Tag: pubmed

Cell Rep Methods. 2021 Nov 16;1(8):100120. doi: 10.1016/j.crmeth.2021.100120. Epub 2021 Nov 22.

ABSTRACT

To estimate a study design’s power to detect differential abundance, we require a framework that simulates many multi-sample single-cell datasets. However, current simulation methods are challenging for large-scale power analyses because they are computationally resource intensive and do not support easy simulation of multi-sample datasets. Current methods also lack modeling of important inter-sample variation, such as the variation in the frequency of cell states between samples that is observed in single-cell data. Thus, we developed single-cell POwer Simulation Tool (scPOST) to address these limitations and help investigators quickly simulate multi-sample single-cell datasets. Users may explore a range of effect sizes and study design choices (such as increasing the number of samples or cells per sample) to determine their effect on power, and thus choose the optimal study design for their planned experiments.

PMID:35005693 | PMC:PMC8740883 | DOI:10.1016/j.crmeth.2021.100120

Lancet Reg Health West Pac. 2022 Feb;19:100347. doi: 10.1016/j.lanwpc.2021.100347. Epub 2021 Dec 31.

ABSTRACT

BACKGROUND: The COVID-19 pandemic has had widespread adverse collateral effects on health care delivery for non-COVID-19 disease conditions. Paediatric oncology care is reliant on prompt testing and diagnosis and on timely and coordinated multimodal treatment, all of which have been impacted by the pandemic. This study aimed to quantify the initial and enduring effects of the COVID-19 pandemic on the utilization of paediatric cancer care and to examine whether the pandemic differentially impacted specific demographic groups.

METHOD: We performed an interrupted time series analysis using negative binomial regression to estimate the change in the monthly admissions for paediatric cancer patients (Age 0-17) associated with the COVID-19 pandemic and subsequent lockdown policies. We obtained data from deidentified individual electronic medical records of paediatric cancer inpatients admitted between January 1, 2015 and May 31, 2021 to a tertiary hospital that provides general and specialized healthcare services to an estimated population of 8.4 million in Jining China. Relative risk (RR) estimates representing monthly admissions compared with expected admissions had the pandemic not occurred were derived. The number of inpatient admissions lost due to the pandemic were estimated.

FINDINGS: The overall denominator for the paediatric population was 1 858 209 individuals in January 2015, which increased to 2 043 803 by May 2021. In total, there were 4 901 admissions for paediatric cancer during the study period, including 1 479 (30%) since February 2020 when the lockdown was implemented. A 33% reduction (95% CI: -43% to -22%) in admissions was observed in February 2020, with the largest relative reduction (-48%, 95% CI: -64% to -24%) among first-time admissions and admissions for patients from rural districts (-46%, 95% CI: -55% to -36%). Admissions quickly rebounded in March 2020 when many government-imposed mobility restrictions were lifted, and continued to resume gradually over time since April 2020, leading to a full recovery as of November 2020. However, the recovery for first-time admissions, and among female patients, younger patients (<5 years) and patients from rural districts was slower over time and incomplete (first-time admissions and rural patients) as of January 2021.

INTERPRETATION: The COVID-19 pandemic has had substantial impact on the timely utilization of paediatric oncology services in China, particularly in the early stage of the first wave. Importantly, some population groups were disproportionately affected and the recovery of admissions among those subgroups has been slow and incomplete, warranting targeted approaches to address potentially exacerbated gender and socio-economic inequalities in access to healthcare resources.

PMID:35005670 | PMC:PMC8718443 | DOI:10.1016/j.lanwpc.2021.100347

Curr Res Microb Sci. 2021 Dec 20;3:100093. doi: 10.1016/j.crmicr.2021.100093. eCollection 2022.

ABSTRACT

Analysis of Escherichia coli taxonomy has expanded into a species-complex with the identification of divergent cryptic clades. A key question is the evolutionary trajectory of these clades and their relationship to isolates of clinical or veterinary importance. Since they have some environmental association, we screened a collection of E. coli isolated from a long-term spring barley field trial for their presence. While most isolates clustered into the enteric-clade, four of them clustered into Clade-V, and one in Clade-IV. The Clade -V isolates shared >96% intra-clade average nucleotide sequence identity but <91% with other clades. Although pan-genomics analysis confirmed their taxonomy as Clade -V (E. marmotae), retrospective phylogroup PCR did not discriminate them correctly. Differences in metabolic and adherence gene alleles occurred in the Clade -V isolates compared to E. coli sensu scricto. They also encoded the bacteriophage phage-associated cyto-lethal distending toxin (CDT) and antimicrobial resistance (AMR) genes, including an ESBL, blaOXA-453. Thus, the isolate collection encompassed a genetic diversity, and included cryptic clade isolates that encode potential virulence factors. The analysis has determined the phylogenetic relationship of cryptic clade isolates with E. coli sensu scricto and indicates a potential for horizontal transfer of virulence factors.

PMID:35005658 | PMC:PMC8718834 | DOI:10.1016/j.crmicr.2021.100093

HGG Adv. 2022 Jan 1:100084. doi: 10.1016/j.xhgg.2021.100084. Online ahead of print.

ABSTRACT

COVID-19 vaccines are safe and highly effective, but some individuals experience unpleasant reactions to vaccination. As the majority of adults in the US have received a COVID-19 vaccine this year, there is an unprecedented opportunity to study the genetics of reactions to vaccination via surveys of individuals who are already part of genetic research studies. Here, we have queried 17,440 participants in the Helix DNA Discovery Project and Healthy Nevada Project about their reactions to COVID-19 vaccination. Our GWAS identifies an association between severe difficulties with daily routine after vaccination and HLA-A*03:01. This association was statistically significant only for those who received the Pfizer-BioNTech vaccine (BNT162b2; n=3,694; p=4.70E-11; OR=2.07 (95%CI 1.67-2.56)), and showed a smaller effect size in those who received the Moderna vaccine (mRNA-1273; n=3,610; p=0.005; OR=1.32 (95%CI 1.09-1.59)). In Pfizer-BioNTech recipients, HLA-A*03:01 was associated with a two-fold increase in risk of self-reported severe difficulties with daily routine following vaccination. The effect was consistent across ages, sexes, and whether the person had previously had a COVID-19 infection. The reactions experienced by HLA-A*03:01 carriers were driven by associations with chills, fever, fatigue, and in general feeling unwell.

PMID:35005651 | PMC:PMC8719913 | DOI:10.1016/j.xhgg.2021.100084

Pediatr Neonatol. 2021 Dec 4:S1875-9572(21)00230-8. doi: 10.1016/j.pedneo.2021.09.007. Online ahead of print.

ABSTRACT

BACKGROUND: Preterm formulas containing greater protein:energy ratio are beneficial for non-breastfed infants, since protein is critical for promoting catch-up growth and synthesis of lean body mass. Additionally, formulas containing enriched sn-2 palmitate (sn-2) and reduced medium chain triglycerides (MCTs) may support better feeding tolerance and nutrient utilization.

METHODS: The objective of this randomized, controlled, double-blinded clinical trial is to evaluate growth, feeding tolerance and nutritional biomarkers of preterm infants with birth weight ≤2000g and gestational age ≤33wks from one neonatal unit in Vietnam receiving experimental formula (EF, n = 80) containing higher protein level of 3.4 g/100 kcal and improved fat blend with enriched sn-2 and modified level of MCTs or isocaloric control formula (CF, n = 80) containing protein level of 2.9 g/100 kcal and standard fat blend. The differences in weight gain (g/d; primary endpoint) from day 1 (D1) of full enteral feeding (FEF) until D21 between groups was evaluated for non-inferiority (margin = -2.5 g/d) and superiority (margin = 0 g/d).

RESULTS: Mean weight gain was 3.09 g/d greater in EF than CF; the lower limit of 95% CI (0.31 g/d) exceeded both non-inferiority and superiority margins. There was no significant difference in length-for-age and head circumference-for-age z-score. By D79, the mean change in weight-for-age z-scores from D1 in EF group (+0.76 SDs) surpassed the criteria for catch-up growth (+0.67 SDs). Infants in the EF group (vs. CF) tended to have softer stools (EF = 3.2 ± 0.59 vs. CF = 3.4 ± 0.58; P = 0.07) based on 5-point scale (1 = watery, 5 = hard). Difference in blood urea nitrogen and biomarkers for bone mineral status (i.e., plasma phosphorus, alkaline phosphatase and urinary calcium/phosphorus ratio) between EF and CF on FEF Day 21 reached statistical significance (P < 0.05) but all mean values stayed within normal clinical ranges for both groups.

CONCLUSION: Preterm formula with greater protein:energy ratio and new fat blend is safe, nutritionally suitable, well-tolerated, and improves catch-up weight gain of preterm infants. Clinical trial registry identifier is NCT03055052 (ClinicalTrials.gov).

PMID:35000893 | DOI:10.1016/j.pedneo.2021.09.007

Radiography (Lond). 2022 Jan 6:S1078-8174(21)00195-4. doi: 10.1016/j.radi.2021.12.004. Online ahead of print.

ABSTRACT

INTRODUCTION: This study assessed the inter-observer agreement of reporting radiographers and consultant radiologists compared with an index radiologist when reporting General Practitioner (GP) requested musculoskeletal radiographs. The potential effect of discordant reports on patient management and outcome was also examined.

METHODS: Three reporting radiographers, three consultant radiologists and an index radiologist reported on a retrospective randomised sample of 219 GP requested musculoskeletal radiographs, in conditions simulating clinical practice. A speciality doctor in radiology compared the observers’ reports with the index radiologist report for agreement and assessed whether any discordance between reports was clinically important.

RESULTS: Overall agreement with the index radiologist was 47.0% (95% CI, 40.5-53.6) and 51.6% (95% CI, 45.0-58.1) for the consultant radiologists and reporting radiographers, respectively. The results for the appendicular and axial skeleton were 48.6% (95% CI, 41.3-55.9) and 40.9% (95% CI, 27.7-55.6) for the radiologists, and 52.6% (95% CI, 45.2-59.8) and 47.7% (95% CI, 33.8-62.1) for the radiographers, respectively. The difference in overall observer agreement between the two professional groups with the index radiologist was not statistically significant (p = 0.34). Discordance with the index radiologist’s reports was judged to be clinically important in less than 10% of the observer’s reports.

CONCLUSION: Reporting radiographers and consultant radiologists demonstrate similar levels of concordance with an index radiologist when reporting GP requested musculoskeletal radiographs.

IMPLICATIONS FOR PRACTICE: These findings contribute to the wider evidence base that selected radiographers with appropriate postgraduate education and training are proficient to report on musculoskeletal radiographs, irrespective of referral source.

PMID:35000869 | DOI:10.1016/j.radi.2021.12.004

Radiography (Lond). 2022 Jan 6:S1078-8174(21)00213-3. doi: 10.1016/j.radi.2021.12.013. Online ahead of print.

ABSTRACT

INTRODUCTION: Recent guidance from the British Institute of Radiology (BIR) and the American Association of Physicists in Medicine (AAPM) focuses on cessation of patient Lead-rubber (Pb) shielding placed within the Field of View (FOV) that may influence image exposure or quality. Furthermore, the BIR assert shielding organs greater than 5 cm from the primary X-ray beam will have a negligible effect to the received radiation dose. Bilateral hand X-rays are frequently and repeatedly requested for the diagnosis and ongoing management of arthritic conditions. There is a lack of literature regarding the effect of Pb shielding during bilateral hand X-ray examinations. This research aimed to investigate the scattered secondary radiation dose to the gonads during a bilateral hand X-ray, with and without the use of Pb shielding outside the FOV at a greater distance than 5 cm from the primary beam.

METHODS: Using an anthropomorphic phantom and constructed upper limbs, radiation was recorded to the male and female gonads. Thermoluminescent dosimeters (TLD’s) (⅛” x ⅛” x 0.15″ TLD-100H) were placed in groups of three upon the testes and within the left and right ovary to record the ionising radiation dose. Three collimated exposures were completed using a standard clinical practice hand X-ray protocol of 60 kVp and 2.5 mAs with a source to image distance (SID) of 100 cm. The mean and standard deviation of the radiation dose was calculated for both with and without Pb shielding. A paired two-sample t-test was conducted to determine statistical significance (p ≤ 0.05).

RESULTS: Data analysis demonstrated dose measured to the testes of 5.3 μGy (SD 0.8) without Pb shielding and 2.3 μGy (SD 0.2) with Pb (reduction of 3 μGy; 56.6%). Left ovary doses measured 40.6 μGy (SD 1.2) without Pb shielding and 28.8 μGy (SD 1.7) with Pb (reduction of 11.9 μGy; 29.2%) and right ovary doses measured 39.5 μGy (SD 1.9) without Pb shielding and 26.6 μGy (SD 1.0) with Pb (reduction of 12.8 μGy; 32.4%). The paired two-sample t-test presented a statistically significant dose reduction (p = 0.0039).

CONCLUSION: The study demonstrated dose limitation from scattered secondary radiation to the gonads when Pb shielding was used during a bilateral hand X-ray at distances greater than 5 cm from the primary X-ray beam on anatomy outside the FOV.

IMPLICATIONS FOR PRACTICE: The use of Pb shielding over the gonad area during a bilateral hand X-ray examination aligns to ALARP best practice and provides prospects for patient (male and female) dose reduction.

PMID:35000868 | DOI:10.1016/j.radi.2021.12.013

J Voice. 2022 Jan 6:S0892-1997(21)00433-1. doi: 10.1016/j.jvoice.2021.12.010. Online ahead of print.

ABSTRACT

INTRODUCTION: In recent years cepstral analysis and specific cepstrum-based measures such as smoothed cepstral peak prominence (CPPS) has become increasingly researched and utilized in attempts to determine the extent of overall dysphonia in voice signals. Yet, few studies have extensively examined how specific voice-source parameters affect CPPS values.

OBJECTIVE: Using a range of synthesized tones, this exploratory study sought to systematically analyze the effect of fundamental frequency (f_o), vibrato extent, source-spectrum tilt, and the amplitude of the voice-source fundamental on CPPS values.

MATERIALS AND METHODS: A series of scales were synthesised using the freeware Madde. Fundamental frequency, vibrato extent, source-spectrum tilt, and the amplitude of the voice-source fundamental were systematically and independently varied. The tones were analysed in PRAAT, and statistical analyses were conducted in SPSS.

RESULTS: CPPS was significantly affected by both f_o and source-spectrum tilt, independently. A nonlinear association was seen between vibrato extent and CPPS, where CPPS values increased from 0 to 0.6 semitones (ST), then rapidly decreased approaching 1.0 ST. No relationship was seen between the amplitude of the voice-source fundamental and CPPS.

CONCLUSION: The large effect of f_o should be taken into account when analyzing the voice, particularly in singing-voice research, when comparing pre and posttreatment data, and when comparing inter-subject CPPS data.

PMID:35000836 | DOI:10.1016/j.jvoice.2021.12.010

J Nutr Educ Behav. 2022 Jan 6:S1499-4046(21)00859-9. doi: 10.1016/j.jneb.2021.10.002. Online ahead of print.

ABSTRACT

OBJECTIVE: To refine a measure of home cooking quality (defined as the usage level of practices with the potential to influence the nutrient content of prepared foods) and conduct a construct validation of the revised tool, the Healthy Cooking Questionnaire 2 (HCQ2).

DESIGN: Two validation approaches are described: (1) a community science approach used to refine and validate Healthy Cooking Questionnaire (HCQ) constructs, and (2) responses to the revised HCQ (HCQ2) in a sample of Amazon Mechanical Turk (MTurk) workers to determine questionnaire comprehension.

SETTING: The Community Scientist Program at the University of Texas MD Anderson Cancer Center facilitated discussion groups to refine the HCQ questions and validate constructs. MTurk workers were subsequently recruited to complete the refined survey so that comprehension and associations with demographic variables could be explored.

PARTICIPANTS: Ten community scientists participated in the refinement of the HCQ. The revised tool (HCQ2) was completed by 267 adult US-based MTurk workers.

VARIABLES MEASURED: Demographics, HCQ concepts, HCQ2, Self-Reported Questionnaire Comprehension.

ANALYSIS: Comprehension items were examined using descriptive statistics. Exploratory analysis the relationships between cooking quality and demographic characteristics, meal type, cooking frequency, as well as patterns of food preparation behavior was conducted on the MTurk sample RESULTS: The HCQ was refined through activities and consensus-building. MTurk responses to the HCQ2 indicated high comprehension and significant differences in cooking quality scores by demographic factors.

CONCLUSIONS AND IMPLICATIONS: This study refined and validated a self-report measure of cooking quality. Cooking quality measures offer critical evaluation methods for culinary programs.

PMID:35000831 | DOI:10.1016/j.jneb.2021.10.002

Am J Prev Med. 2022 Jan 6:S0749-3797(21)00593-6. doi: 10.1016/j.amepre.2021.10.018. Online ahead of print.

ABSTRACT

INTRODUCTION: Research is equivocal about how the social relationship between victims and offenders is linked to the emotional, social, and physical consequences of violence. This study examines the association of victim-offender relationship with the adverse outcomes reported by injured and uninjured victims of violence.

METHODS: The study analyzed 16,723 violent victimizations recorded by the National Crime Victimization Survey from 2008 to 2018. Multivariable quasi-Poisson models estimated the associations between the victim-offender relationship and victims’ emotional distress, social distress, and physical and emotional symptoms. These models also estimated a statistical interaction between victim-offender relationship and violent injury to examine how this association differed for injured and uninjured victims. The analyses occurred during 2020 and 2021.

RESULTS: Uninjured victims were more likely to report emotional distress (risk ratio=1.41, 95% CI=1.33, 1.50), social distress (risk ratio=3.12, 95% CI=2.78, 3.51), more physical symptoms (symptom frequency ratio=1.68, 95% CI=1.51, 1.87), and more emotional symptoms (symptom frequency ratio=1.13, 95% CI=1.08, 1.18) in family member/intimate partner violence than in stranger violence. Victims also reported worse outcomes after acquaintance violence than after stranger violence. For injured victims, these differences narrowed-but were still significant-in emotional and social distress models. However, the number of emotional and physical symptoms reported by injured victims did not significantly vary across victim-offender relationships.

CONCLUSIONS: Relational closeness between victims and offenders is a risk factor for adverse outcomes after violent victimization, and it is more strongly associated with these outcomes for uninjured victims than for injured victims.

PMID:35000834 | DOI:10.1016/j.amepre.2021.10.018