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Background: The last three decades have seen a growth in the number of children requiring long-term ventilation. Children with long-term ventilation present with underlying respiratory and neurological conditions that place them at risk of feeding and swallowing difficulties. To date, a scoping review or systematic review investigating the feeding and swallowing outcomes of children with long-term ventilation needs has not been conducted. Aims: This paper describes a protocol for a scoping review of the feeding and swallowing outcomes of children receiving long-term ventilation. Methods: This scoping review protocol will utilize the Joanna Briggs Institute scoping review methodology guideline. Our review will focus on the feeding and swallowing outcomes of children aged 0 to 18 years with long-term ventilation needs. A full search strategy initially created by the authors and a research librarian was conducted on the PubMed database. Following this, pilot testing took place to determine discrepancies in eligibility criteria. A full search strategy will be conducted across several databases. A data extraction form has been developed by the authors and will be used during the scoping review process. Discussion: This protocol has been created to provide a rigorous and comprehensive basis for undertaking a scoping review. All necessary steps have been completed in order to commence the scoping review. Registration: This scoping review protocol was registered on Open Science Framework on the 26th November 2021 (Registration DOI 10.17605/OSF.IO/NQBPD). [ABSTRACT FROM AUTHOR]

Objective: To determine the prevalence of vitamin D deficiency in Indonesian children hospitalized with pneumonia and evaluate the association between vitamin D status and severity of pneumonia. Methods: A hospital-based cross-sectional study was conducted from February 2016 to July 2017 in two district hospitals in Yogyakarta province, Indonesia. Infants and young children aged 2–59 months hospitalized with pneumonia were recruited. Serum blood samples were collected on admission and analyzed for total serum 25-hydroxyvitamin D3 and 25-hydroxyvitamin D2 concentrations using liquid chromatography-tandem mass spectrometry. Vitamin D deficiency was defined as a level of serum vitamin D <50 nmol/L. The association between vitamin D deficiency and severity of hospitalized pneumonia according to WHO criteria, including the presence of danger signs, hypoxemia (SpO2 in air below 90%), duration of hospitalization, and admission to Intensive Care Unit (ICU), was analyzed using logistic regression. Results: 133 children with WHO-defined pneumonia were enrolled in the study and 127 (96%) had their vitamin D status determined. The mean vitamin D concentration was 67 (± 24 SD) nmol/L and 19% of participants were vitamin D deficient. Age younger than 6 months was associated with prolonged hospitalization (> 5 days) and low birth weight and poor nutritional status on admission were risk factors for hypoxemia. However, vitamin D status was not associated with the presence of danger signs, duration of hospitalization, or hypoxemia. Conclusions: One in every five children hospitalized with pneumonia was vitamin D deficient. Vitamin D status was not associated with the severity of pneumonia. [ABSTRACT FROM AUTHOR]

Background: Vitamin D deficiency has been associated with acute respiratory infection (ARI) in early life, but this has not been evaluated in Indonesia. We aimed to determine the incidence of ARI in Indonesian infants, and to evaluate the association with vitamin D deficiency. Methods: From 23 December 2015 to 31 December 2017, we conducted a community-based prospective cohort study in Yogyakarta province. We enrolled 422 pregnant women and followed their infants from birth until 12 months of age for ARI episodes. Vitamin D status was measured at birth and at age six months. We performed Cox proportional hazard regression analysis to evaluate the association between vitamin D deficiency and pneumonia incidence. Results: At study completion, 95% (400/422) of infants retained with a total of 412 child years of observation (CYO). The incidence of all ARI and of WHO-defined pneumonia was 3.89 (95% CI 3.70–4.08) and 0.25 (95% CI 0.21–0.30) episodes per CYO respectively. Vitamin D deficiency at birth was common (90%, 308/344) and associated with more frequent episodes of ARI non-pneumonia (adjusted odds ratio 4.48, 95% CI:1.04–19.34). Vitamin D status at birth or six months was not associated with subsequent pneumonia incidence, but greater maternal sun exposure during pregnancy was associated with a trend to less frequent ARI and pneumonia in infants. Conclusion: ARI, pneumonia, and vitamin D deficiency at birth were common in Indonesian infants. Minimising vitamin D deficiency at birth such as by supplementation of mothers or safe sun exposure during pregnancy has the potential to reduce ARI incidence in infants in this setting. [ABSTRACT FROM AUTHOR]

Background: Vitamin D deficiency in infants has been associated with an increased risk of a number of diseases but there are limited data on the prevalence and determinants of vitamin D deficiency from tropical settings with high infant morbidity and mortality. Objective: To determine the prevalence and determinants of vitamin D deficiency in infants at birth and at six months of age in Yogyakarta province, Indonesia. Design: Serum vitamin D of eligible infants was measured in cord blood at birth and at six months of age. Factors associated with vitamin D deficiency (serum 25-hydroxyvitamin D <50 nmol/L) were collected prospectively monthly from birth and concentrations measured by liquid chromatography-tandem mass spectrometry. Independent risk factors were identified by multiple logistic regression. Results: Between December 2015 to December 2017, 350 maternal-newborn participants were recruited and followed up. Vitamin D deficiency was detected in 90% (308/344) of cord blood samples and 13% (33/255) of venous blood samples at six months. Longer time outdoors (≥2 hours per day) and maternal multivitamin intake containing vitamin D during pregnancy were protective against vitamin D deficiency at birth (AOR: 0.10, 95% CI: 0.01–0.90 and AOR: 0.21, 95% CI: 0.06–0.68, respectively). Risk factors for vitamin D deficiency at six months included lower cumulative skin-sun exposure score (AOR: 1.12, 95% CI: 1.04–1.20), severe vitamin D deficiency at birth (AOR: 7.73, 95% CI: 1.20–49.60) and exclusive breastfeeding (AOR: 2.64, 95% CI: 1.07–6.49) until six months. Among exclusively breast fed (EBF) infants, a higher skin-sun exposure score was associated with reduced vitamin D deficiency risk. Conclusion: In equatorial regions, the role of 'safe' morning sun exposure in infants and mothers in populations with medium to dark brown skin pigmentation and effective interventions to prevent vitamin D deficiency in newborns and EBF infants, need further consideration and evaluation. [ABSTRACT FROM AUTHOR]

Purpose: To comprehensively assess the Randot Preschool stereo test in young children, including testability, normative values, test/retest reliability and sensitivity and specificity for detecting binocular vision disorders. Methods: We tested 1005 children aged 2–11 years with the Randot Preschool stereo test, plus a cover/uncover test to detect heterotropia. Monocular visual acuity was assessed in both eyes using Keeler Crowded LogMAR visual acuity test for children aged 4 and over. Results: Testability was very high: 65% in two-year-olds, 92% in three-year-olds and ~100% in older children. Normative values: In 389 children aged 2–5 with apparently normal vision, 6% of children scored nil (stereoblind). In those who obtained a threshold, the mean log threshold was 2.06 log10 arcsec, corresponding to 114 arcsec, and the median threshold was 100 arcsec. Most older children score 40 arcsec, the best available score. We found a small sex difference, with girls scoring slightly but significantly better. Test/retest reliability: ~99% for obtaining any score vs nil. Agreement between stereo thresholds is poor in children aged 2–5; 95% limit of agreement = 0.7 log10 arcsec: five-fold change in stereo threshold may occur without any change in vision. In children over 5, the test essentially acts only as a binary classifier since almost all non-stereoblind children score 40 arcsec. Specificity (true negative rate): >95%. Sensitivity (true positive rate): poor, <50%, i.e. around half of children with a demonstrable binocular vision abnormality score well on the Randot Preschool. Conclusions: The Randot Preschool is extremely accessible for even very young children, and is very reliable at classifying children into those who have any stereo vision vs those who are stereoblind. However, its ability to quantify stereo vision is limited by poor repeatability in children aged 5 and under, and a very limited range of scores relevant to children aged over 5. [ABSTRACT FROM AUTHOR]

Antenatal corticosteroids (ACS) are standard of care for women at risk of preterm delivery, although choice of drug, dose or route have not been systematically evaluated. Further, ACS are infrequently used in low resource environments where most of the mortality from prematurity occurs. We report proof of principle experiments to test betamethasone-phosphate (Beta-P) or dexamethasone-phosphate (Dex-P) given orally in comparison to the clinical treatment with the intramuscular combination drug beta-phosphate plus beta-acetate in a Rhesus Macaque model. First, we performed pharmacokinetic studies in non-pregnant monkeys to compare blood levels of the steroids using oral dosing with Beta-P, Dex-P and an effective maternal intramuscular dose of the beta-acetate component of the clinical treatment. We then evaluated maternal and fetal blood steroid levels with limited fetal sampling under ultrasound guidance in pregnant macaques. We found that oral Beta is more slowly cleared from plasma than oral Dex. The blood levels of both drugs were lower in maternal plasma of pregnant than in non-pregnant macaques. Using the pharmacokinetic data, we treated groups of 6–8 pregnant monkeys with oral Beta-P, oral Dex-P, or the maternal intramuscular clinical treatment and saline controls and measured pressure-volume curves to assess corticosteroid effects on lung maturation at 5d. Oral Beta-P improved the pressure-volume curves similarly to the clinical treatment. Oral Dex-P gave more variable and nonsignificant responses. We then compared gene expression in the fetal lung, liver and hippocampus between oral Beta-P and the clinical treatment by RNA-sequencing. The transcriptomes were largely similar with small gene expression differences in the lung and liver, and no differences in the hippocampus between the groups. As proof of principle, ACS therapy can be effective using inexpensive and widely available oral drugs. Clinical dosing strategies must carefully consider the pharmacokinetics of oral Beta-P or Dex-P to minimize fetal exposure while achieving the desired treatment responses. [ABSTRACT FROM AUTHOR]

It is suggested that testosterone may play a part in the higher prevalence of Autism Spectrum Disorder (ASD) in males compared to females. Previous studies have reported elevated postnatal testosterone levels in children and women with ASD but not in men. We compared levels of salivary testosterone across 67 undergraduate males (Mage 19.5 yrs, SD 1.92) selected for low, mid-range and high levels of autistic traits assessed using the Autism-spectrum Quotient. Analyses revealed no significant differences in testosterone concentrations across the three groups. The current data add to the increasing evidence for the lack of relationship between autistic traits and postnatal levels of testosterone in men. [ABSTRACT FROM AUTHOR]

Influenza polymerase is a heterotrimer protein with both endonuclease and RNA-dependent RNA polymerase (RdRp) activity. It plays a critical role in viral RNA replication and transcription and has been targeted for antiviral drug development. In this study, we characterized the activity of recombinant RdRp purified at 1:1:1 ratio in both ApG-primed RNA replication and mRNA-initiated RNA transcription. The heterotrimer complex showed comparable activity profiles to that of viral particle derived crude replication complex, and in contrast to the crude replication complex, was suitable for detailed mechanistic studies of nucleotide incorporation. The recombinant RdRp was further used to examine distinct modes of inhibition observed with five different nucleotide analog inhibitors, and the apparent steady-state binding affinity Kapp was measured for selected analogs to correlate antiviral activity and enzymatic inhibition with substrate efficiency. [ABSTRACT FROM AUTHOR]

Influenza polymerase is a heterotrimer composed of polymerase acidic protein A (PA) and basic proteins 1 (PB1) and 2 (PB2). The endonuclease active site, located in the PA subunit, cleaves host mRNA to prime viral mRNA transcription, and is essential for viral replication. To date, the human influenza A endonuclease activity has only been studied on the truncated active-site containing N-terminal domain of PA (PAN) or full-length PA in the absence of PB1 or PB2. In this study, we characterized the endonuclease activity of recombinant proteins of influenza A/PR8 containing full length PA, PA/PB1 dimer, and PA/PB1/PB2 trimer, observing 8.3-, 265-, and 142-fold higher activity than PAN, respectively. Using the PA/PB1/PB2 trimer, we developed a robust endonuclease assay with a synthetic fluorogenic RNA substrate. The observed Km (150 ± 11 nM) and kcat [(1.4 ± 0.2) x 10-3s-1] values were consistent with previous reports using virion-derived replication complex. Two known influenza endonuclease phenylbutanoic acid inhibitors showed IC50 values of 10–20 nM, demonstrating the utility of this system for future high throughput screening. [ABSTRACT FROM AUTHOR]

Understanding the age structure of vegetation is important for effective land management, especially in fire-prone landscapes where the effects of fire can persist for decades and centuries. In many parts of the world, such information is limited due to an inability to map disturbance histories before the availability of satellite images (~1972). Here, we describe a method for creating a spatial model of the age structure of canopy species that established pre-1972. We built predictive neural network models based on remotely sensed data and ecological field survey data. These models determined the relationship between sites of known fire age and remotely sensed data. The predictive model was applied across a 104,000 km2 study region in semi-arid Australia to create a spatial model of vegetation age structure, which is primarily the result of stand-replacing fires which occurred before 1972. An assessment of the predictive capacity of the model using independent validation data showed a significant correlation (rs = 0.64) between predicted and known age at test sites. Application of the model provides valuable insights into the distribution of vegetation age-classes and fire history in the study region. This is a relatively straightforward method which uses widely available data sources that can be applied in other regions to predict age-class distribution beyond the limits imposed by satellite imagery. [ABSTRACT FROM AUTHOR]

Termites play an important ecological role in many ecosystems, particularly in nutrient-poor arid and semi-arid environments. We examined the distribution and occurrence of termites in the fire-prone, semi-arid mallee region of south-eastern Australia. In addition to periodic large wildfires, land managers use fire as a tool to achieve both asset protection and ecological outcomes in this region. Twelve taxa of termites were detected by using systematic searches and grids of cellulose baits at 560 sites, clustered in 28 landscapes selected to represent different fire mosaic patterns. There was no evidence of a significant relationship between the occurrence of termite species and time-since-fire at the site scale. Rather, the occurrence of species was related to habitat features such as the density of mallee trees and large logs (>10 cm diameter). Species richness was greater in chenopod mallee vegetation on heavier soils in swales, rather than Triodia mallee vegetation of the sandy dune slopes. At the landscape scale, there was little evidence that the frequency of occurrence of termite species was related to fire, and no evidence that habitat heterogeneity generated by fire influenced termite species richness. The most influential factor at the landscape scale was the environmental gradient represented by average annual rainfall. Although termites may be associated with flammable habitat components (e.g. dead wood), they appear to be buffered from the effects of fire by behavioural traits, including nesting underground, and the continued availability of dead wood after fire. There is no evidence to support the hypothesis that a fine-scale, diverse mosaic of post-fire age-classes will enhance the diversity of termites. Rather, termites appear to be resistant to the effects of fire at multiple spatial scales. [ABSTRACT FROM AUTHOR]

Measured serum 25-hydroxyvitamin D concentrations vary depending on the type of assay used and the specific laboratory undertaking the analysis, impairing the accurate assessment of vitamin D status. We investigated differences in serum 25-hydroxyvitamin D concentrations measured at three laboratories (laboratories A and B using an assay based on liquid chromatography-tandem mass spectrometry and laboratory C using a DiaSorin Liaison assay), against a laboratory using an assay based on liquid chromatography-tandem mass spectrometry that is certified to the standard reference method developed by the National Institute of Standards and Technology and Ghent University (referred to as the ‘certified laboratory’). Separate aliquots from the same original serum sample for a subset of 50 participants from the Ausimmune Study were analysed at the four laboratories. Bland-Altman plots were used to visually check agreement between each laboratory against the certified laboratory. Compared with the certified laboratory, serum 25-hydroxyvitamin D concentrations were on average 12.4 nmol/L higher at laboratory A (95% limits of agreement: -17.8,42.6); 12.8 nmol/L higher at laboratory B (95% limits of agreement: 0.8,24.8); and 10.6 nmol/L lower at laboratory C (95% limits of agreement: -48.4,27.1). The prevalence of vitamin D deficiency (defined here as 25-hydroxyvitamin D <50 nmol/L) was 24%, 16%, 12% and 41% at the certified laboratory, and laboratories A, B, and C, respectively. Our results demonstrate considerable differences in the measurement of 25-hydroxyvitamin D concentrations compared with a certified laboratory, even between laboratories using assays based on liquid chromatography-tandem mass spectrometry, which is often considered the gold-standard assay. To ensure accurate and reliable measurement of serum 25-hydroxyvitamin D concentrations, all laboratories should use an accuracy-based quality assurance system and, ideally, comply with international standardisation efforts. [ABSTRACT FROM AUTHOR]

Context: Since September 2005, the International Committee of Medical Journal Editors (ICMJE) has required that randomised controlled trials (RCTs) are prospectively registered in a publicly accessible database. After registration, a trial registration number (TRN) is assigned to each RCT, which should make it easier to identify future publications and cross-check published results with associated registry entries, as long as the unique identification number is reported in the article. Objective: Our primary objective was to evaluate the reporting of trial registration numbers in biomedical publications. Secondary objectives were to evaluate how many published RCTs had been registered and how many registered RCTs had resulted in a publication, using a sample of trials from the Netherlands Trials Register (NTR). Design, Setting: Two different samples of RCTs were examined: 1) RCTs published in November 2010 in core clinical journals identified in MEDLINE; 2) RCTs registered in the NTR with a latest expected end date of 31 August 2008. Results: Fifty-five percent (166/302) of the reports of RCTs found in MEDLINE and 60% (186/312) of the published reports of RCTs from the NTR cohort contained a TRN. In both samples, reporting of a TRN was more likely in RCTs published in ICMJE member journals as compared to non-ICMJE member journals (MEDLINE 58% vs. 45%; NTR: 70% vs. 49%). Thirty-nine percent of published RCTs in the MEDLINE sample appear not to have been registered, and 48% of RCTs registered in the NTR seemed not to have been published at least two years after the expected date for study completion. Conclusion: Our results show that further promotion and implementation of trial registration and accurate reporting of TRN is still needed. This might be helped by inclusion of the TRN as an item on the CONSORT checklist. [ABSTRACT FROM AUTHOR]

Background: We sought to determine if a common polymorphism can influence vulnerability to LDL cholesterol, and thereby influence the clinical benefit derived from therapies that reduce LDL cholesterol. Methods: We conducted a meta-analysis of the association between a common Trp719Arg polymorphism in the kinesin-like protein 6 (KIF6) gene and the risk of cardiovascular disease (CVD), and a meta-regression analysis to measure the effect modification of this polymorphism on the association between LDL cholesterol and the risk of CVD. We used this measure of genetic effect modification to predict the expected difference in clinical benefit among KIF6 719Arg allele carriers and non-carriers in response to therapies that reduce LDL cholesterol. We then conducted a meta-analysis of statin trials to compare the expected difference in clinical benefit with the observed difference during treatment with a statin. Results: In a meta-analysis involving 144,931 participants, the KIF6 719Arg allele was not associated with the relative risk (RR) of CVD (RR: 1.02, 95%CI: 0.98-1.07, p = 0.288). Meta-regression analysis involving 88,535 participants, however, showed that the 719Arg allele appears to influence the effect of LDL cholesterol on the risk of CVD. KIF6 carriers experienced a 13% greater reduction in the risk of CVD per mmol/L decrease in LDL cholesterol than non-carriers. We interpreted this difference as the expected difference in clinical benefit among KIF6 carriers and non-carriers in response to therapies that lower LDL cholesterol. The difference in clinical benefit predicted by the increased vulnerability to LDL cholesterol among KIF6 carriers (ratio of RR: 0.87, 95%CI: 0.80-0.94, p = 0.001) agreed very closely with the observed difference among 50,060 KIF6 carriers and non-carriers enrolled in 8 randomized trials of statin therapy (ratio of RR: 0.87, 95%CI: 0.77-0.99, p = 0.038). Conclusion: The KIF6 719Arg allele increases vulnerability to LDL cholesterol and thereby influences the expected clinical benefit of therapies that reduce LDL cholesterol. [ABSTRACT FROM AUTHOR]

Background: Adherence to good methodological quality is necessary to minimise bias in randomised conrolled trials (RCTs). Specific trial characteristics are associated with better trial quality, but no studies to date are specific to HIV/AIDS or African trials. We postulated that location may negatively impact on trial quality in regions where resources are scarce. Methods: 1) To compare the methodological quality of all HIV/AIDS RCTs conducted in Africa with a random sample of similar trials conducted in North America; 2) To assess whether location is predictive of trial quality. We searched MEDLINE, EMBASE, CENTRAL and LILACS. Eligible trials were 1) randomized, 2) evaluations of preventive or treatment interventions for HIV/AIDS, 3) reported before 2004, and 4) conducted wholly or partly (if multi-centred) in Africa or North America. We assessed adequacy of random generation, allocation concealment and masking of assessors. Using univariate and multivariate logistic regression analyses we evaluated the association between location (Africa versus North America) and these domains. Findings: The African search yielded 12,815 records, from which 80 trials were identified. The North American search yielded 13,158 records from which 785 trials were identified and a random sample of 114 selected for analysis. African trials were three times more likely than North American trials to report adequate allocation concealment (OR = 3.24; 95%CI: 1.59 to 6.59; p,0.01) and twice as likely to report adequate generation of the sequence (OR = 2.36; 95%CI: 1.20 to 4.67; p = 0.01), after adjusting for other confounding factors. Additional significant factors positively associated with quality were an a priori sample size power calculation, restricted randomization and inclusion of a flow diagram detailing attrition. We did not detect an association between location and outcome assessor masking. Conclusions: The higher quality of reporting of methodology in African trials is noteworthy. Most African trials are externally funded, and it is possible that stricter agency requirements when leading trials in other countries and greater experience and training of principal investigators of an international stature, may account for this difference. [ABSTRACT FROM AUTHOR]

Background: Patients generally die of cancer after the failure of current therapies to eliminate residual disease. A subpopulation of tumor cells, termed cancer stem cells (CSC), appears uniquely able to fuel the growth of phenotypically and histologically diverse tumors. It has been proposed, therefore, that failure to effectively treat cancer may in part be due to preferential resistance of these CSC to chemotherapeutic agents. The subpopulation of human colorectal tumor cells with an ESA+CD44+ phenotype are uniquely responsible for tumorigenesis and have the capacity to generate heterogeneous tumors in a xenograft setting (i.e. CoCSC). We hypothesized that if non-tumorigenic cells are more susceptible to chemotherapeutic agents, then residual tumors might be expected to contain a higher frequency of CoCSC. Methods and Findings: Xenogeneic tumors initiated with CoCSC were allowed to reach ∼400 mm3, at which point mice were randomized and chemotherapeutic regimens involving cyclophosphamide or Irinotecan were initiated. Data from individual tumor phenotypic analysis and serial transplants performed in limiting dilution show that residual tumors are enriched for cells with the CoCSC phenotype and have increased tumorigenic cell frequency. Moreover, the inherent ability of residual CoCSC to generate tumors appears preserved. Aldehyde dehydrogenase 1 gene expression and enzymatic activity are elevated in CoCSC and using an in vitro culture system that maintains CoCSC as demonstrated by serial transplants and lentiviral marking of single cell-derived clones, we further show that ALDH1 enzymatic activity is a major mediator of resistance to cyclophosphamide: a classical chemotherapeutic agent. Conclusions: CoCSC are enriched in colon tumors following chemotherapy and remain capable of rapidly regenerating tumors from which they originated. By focusing on the biology of CoCSC, major resistance mechanisms to specific chemotherapeutic agents can be attributed to specific genes, thereby suggesting avenues for improving cancer therapy. [ABSTRACT FROM AUTHOR]