We and others have suggested that pioneer activity - a transcription factor's (TF's) ability to bind and open inaccessible loci - is not a qualitative trait limited to a select class of pioneer TFs. ...We hypothesize that most TFs display pioneering activity that depends on the TF concentration and the motif content at their target loci.
Here, we present a quantitative in vivo measure of pioneer activity that captures the relative difference in a TF's ability to bind accessible versus inaccessible DNA. The metric is based on experiments that use CUT&Tag to measure the binding of doxycycline-inducible TFs. For each location across the genome, we determine the concentration of doxycycline required for a TF to reach half-maximal occupancy; lower concentrations reflect higher affinity. We propose that the relative difference in a TF's affinity between ATAC-seq labeled accessible and inaccessible binding sites is a measure of its pioneer activity. We estimate binding affinities at tens of thousands of genomic loci for the endodermal TFs FOXA1 and HNF4A and show that HNF4A has stronger pioneer activity than FOXA1. We show that both FOXA1 and HNF4A display higher binding affinity at inaccessible sites with more copies of their respective motifs. The quantitative analysis of binding suggests different modes of binding for FOXA1, including an anti-cooperative mode of binding at certain accessible loci.
Our results suggest that relative binding affinities are reasonable measures of pioneer activity and support the model wherein most TFs have some degree of context-dependent pioneer activity.
To assess if SARS-CoV-2 (COVID-19) systemic disease can be determined by available nucleoprotein assays, we compared the performance of three commercial SARS-CoV-2 nucleoprotein (N) assays in plasma. ...A total of 272 plasma samples collected in the period November-December 2021 were analyzed by the methods Simoa SARS CoV-2 N Protein Advantage Kit Quanterix Simoa, Solsten SARS-CoV-2 Antigen enzyme immunosorbent assay (ELISA) Solsten ELISA, and Elecsys SARS-CoV-2 Antigen electrochemiluminescence immunoassay Elecsys ECLIA. Additionally, a dilution series of inactivated virus culture was analyzed by the three assays. The SARS CoV-2 PCR-status was not known for the patients. Linear correlation in the pairwise correlation between assays as well as linearity of dilution series of inactivated virus culture was estimated by Spearman score. Sensitivity and specificity were estimated by pairwise comparison. The three assays showed poor agreement on patient samples with regards to concentration. Performance on virus culture was excellent but with different level of detection (LOD). Positive vs negative results show comparable sensitivity and specificity of Quanterix Simoa and Solsten ELISA, with a higher LOD in Elecsys ECLIA and thus lower sensitivity and high specificity. N by all tested assays can be used as a marker for systemic COVID-19 disease.
This review summarizes the results of past research on films and coatings from hemicelluloses, biopolymers that are as yet relatively unexploited commercially. The targeted uses of hemicelluloses ...have primarily been packaging films and coatings for foodstuffs as well as biomedical applications. Oxygen permeability of hemicellulose films, an important characteristic for food packaging, was typically comparable to values found for other biopolymer films such as amylose and amylopectin. As expected, the modification of hemicelluloses to create more hydrophobic films reduced the water vapor permeability. However, modified hemicellulose coatings intended for food still exhibited water vapor permeabilities several magnitudes higher than those of other polymers currently used for this purpose. Research on hemicelluloses for biomedical applications has included biocompatible hydrogels and coatings and material surfaces with enhanced cell affinity. Numerous possibilities exist for chemically modifying hemicelluloses, and fundamental studies of films from modified hemicelluloses have identified other potential applications, including selective membranes.
We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with the sample compartmentalization and ...dispersion-free transport that is inherent to droplets. The device allows for the execution of user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging programmable sequences of picoliter-volume droplets containing reagents or cells. This functionality is enabled by "flow-controlled wetting," a droplet docking and merging mechanism that exploits the physics of droplet flow through a channel to control the precise location of droplet wetting. The device also allows for automated cross-contamination-free recovery of reaction products from individual chambers into standard microfuge tubes for downstream analysis. The combined features of programmability, addressability, and selective recovery provide a general hardware platform that can be reprogrammed for multiple applications. We demonstrate this versatility by implementing multiple single-cell experiment types with this device: bacterial cell sorting and cultivation, taxonomic gene identification, and high-throughput single-cell whole genome amplification and sequencing using common laboratory strains. Finally, we apply the device to genome analysis of single cells and microbial consortia from diverse environmental samples including a marine enrichment culture, deep-sea sediments, and the human oral cavity. The resulting datasets capture genotypic properties of individual cells and illuminate known and potentially unique partnerships between microbial community members.
Objectives
To assess cancer detection rates of different target‐dependent transperineal magnetic resonance (MR)/ultrasonography (US) fusion‐guided biopsy templates with reduced number of systematic ...cores.
Patients and Methods
Single‐centre outcome of transperineal MR/US fusion‐guided biopsies of 487 men with a single target MR imaging (MRI) lesion, prospectively collected between 2012 and 2016. All men underwent transperineal targeted biopsy (TB) with two cores, followed by 18–24 systematic sector biopsies (SB) using the Ginsburg protocol. Gleason score ≥7 prostate cancer detection rates for two‐core TB, four‐core extended TB (eTB), 10‐ to 20‐core saturation TB (sTB) including cores from sectors adjacent to the target, and 14 core ipsilateral TB (iTB) were compared to combined TB+SB.
Results
Cancer was detected in 345 men and Gleason score 7–10 cancer in 211 men. TB alone detected 67%, eTB 76%, sTB 91% and iTB 91% of these Gleason score 7–10 cancers. In the subgroup of 33 men (7% of cohort) with an anterior >0.5 mL highly suspicious MRI lesion and a prostate volume ≤45 mL, four‐core eTB detected 31 of 32 cancers (97%) and all 26 Gleason score 7–10 cancers.
Conclusion
sTB detected Gleason score 7–10 cancer in 25% more of the men than a two‐core TB approach, and in almost as many men (91%) as the 20–26‐core combined TB+SB, while needing only 10–20 cores. A four‐core extended TB may suffice for large, highly suspicious anterior lesions in small or slightly enlarged prostates.
Insight into the location, state, and function of a promoter in heterogeneous catalysis was obtained through atomic-resolution in situ transmission electron microscopy. In the most active ruthenium ...catalyst for ammonia synthesis known so far, the barium promoter is shown to be located in two different phases in the catalyst. The increased activity is suggested to be related to a two-dimensional barium-oxygen overlayer on the ruthenium crystals. The possibility for conducting such studies for other reactions could add substantially to our current understanding of heterogeneous catalysis. Heterogeneous catalysis plays an increasingly important role in environmental protection processes, in fuel upgrading, and in providing the majority of the chemical building blocks required by contemporary society. Most heterogeneous catalysts of industrial importance are multicomponent materials that are designed by trial-and-error experimentation. Application of even the most sophisticated physical-chemical characterization techniques is usually not sufficient to obtain a complete understanding of the structure of the active site, the reaction mechanism and kinetics, the structural dynamics, and the specific roles of all catalyst components.
•Research proposes the benefit of introducing positive interventions early in life.•A good correlation between quantitative PCR and enumeration is identified.•Early probiotic inoculation reduces ...shedding E. coli F18 and STb toxin in faeces.•Probiotic intervention early in life causes a faster clearance of E. coli F18.•Probiotics to newborn piglets may promote resilience in newly weaned pigs.
Postweaning diarrhoea caused by Enterotoxigenic Escherichia coli (ETEC) is a threat to the pig industry. With an intensified focus on finding alternatives to the use of medical zinc oxide and antibiotics in newly weaned pigs, the objective of this study was to investigate the effect of early inoculation of probiotics to suckling piglets on subsequently ETEC faecal shedding and immune parameters in ETEC F18-challenged weaned piglets. Sixty pigs weaned on day 28 of age were assigned to three treatment groups: (i) Negative Control (non-challenged), (ii) Positive Control (challenged) and (iii) Probiotic (challenged and inoculated with a multi-species probiotic product during suckling). On days 1 and 2 postweaning, pigs in the Positive Control and Probiotic groups were challenged with 5 × 108 colony-forming unit ETEC F18/pig/day, whereas pigs in the Negative Control group were provided with NaCl. Growth and diarrhoea incidence were not significantly affected by ETEC challenge or probiotic administration. ETEC F18 shedding and C-reactive protein concentration in plasma were significantly lower in the Negative Control group, confirming a successful challenge model. Pigs in the Probiotic group had a significantly reduced number of pigs shedding ETEC F18 and STb toxin in faeces compared with the Positive Control group. Probiotic application did not significantly impact the concentration of C-reactive protein, haptoglobin and cytokines in plasma nor haematology numbers. In conclusion, weaned pigs administered with a multi-species probiotic product early in life had a more rapid response towards the pathogen challenge and a faster clearance of ETEC compared with the Positive Control group. Administration of a multi-species probiotic to newborn piglets may thus promote resilience in the newly weaned pig. However, further studies with pigs subjected to a more severe pathogen challenge are needed to confirm these results and to investigate the mechanism of action of the probiotic intervention.
CONTEXT Pediatric hypertension is increasing in prevalence with the pediatric obesity epidemic. Diagnosis of hypertension in children is complicated because normal and abnormal blood pressure values ...vary with age, sex, and height and are therefore difficult to remember. OBJECTIVES To determine the frequency of undiagnosed hypertension and prehypertension and to identify patient factors associated with this underdiagnosis. DESIGN, SETTING, AND PARTICIPANTS A cohort study of 14 187 children and adolescents aged 3 to 18 years who were observed at least 3 times for well-child care between June 1999 and September 2006 in the outpatient clinics in a large academic urban medical system in northeast Ohio. For children and adolescents who met criteria for hypertension or prehypertension at 3 or more well-child care visits, the proportion with a hypertension-related International Classification of Diseases, Ninth Revision code in the diagnoses list, problem list, or past medical history list of any visit was determined. MAIN OUTCOME MEASURES Proportion of children and adolescents with 3 or more elevated age-adjusted and height-adjusted blood pressure measurements at well-child care visits and with a diagnosis of hypertension or prehypertension documented in the electronic medical record. Multivariate logistic regression identified patient factors associated with a correct diagnosis. RESULTS Of 507 children and adolescents (3.6%) who had hypertension, 131 (26%) had a diagnosis of hypertension or elevated blood pressure documented in the electronic medical record. Patient factors that increased the adjusted odds of a correct diagnosis were a 1-year increase in age over age 3 (odds ratio OR, 1.09; 95% confidence interval CI, 1.03-1.16), number of elevated blood pressure readings beyond 3 (OR, 1.77; 95% CI, 1.21-2.57), increase of 1% in height-for-age percentile (OR, 1.02; 95% CI, 1.01-1.03), having an obesity-related diagnosis (OR, 2.61; 95% CI, 1.49-4.55), and number of blood pressure readings in the stage 2 hypertension range (OR, 1.68; 95% CI, 1.29-2.19). Of 485 children and adolescents (3.4%) who had prehypertension, 55 (11%) had an appropriate diagnosis documented in the electronic medical record. Patient factors that increased the adjusted odds of being diagnosed with prehypertension included a 1-year increase in age over age 3 (OR, 1.21; 95% CI, 1.09-1.34) and number of elevated blood pressure readings beyond 3 (OR, 3.07; 95% CI, 2.20-4.28). CONCLUSIONS Hypertension and prehypertension were frequently undiagnosed in this pediatric population. Patient age, height, obesity-related diagnoses, and magnitude and frequency of abnormal blood pressure readings all increased the odds of diagnosis.
To determine the relation of neuritic plaques (NPs) and neurofibrillary tangles (NFTs) to the development and evolution of Alzheimer disease (AD).
An autopsy series of 102 patients with dementia and ...pathologically confirmed AD and 29 normal control subjects (NCs) was studied. AD cases were stratified according to their last Mini-Mental State Examination (MMSE) before death as mild, moderate, severe, or very severe. NPs and NFTs were enumerated in the midfrontal (MF), inferior parietal (IP), superior temporal (ST), hippocampal (Hip), or entorhinal cortices using thioflavin-S preparations.
Most (87%) of the NCs had allocortical NFTs, whereas only a minority (37%) displayed neocortical NPs, and even fewer (19%) showed Hip NPs. In contrast, none of the NCs exhibited neocortical NFTs, except one case with a single ST tangle. However, neocortical NFTs were not detected in even 10% of the patients with AD and, in particular, were absent in nearly 50% of those with mild disease at death. Thus, their sensitivity as a marker of AD was lower than that of NPs, which, conversely, were found in all patients with AD. Comparing NCs and patients with mild AD, significant differences were found for numbers of NPs only. Across the AD groups, in contrast, although NP and NFT density increased with dementia severity, significant differences consistently emerged for NFTs alone.
Deterioration in Alzheimer disease appears to be driven by neuritic plaques and neurofibrillary tangles at different stages of the disease. The significant increase in neuritic plaques, but not neurofibrillary tangles, in patients with even mild Alzheimer disease at death compared with normal control subjects suggests that only neuritic plaques are associated with the earliest symptoms of Alzheimer disease.
Lingual nerve injury (LNI) is a rare, serious complication and previous studies include limited numbers of cases. The aim of this retrospective study was to report the neurosensory outcomes for a ...large patient cohort with permanent LNI and correlate the mechanism of injury (surgical vs non-surgical) to neurosensory characteristics. Demographics, procedural parameters, mandibular third molar (M3) position, surgeon type, neurosensory test results, and symptoms were recorded for 228 patients and analysed. The majority were female (67.1%). Overall, 59.6% of LNIs were caused by M3 removal and 36.4% by local anaesthesia. Complete loss occurred more frequently in surgical LNIs (P = 0.013). The presence of pain did not differ significantly, however the burning type of pain was significantly more frequent in non-surgical LNIs (P = 0.008) along with altered gustation (P = 0.025). The most common M3 position related to LNI was distoangular (40.4%), class III (63.2%), level A (58.1%) (Winter/Pell and Gregory classifications). The majority of patients undergoing M3 removal were >24 years. A total of 71.7% showed no sign of recovery and 5.5% reported further impairment in their condition. Overall, nine patients underwent microsurgical repair. This study presents neurosensory characteristics potentially decisive for timely referral of operable LNIs.
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