Age estimation based on DNA methylation (DNAm) can be applied to children, adolescents and adults, but many CG dinucleotides (CpGs) exhibit different kinetics of age-associated DNAm across these age ...ranges. Furthermore, it is still unclear how growth disorders impact epigenetic age predictions, and this may be particularly relevant for a forensic application. In this study, we analyzed buccal mucosa samples from 95 healthy children and 104 children with different growth disorders. DNAm was analysed by pyrosequencing for 22 CpGs in the genes
PDE4C
,
ELOVL2
,
RPA2
,
EDARADD
and
DDO
. The relationship between DNAm and age in healthy children was tested by Spearman’s rank correlation. Differences in DNAm between the groups “healthy children” and the (sub-)groups of children with growth disorders were tested by ANCOVA. Models for age estimation were trained (1) based on the data from 11 CpGs with a close correlation between DNAm and age (
R
≥ 0.75) and (2) on five CpGs that also did not present significant differences in DNAm between healthy and diseased children. Statistical analysis revealed significant differences between the healthy group and the group with growth disorders (11 CpGs), the subgroup with a short stature (12 CpGs) and the non-short stature subgroup (three CpGs). The results are in line with the assumption of an epigenetic regulation of height-influencing genes. Age predictors trained on 11 CpGs with high correlations between DNAm and age revealed higher mean absolute errors (MAEs) in the group of growth disorders (mean MAE 2.21 years versus MAE 1.79 in the healthy group) as well as in the short stature (sub-)groups; furthermore, there was a clear tendency for overestimation of ages in all growth disorder groups (mean age deviations: total growth disorder group 1.85 years, short stature group 1.99 years). Age estimates on samples from children with growth disorders were more precise when using a model containing only the five CpGs that did not present significant differences in DNAm between healthy and diseased children (mean age deviations: total growth disorder group 1.45 years, short stature group 1.66 years). The results suggest that CpGs in genes involved in processes relevant for growth and development should be avoided in age prediction models for children since they may be sensitive for alterations in the DNAm pattern in cases of growth disorders.
Zika virus (ZIKV) infection during pregnancy results in a spectrum of birth defects and neurodevelopmental deficits in prenatally exposed infants, with no clear understanding of why some pregnancies ...are more severely affected. Differential control of maternal ZIKV infection may explain the spectrum of adverse outcomes.
Here, we investigated whether the magnitude and breadth of the maternal ZIKV-specific antibody response is associated with better virologic control using a rhesus macaque model of prenatal ZIKV infection. We inoculated 18 dams with an Asian-lineage ZIKV isolate (PRVABC59) at 30-45 gestational days. Plasma vRNA and infectious virus kinetics were determined over the course of pregnancy, as well as vRNA burden in the maternal-fetal interface (MFI) at delivery. Binding and neutralizing antibody assays were performed to determine the magnitude of the ZIKV-specific IgM and IgG antibody responses throughout pregnancy, along with peptide microarray assays to define the breadth of linear ZIKV epitopes recognized.
Dams with better virologic control (n= 9) cleared detectable infectious virus and vRNA from the plasma by 7 days post-infection (DPI) and had a lower vRNA burden in the MFI at delivery. In comparison, dams with worse virologic control (n= 9) still cleared detectable infectious virus from the plasma by 7 DPI but had vRNA that persisted longer, and had higher vRNA burden in the MFI at delivery. The magnitudes of the ZIKV-specific antibody responses were significantly lower in the dams with better virologic control, suggesting that higher antibody titers are not associated with better control of ZIKV infection. Additionally, the breadth of the ZIKV linear epitopes recognized did not differ between the dams with better and worse control of ZIKV infection.
Thus, the magnitude and breadth of the maternal antibody responses do not seem to impact maternal virologic control. This may be because control of maternal infection is determined in the first 7 DPI, when detectable infectious virus is present and before robust antibody responses are generated. However, the presence of higher ZIKV-specific antibody titers in dams with worse virologic control suggests that these could be used as a biomarker of poor maternal control of infection and should be explored further.
To test the hypothesis that term-born small for gestational age (SGA) neonates have elevated thyroid-stimulating hormone (TSH) concentrations and an increased incidence of congenital hypothyroidism ...compared with non-SGA term neonates.
This retrospective cohort study included all term neonates screened in Wisconsin in 2015 and 2016. The cohort was divided based on SGA status, defined as birth weight <10th percentile as calculated from the World Health Organization's sex-specific growth charts for age 0-2 years. TSH concentration on first newborn screening performed between birth and 96 hours of life and incidence of congenital hypothyroidism were compared between the SGA and non-SGA groups.
A total of 115 466 term neonates, including 11 498 (9.96%) SGA neonates, were included in the study. TSH concentration and incidence of congenital hypothyroidism was significantly higher in the SGA group, but only TSH concentration remained significant when adjusted for potential confounding variables.
Our data do not support a higher incidence of congenital hypothyroidism in term SGA neonates after adjusting for potential confounders. However, TSH concentrations were higher in term SGA neonates compared with term non-SGA neonates. The effects of mild thyroid hormone dysfunction on neurodevelopmental outcomes and development of chronic medical conditions merit long-term study.
Background and aim Biological soil crusts (biocrusts) play numerous crucial roles in drylands, which comprise over 40% of Earth's terrestrial surface. Among these key contributions is the fixation of ...atmospheric nitrogen. Yet, relatively little is known about the N2 fixation capabilities of different lichen species that are found in late successional biocrust communities across diylands globally. Methods In order to improve our species-specific understanding of biocrust lichen N2 fixation, we collected biocrusts dominated by four common species of lichens – Collema spp., Gyalolechia desertorum, Psora decipiens, and Squamarina lentigera – that represent a range of lichen families and morphological types. Nitrogenase activity of the biocrust community dominated by these lichens was evaluated using the acetylene reduction assay. Additionally, biocrust community composition was assessed using the point-intercept method along transects at varied distances from exposed bedrock. Results As expected, Collema spp.-dominated biocrusts had the highest rates of nitrogenase activity, with rates up to seven times larger than those of the other three target species. Nitrogen concentrations and carbon:nitrogen ratios of lichen tissue differed among lichen species. However, when the composite biocrust profile was assessed (i.e., biocrust tissue, microbial cells, and mineral soil to a 2 cm depth) these among-species differences in total nitrogen disappeared. Community composition changed according to distance from exposed bedrock, with a higher diversity of lichens closer to the bedrock. Conclusion Multiple drivers, including climate and land use change, affect biocrust community composition and species-specific functional information, even within a group such as late successional biocrusts, could help in forecasting the potential effects of global change on N2 fixation, and consequently, soil fertility in drylands.
Net synthesis of pancreatic β-cells peaks before 2 years of life. β-Cell mass is set within the first 5 years of life. In-frame translational readthrough of the NRP1 gene exon 9 into intron 9 ...generates a truncated neuropilin-1 protein lacking downstream sequence necessary for binding VEGF that stimulates β-cell replication. VEGF is critical for developing but not adult islet neogenesis. Herein we show that cells in human pancreatic islets containing the full-length neuropilin-1 possess insulin but cells that contain the truncated neuropilin-1 are devoid of insulin. Decreased insulin cells increases susceptibility to onset of type 1 diabetes at a younger age. We also show that the frequency of a genetic marker in NRP1 intron 9 is higher among patients with onset of type 1 diabetes before age 4 years (31.8%), including those with onset at 0.67–2.00 and 2–4 years, compared with that in patients with onset at 4–8 years, at 8–12 years, and after 16 years (16.1%) with frequency equal to that in subjects without diabetes (16.0%). Decreased insulin cells plus the genetic data are consistent with a low effect mechanism that alters the onset of type 1 diabetes to a very young age in some patients, thus supporting the endotype concept that type 1 diabetes is a heterogeneous disease.
Conventional mass-univariate analyses have been previously used to test for group differences in neural signals. However, machine learning algorithms represent a multivariate decoding approach that ...may help to identify neuroimaging patterns associated with functional impairment in "individual" patients. We investigated whether fMRI allows classification of individual motor impairment after stroke using support vector machines (SVMs). Forty acute stroke patients and 20 control subjects underwent resting-state fMRI. Half of the patients showed significant impairment in hand motor function. Resting-state connectivity was computed by means of whole-brain correlations of seed time-courses in ipsilesional primary motor cortex (M1). Lesion location was identified using diffusion-weighted images. These features were used for linear SVM classification of unseen patients with respect to motor impairment. SVM results were compared with conventional mass-univariate analyses. Resting-state connectivity classified patients with hand motor deficits compared with controls and nonimpaired patients with 82.6-87.6% accuracy. Classification was driven by reduced interhemispheric M1 connectivity and enhanced connectivity between ipsilesional M1 and premotor areas. In contrast, lesion location provided only 50% sensitivity to classify impaired patients. Hence, resting-state fMRI reflects behavioral deficits more accurately than structural MRI. In conclusion, multivariate fMRI analyses offer the potential to serve as markers for endophenotypes of functional impairment.
Introduction One of the key symptoms of Parkinson’s disease (PD) is the impairment of spontaneous movement also known as akinesia ( Berardelli et al., 2001 ). Correspondingly, patients performing ...motor tasks feature abnormal activation in regions such as posterior medial frontal cortex (pMFC) and putamen ( Herz et al., 2013 ). These areas play crucial roles in the internal timing of volitional movements in healthy individuals ( Hoffstaedter et al., 2013 ). Yet, little is known about these regions’ functional connectivity (FC) in PD and its relationship with akinesia. The present study investigated FC alterations of the ’motor initiation network’ in PD, using a seed-based resting-state (RS) analysis. Methods RS fMRI data of 60 patients diagnosed with idiopathic PD (mean age 61.6 ± 10.2; mean disease duration 6.5 ± 5.5 years) and 72 healthy volunteers (mean age 60.1 ± 8.8, matched for age, gender and within-scanner movement) was acquired at two sites. After spatial preprocessing (realignment, normalization, smoothing), temporal filtering was conducted including motion confound removal and band-pass filtering. Seeds in bilateral putamen and pMFC were derived from a meta-analysis on volitional movements ( Hoffstaedter et al., 2014 ). Two more seeds were selected in bilateral primary motor cortex (M1). For each seed, (i) whole-brain FC and (ii) its interaction with akinesia (UPDRS item 3.14) were assessed. RS networks for the aforementioned regions were first mapped in healthy controls only: Contrasting each region’s FC to the FC of all respective other seeds yielded maps of specific connectivity with either seed. These networks were then used to map whole-brain corrected changes of FC in PD. Results were cluster-level corrected for multiple comparisons ( p < 0.05). Results In healthy participants, RS analysis differentiated three networks, specifically (more than all other seeds) connected to bilateral putamen, bilateral M1, and pMFC. In PD, all seeds consistently featured decreased FC with regions in their most related network. That is, M1 mainly showed FC decrease within the M1-related network, pMFC lost FC with anterior insulae and left dorsolateral prefrontal cortex (DLPFC; pMFC-related network), and putamen lost FC with caudate nucleus, pallidum and thalamus (Putamen-related network). Additionally, putamen FC decreased extensively also in those regions more related to M1 and pMFC, including visual, superior parietal, primary somatosensory, M1, pMFC and DLPFC. Testing for each seed’s interaction with akinesia, pMFC showed a decreased FC with inferior parietal lobe (IPL) in the pMFC-related network. In turn, FC of the other seeds did not significantly relate to akinesia. Conclusions The present study examined RS FC changes of bilateral putamen, M1 and pMFC in PD. In patients, putamen FC suggests a marked cortico-striatal decoupling, in line with pathophysiological models of the disease ( Braak et al., 2004 ). In contrast, pMFC featured more selective FC decreases, predominantly in regions involved in motor control ( Hoffstaedter et al., 2013; Hoffstaedter et al., 2014 ). Notably, akinesia was exclusively related to pMFC-connectivity. With increasing impairment, pMFC decoupled from the right IPL. In sum, the present study demonstrates a disruption of cortico-striatal FC and specifies the role of pMFC - IPL connectivity for movement initiation in PD.
A controlled human infection model for assessing tuberculosis (TB) immunity can accelerate new vaccine development.
In this phase 1 dose escalation trial, 92 healthy adults received a single ...intradermal injection of 2 × 106 to 16 × 106 colony-forming units of Bacillus Calmette-Guérin (BCG). The primary endpoints were safety and BCG shedding as measured by quantitative polymerase chain reaction, colony-forming unit plating, and MGIT BACTEC culture.
Doses up to 8 × 106 were safe, and there was evidence for increased BCG shedding with dose escalation. The MGIT time-to-positivity assay was the most consistent and precise measure of shedding. Power analyses indicated that 10% differences in MGIT time to positivity (area under the curve) could be detected in small cohorts (n = 30). Potential biomarkers of mycobacterial immunity were identified that correlated with shedding. Transcriptomic analysis uncovered dose- and time-dependent effects of BCG challenge and identified a putative transcriptional TB protective signature. Furthermore, we identified immunologic and transcriptomal differences that could represent an immune component underlying the observed higher rate of TB disease incidence in males.
The safety, reactogenicity, and immunogenicity profiles indicate that this BCG human challenge model is feasible for assessing in vivo TB immunity and could facilitate the vaccine development process.
NCT01868464 (ClinicalTrials.gov).
This study characterizes the morphologic features and the endogenous fluorescence in the stratified squamous epithelia of the 7,12-dimethylbenz(a)anthracene-treated hamster cheek pouch model of ...carcinogenesis using multiphoton laser scanning microscopy (MPLSM). MPLSM allows high-resolution, three-dimensional image data to be collected deeper within thick tissue samples with reduced phototoxicity compared with single-photon imaging. Three-dimensional image stacks of normal (n = 13), precancerous (dysplasia, n = 12; carcinoma in situ, n = 9) and cancerous tissue nonpapillary squamous cell carcinoma (SCC), n = 10, and papillary SCC, n = 7 sites in the hamster cheek pouch were collected in viable, unsectioned tissue biopsies at a two-photon excitation wavelength of 780 nm. Five features were quantified from the MPLSM images. These included nuclear density versus depth, keratin layer thickness, epithelial thickness, and the fluorescence per voxel in the keratin and epithelial layers. Statistically significant differences in all five features were found between normal and both precancerous and cancerous tissues. The only exception to this was a lack of statistically significant differences in the keratin fluorescence between normal tissues and papillary SCCs. Statistically significant differences were also observed in the epithelial thickness of dysplasia and carcinoma in situ, and in the keratin layer thickness of dysplasia and SCCs (both nonpapillary and papillary). This work clearly shows that three-dimensional images from MPLSM of endogenous tissue fluorescence can effectively distinguish between normal, precancerous, and cancerous epithelial tissues. This study provides the groundwork for further exploration into the application of multiphoton fluorescence endoscopy in a clinical setting.
The diagnostic approach to newly detected space-occupying lesions in the liver can be difficult and a histogenetic classification of the primary tumor is impossible in some cases. Such cases of ...metastatic disease without a detectable primary tumor are classified as cancer of unknown primary site (CUP). The incidence of this diagnosis depends on the clinical and histochemical methods used. It was the main aim of this study to analyze the true incidence of adenocarcinoma metastases of the liver with an unknown primary cancer after application of a standardized protocol of clinical and immunhistochemical diagnostic tests and a long-term follow-up.
Between January 2000 and January 2003 127 consecutive patients underwent diagnostic ultrasound-guided biopsy of a space-occupying lesion in the liver. Based on the histopathology and immunochemistry a well defined and individually adapted diagnostic algorithm was employed (endoscopy, imaging).
44 females and 83 males, median age 66.8 years, were enrolled into the study. Primary tumors of the liver were found in 21 cases and non-hepatocellular tumors (metastases) were documented in 106 patients, 82 of the latter (77%) had metastases of an adenocarcinoma. The further diagnostic approach was based on histochemistry, immunhistochemistry and imaging techniques, making possible a full diagnosis of primary tumor in a further 59 (72%) cases. Thus the incidence of an adenocarcinoma of the liver of unknown primary site was 23 of 127 cases (18%).
Although there is a wide variety of modern diagnostic methods today, the histogenetic classification of hepatic metastases is not always possible. However, in the last few years diagnostic advances have occurred based on modern immunhistochemical methods. This immunhistochemical definition has made it possible to avoid an oppressive "overdiagnosis" and offer patients early and appropriate therapeutic options.
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