resistant Klebsiella pneumoniae has been highlighted to be a critical pathogen by the World Health Organization. The objectives of this study were to assess the efficacy of lactic acid (LA) against planktonic cells and biofilms formed by carbapenem-hydrolyzing K. pneumoniae isolates obtained from the nares of preterm neonates. Time-kill assays with graded percentages of (v/v) LA in water were initially carried out against planktonic cells of a meropenem (MRP)-resistant K. pneumoniae isolate, JNM11.C4. The efficacy parameters such as optimal incubation time and minimum inhibitory concentration were determined by comparing colony-forming unit counts (log(10) CFU). Scanning electron microscopy was used to visualize cell damage. Likewise, JNM11.C4 biofilms were treated with graded series of (v/v) LA. Six carbapenem-hydrolyzing isolates were next used to validate the results. A reduction of 3.6 ± 0.6 log(10) CFU/mL in JNM11.C4 planktonic cells and >3 ± 0.03log(10) CFU/mL in biofilm-forming cells were observed using 0.225% and 2% LA, respectively, after three hours. Similar decreases in viable cell-counts were observed both in the case of planktonic (˃3.6 ± 0.3log(10) CFU/mL) and biofilm-forming cells (3.8 ± 0.3log(10) CFU/mL) across all the six clinical isolates. These results indicate that LA is an effective antimicrobial against planktonic carbapenem-hydrolyzing K. pneumoniae cells and biofilms.
Trajectory and mortality of preserved ratio impaired spirometry: the Rotterdam Study

Preserved ratio impaired spirometry (PRISm) is a heterogeneous condition but its course and disease progression remain to be elucidated. We aimed to examine its prevalence, trajectories and prognosis in the general population. In the Rotterdam Study (population-based prospective cohort) we examined prevalence, trajectories and prognosis of subjects with normal spirometry (controls; forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) ≥0.7, FEV1 ≥80%), PRISm (FEV1/FVC ≥0.7, FEV1 <80%) and chronic obstructive pulmonary disease (COPD) (FEV1/FVC <0.7) at two study visits. Hazard ratios with 95% confidence intervals for mortality (until December 30, 2018) were adjusted for age, sex, body mass index, current smoking and pack-years. Of 5487 subjects (age 69.1±8.9 years; 7.1% PRISm), 1603 were re-examined after 4.5 years. Of the re-examined PRISm subjects, 15.7% transitioned to normal spirometry and 49.4% to COPD. Median lung function decline was highest in subjects with incident PRISm (FEV1 −92.8 mL·year−1, interquartile range (IQR) −131.9– −65.8 mL·year−1; FVC −93.3 mL·year−1, IQR −159.8– −49.1 mL·year−1), but similar in persistent PRISm (FEV1 −30.2 mL·year−1, IQR −67.9– −7.5 mL·year−1; FVC −20.1 mL·year−1, IQR −47.7–21.7 mL·year−1) and persistent controls (FEV1 −39.6 mL·year−1, IQR −64.3–−12.7 mL·year−1; FVC −20.0 mL·year−1, IQR −55.4–18.8 mL·year−1). Of 5459 subjects with informed consent for follow-up, 692 (12.7%) died during 9.3 years (maximum) follow-up: 10.3% of controls, 18.7% of PRISm subjects and 20.8% of COPD subjects. Relative to controls, subjects with PRISm and COPD Global Initiative for Chronic Obstructive Lung Disease (GOLD) 2–4 had increased all-cause mortality (PRISm: HR 1.6, 95% CI 1.2–2.0; COPD GOLD 2–4: HR 1.7, 95% CI 1.4–2.1) and cardiovascular mortality (PRISm: HR 2.8, 95% CI 1.5–5.1; COPD 2–4: HR 2.1, 95% CI 1.2–3.6). Mortality within <1 year was highest in PRISm, with patients often having cardiovascular comorbidities (heart failure or coronary heart disease; 70.0%). PRISm is associated with increased mortality and this population encompasses at least three distinct subsets: one that develops COPD during follow-up, a second with high cardiovascular burden and early mortality, and a third with persistent PRISm and normal age-related lung function decline. Preserved ratio impaired spirometry, previously called restrictive spirometry, is a condition associated with increased mortality that encompasses distinct clinical subsets http://bit.ly/2ncclac
A bacterium against the tiger: preliminary evidence of fertility reduction after release of Aedes albopictus males with manipulated Wolbachia infection in an Italian urban area.

BACKGROUND Novel tools are needed to reduce nuisance and risk of exotic arbovirus transmission associated with the colonization of temperate regions by Aedes albopictus. Incompatible Insect Technique (IIT) is a population suppression approach based on cytoplasmic incompatibility between males with manipulated endosymbionts and wild females. Here we present the results of the first field experiment in Europe to assess the capacity of an Ae. albopictus line (ARwP) deprived of its natural endosymbiont Wolbachia and transinfected with a Wolbachia strain from the mosquito Culex pipiens - to sterilize wild females. RESULTS We released ~4500 ARwP males weekly for 6 weeks in a green area within urban Rome (Italy) and carried out egg (N = 13 442), female (N = 128) and male (N = 352) collections. Egg (N = 13 783) and female (N = 48) collections were also carried out in two untreated Control Sites. The percentage of viable eggs during releases was on average significantly lower in Treated than in Control Sites, with the highest difference (16%) after the fourth release. The ARwP/wild male ratio in the release spots between day-3 from the first ARwP male release and day-7 after the last release was on average 7:10. Released males survived up to two weeks. About 30% of the females collected in the release spots showed 100% sterility and 20% a strongly reduced fertility compared to Control Sites. CONCLUSIONS Results support the potential of IIT as a tool to contribute to Ae. albopictus control in the urban context and stress the need of larger field trials to evaluate the cost-efficacy of the approach in suppressing wild populations. This article is protected by copyright. All rights reserved.
A Phase II Trial of Hu14.18K322A in Combination with Induction Chemotherapy in Children with Newly Diagnosed High-Risk Neuroblastoma

Purpose: We sought to evaluate whether combining a humanized antidisialoganglioside mAb (hu14.18K322A) with induction chemotherapy improves early responses and outcomes in children with newly diagnosed high-risk neuroblastoma. Patients and Methods: We conducted a prospective nonrandomized, single-arm, two-stage, phase II clinical trial. Six courses of induction chemotherapy were coadministered with hu14.18K322A and followed with granulocyte–macrophage colony-stimulating factor (GM-CSF) and low-dose IL2. Consolidation was performed with a busulfan/melphalan preparative regimen. An additional course of hu14.18K322A was administered with parent-derived natural killer cells, when available, during consolidation. Hu14.18K322A, GM-CSF, IL2, and isotretinoin were then administered. Secondary outcomes included reduced tumor volume and semiquantitative 123I-metaiodobenzylguanidine scoring [i.e., Curie scores (CS)] at the end of induction. Results: Forty-two patients received hu14.18K322A and induction chemotherapy. This regimen was well tolerated, with continuous-infusion narcotics adjusted to patient tolerance. Partial responses (PR) or better after the first two chemoimmunotherapy courses occurred in 32 patients [76.2%; 95% confidence interval (CI), 60.6–88.0]. This was accompanied by primary tumor volume reductions (median, –76%; range, –100% to 5%). Of 35 patients with stage IV disease who completed induction, 31 had end-of-induction CSs of 2 or less. No patients experienced progression during induction. Two-year event-free survival (EFS) was 85.7% (95% CI, 70.9–93.3). Conclusions: Adding hu14.18K322A to induction chemotherapy produced early PR or better in most patients, reduced tumor volumes, improved CSs at the end of induction, and yielded an encouraging 2-year EFS. These results, if validated in a larger study, may change the standard of care for children with high-risk neuroblastoma.
MANAGEMENT OF ENDOCRINE DISEASE: Are all GLP-1 agonist equal in the treatment of type 2 diabetes?

GLP-1, a peptide hormone secreted from the gut stimulating insulin and suppressing glucagon secretion was identified as a parent compound for novel treatments of diabetes, but was degraded (dipeptidyl peptidase-4) eliminated (mainly kidneys) too fast (half-life 1-2 min) to be useful as a therapeutic agent. GLP-1 receptor agonist have been used to treat patients with type 2 diabetes since 2007, when exenatide (twice daily) was approved in 2007. Compounds with longer duration of action (once daily, once weekly) and with increasingly better efficacy with respect to glycaemic control and body weight reduction have been developed, and in a recent ADA/EASD consensus statement were recommended as the first injectable diabetes therapy after failure of oral glucose-lowering medications. Most GLP-1 receptor agonists (lixisenatide q.d., liraglutide q.d., exenatide q.w., albiglutide q.w., albiglutide q.w., semaglutide q.w., all for subcutaneous injection, and the first oral preparation, oral semaglutide) have been examined in cardiovascular outcomes studies. Beyond proving their safety in vulnerable patients, most of whom had pre-existing heart disease, liraglutide, semaglutide, albiglutide, and dulaglutide reduced the time to first major adverse cardiovascular events (non-fatal myocardial infarction and stroke, cardiovascular death). Liraglutide, in addition, reduced cardiovascular and all-cause mortality. It is the purpose of the present review to describe clinically important differences, regarding pharmacokinetic behaviour, glucose-lowering potency, effectiveness of reducing body weight and controlling other cardiovascular risk factors, and of the influence of GLP-1 receptor agonist treatment on cardiovascular outcomes in patients either presenting with or without pre-existing cardiovascular disease (atherosclerotic, ischemic or congestive heart failure).
Physical fitness and physical self-concept of male and female young adults in Qatar

Background Physical inactivity is high within the Qatari population, particularly within females, and school-based environments, contributing to increased morbidity and mortality. School-based physical activity (PA) outcomes may be mediated by physical self-concept. Low physical self-concept may negatively impact PA engagement, compromising childhood and adolescent physical fitness, which may translate into adulthood. Normative physical fitness data for the Qatari population is unavailable. Stratifying normative physical fitness appears prudent, to not only allow comparisons to be made worldwide, but enable informed decisions for public health policy and future interventions in the Qatari population. Purpose To establish the physical fitness of young adults in Qatar, and examine differences between males and females for physical self-concept, and engagement in school-based and extra-curricular PA. Method 186 (females n = 85) healthy participants [median (minimum—maximum) age: males = 21 (18–26), females = 21 (18–24) y; height: males = 1.74 (1.57–1.99), females = 1.61 (1.46–1.76) m; body mass: males = 71.9 (49.3–145.0), females = 56.8 (35.7–96.4) kg] completed the ALPHA-FIT test battery for adults (one leg stand, figure of eight run, handgrip strength, jump and reach, modified push-up, dynamic sit-up and 2 km walk), physical self-description questionnaire (measuring physical self-concept), and were asked to answer ‘yes’ or ‘no’ to whether they participated in school-based and extra-curricular PA. Results Data is reported as effect size; ±90% confidence limit. Males compared to females most likely performed better for dynamic sit-up (2.2; ±0.76), very likely better for the figure of eight run (0.86; ±0.42) and likely better for handgrip strength (2.1; ±0.75). Males likely had higher physical self-concept for coordination (0.78; ±0.37) and endurance (0.66; ±0.27) compared to females. There were no differences for school-based PA (p ≥ 0.78) or for extra-curricular PA for males (p ≥ 0.26) or females (p ≥ 0.21). Conclusion The data suggests that the young Qatari adult population has variable, yet generally low, physical fitness traits compared to individuals worldwide, likely due to their low PA. The precise aetiology for this is not well documented, yet such data may be prudent to evidence-inform strategies to improve physical fitness through increased PA (synergistic relationship), given the strong association between physical activity/fitness and morbidity/mortality.
SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting

MOTIVATION Mitochondria are an essential organelle in most eukaryotes. They not only play an important role in energy metabolism but also take part in many critical cytopathological processes. Abnormal mitochondria can trigger a series of human diseases, such as Parkinson's disease, multifactor disorder, and Type-II diabetes. Protein submitochondrial localization enables the understanding of protein function in studying disease pathogenesis and drug design. RESULTS We proposed a new method, SubMito-XGBoost, for protein submitochondrial localization prediction. Three steps are included: (i) the g-gap dipeptide composition (g-gap DC), pseudo-amino acid composition (PseAAC), auto-correlation function (ACF), and Bi-gram position-specific scoring matrix (Bi-gram PSSM) are employed to extract protein sequence features, (ii) Synthetic Minority Oversampling Technique (SMOTE) is used to balance samples, and the ReliefF algorithm is applied for feature selection, and (iii) the obtained feature vectors are fed into XGBoost to predict protein submitochondrial locations. SubMito-XGBoost has obtained satisfactory prediction results by the leave-one-out-cross-validation (LOOCV) compared with existing methods. The prediction accuracies of the SubMito-XGBoost method on the two training datasets M317 and M983 were 97.7% and 98.9%, which are 2.8-12.5% and 3.8-9.9% higher than other methods, respectively. The prediction accuracy of the independent test set M495 was 94.8%, which is significantly better than the existing studies. The proposed method also achieves satisfactory predictive performance on plant and non-plant protein submitochondrial datasets. SubMito-XGBoost also plays an important role in new drug design for the treatment of related diseases. AVAILABILITY AND IMPLEMENTATION The source codes and data are publicly available at https://github.com/QUST-AIBBDRC/SubMito-XGBoost/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Enhanced capabilities of TROPOMI NO2: Estimating NOx from North American cities and power plants.

The Tropospheric Monitoring Instrument (TROPOMI) is used to derive top-down NOx emissions for two large power plants and three megacities in North America. We first re-process the vertical column NO2 with an improved air mass factor to correct for a known systematic low-bias in the operational retrieval near urban centers. For the two power plants, top-down NOx emissions agree to within 10% of the emissions reported by the power plants. We then derive top-down NOx emissions rates for New York City, Chicago, and Toronto, and compare them to projected bottom-up emissions inventories. In this analysis of 2018 NOx emissions, we find a +22% overestimate for New York City, a -21% underestimate in Toronto, and good agreement in Chicago in the projected bottom-up inventories when compared to the top-down emissions. Top-down NOx emissions also capture intra-seasonal variability, such as the weekday vs. weekend effect (emissions are +45% larger on weekdays vs. weekends in Chicago). Finally, we demonstrate the enhanced capabilities of TROPOMI, which allow us to derive a NOx emissions rate for Chicago using a single overpass on July 7, 2018. The large signal-to-noise ratio of TROPOMI is well-suited for estimating NOx emissions from relatively small sources and for sub-seasonal timeframes.
Age-Dependent Signal Intensity Changes in the Structurally Normal Pediatric Brain on Unenhanced T1-Weighted MR Imaging

BACKGROUND AND PURPOSE: Various pathologic and nonpathologic states result in brain parenchymal signal intensity changes on unenhanced T1-weighted MR imaging. However, the absence of quantitative data to characterize typical age-related signal intensity values limits evaluation. We sought to establish a range of age-dependent brain parenchymal signal intensity values on unenhanced T1WI in a sample of individuals (18 years of age or younger) with structurally normal brains. MATERIALS AND METHODS: A single-center retrospective study was performed. Gadolinium-naïve pediatric patients with structurally normal MR brain imaging examination findings were analyzed (n = 114; 50% female; age range, 68 days to 18 years). ROI signal intensity measurements were obtained from the globus pallidus, thalamus, dentate nucleus, pons, and frontal lobe cortex and subcortical white matter. Multivariable linear regression was used to analyze the relationship between signal intensity values and age. RESULTS: Results demonstrated a statistically significant association between signal intensity values and linear age in all neuroanatomic areas tested, except the frontal gray matter, (P < .01). There were no statistically significant differences attributable to patient sex. CONCLUSIONS: Age-dependent signal intensity values were determined on unenhanced T1WI in structurally normal pediatric brains. Increased age correlated with increased signal intensity in all brain locations, except the frontal gray matter, irrespective of sex. The biologic mechanisms underlying our results remain unclear and may be related to chronologic changes in myelin density, synaptic density, and water content. Establishing age-dependent signal intensity parameters in the structurally normal pediatric brain will help clarify developmental aberrations and enhance gadolinium-deposition research by providing an improved understanding of the confounding effect of age.