Tag: pubmed

Front Digit Health. 2021 Dec 23;3:637944. doi: 10.3389/fdgth.2021.637944. eCollection 2021.

ABSTRACT

The SARS-CoV-2 virus, which causes the COVID-19 pandemic, has had an unprecedented impact on healthcare requiring multidisciplinary innovation and novel thinking to minimize impact and improve outcomes. Wide-ranging disciplines have collaborated including diverse clinicians (radiology, microbiology, and critical care), who are working increasingly closely with data-science. This has been leveraged through the democratization of data-science with the increasing availability of easy to access open datasets, tutorials, programming languages, and hardware which makes it significantly easier to create mathematical models. To address the COVID-19 pandemic, such data-science has enabled modeling of the impact of the virus on the population and individuals for diagnostic, prognostic, and epidemiological ends. This has led to two large systematic reviews on this topic that have highlighted the two different ways in which this feat has been attempted: one using classical statistics and the other using more novel machine learning techniques. In this review, we debate the relative strengths and weaknesses of each method toward the specific task of predicting COVID-19 outcomes.

PMID:35005694 | PMC:PMC8734592 | DOI:10.3389/fdgth.2021.637944

Lancet Reg Health West Pac. 2022 Mar;20:100362. doi: 10.1016/j.lanwpc.2021.100362. Epub 2022 Jan 1.

ABSTRACT

BACKGROUND: In early 2020, non-pharmaceutical interventions (NPIs) were implemented in China to reduce and contain the coronavirus disease 2019 (COVID-19) transmission. These NPIs might have also reduced the incidence of hand, foot, and mouth disease (HFMD).

METHODS: The weekly numbers of HFMD cases and meteorological factors in 31 provincial capital cities and municipalities in mainland China were obtained from Chinese Center for Disease Control and Prevention (CCDC) and National Meteorological Information Center of China from 2016 to 2020. The NPI data were collected from local CDCs. The incidence rate ratios (IRRs) were calculated for the entire year of 2020, and for January-July 2020 and August-December 2020. The expected case numbers were estimated using seasonal autoregressive integrated moving average models. The relationships between kindergarten closures and incidence of HFMD were quantified using a generalized additive model. The estimated associations from all cities were pooled using a multivariate meta-regression model.

FINDINGS: Stringent NPIs were widely implemented for COVID-19 control from January to July 2020, and the IRRs for HFMD were less than 1 in all 31 cities, and less than 0·1 for 23 cities. Overall, the proportion of HFMD cases reduced by 52·9% (95% CI: 49·3-55·5%) after the implementation of kindergarten closures in 2020, and this effect was generally consistent across subgroups.

INTERPRETATION: The decrease in HFMD incidence was strongly associated with the NPIs for COVID-19. HFMD epidemic peaks were either absent or delayed, and the final epidemic size was reduced. Kindergarten closure is an intervention to prevent HFMD outbreaks.

FUNDING: This research was supported by the National Natural Science Foundation of China (81973102 & 81773487), Public Health Talents Training Program of Shanghai Municipality (GWV-10.2-XD21), the Shanghai New Three-year Action Plan for Public Health (GWV-10.1-XK16), the Major Project of Scientific and Technical Winter Olympics from National Key Research and Development Program of China (2021YFF0306000), 13th Five-Year National Science and Technology Major Project for Infectious Diseases (2018ZX10725-509) and Key projects of the PLA logistics Scientific research Program (BHJ17J013).

PMID:35005671 | PMC:PMC8720138 | DOI:10.1016/j.lanwpc.2021.100362

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