Tag: statistics

Lab Chip. 2022 Feb 10. doi: 10.1039/d1lc01043c. Online ahead of print.

ABSTRACT

Imaging flow cytometry (IFC) has become a powerful tool for diverse biomedical applications by virtue of its ability to image single cells in a high-throughput manner. However, there remains a challenge posed by the fundamental trade-off between throughput, sensitivity, and spatial resolution. Here we present deep-learning-enhanced imaging flow cytometry (dIFC) that circumvents this trade-off by implementing an image restoration algorithm on a virtual-freezing fluorescence imaging (VIFFI) flow cytometry platform, enabling higher throughput without sacrificing sensitivity and spatial resolution. A key component of dIFC is a high-resolution (HR) image generator that synthesizes “virtual” HR images from the corresponding low-resolution (LR) images acquired with a low-magnification lens (10×/0.4-NA). For IFC, a low-magnification lens is favorable because of reduced image blur of cells flowing at a higher speed, which allows higher throughput. We trained and developed the HR image generator with an architecture containing two generative adversarial networks (GANs). Furthermore, we developed dIFC as a method by combining the trained generator and IFC. We characterized dIFC using Chlamydomonas reinhardtii cell images, fluorescence in situ hybridization (FISH) images of Jurkat cells, and Saccharomyces cerevisiae (budding yeast) cell images, showing high similarities of dIFC images to images obtained with a high-magnification lens (40×/0.95-NA), at a high flow speed of 2 m s^-1. We lastly employed dIFC to show enhancements in the accuracy of FISH-spot counting and neck-width measurement of budding yeast cells. These results pave the way for statistical analysis of cells with high-dimensional spatial information.

PMID:35142325 | DOI:10.1039/d1lc01043c

Ann Ig. 2022 Feb 8. doi: 10.7416/ai.2022.2502. Online ahead of print.

ABSTRACT

FOREWARD: Nurses’ attitudes towards COVID-19 vaccination is a relevant issue, for the protection of the vulnerable people they care for, and the key role they play in promoting health behaviors that encourage trust and adherence to vaccination among population. This study aimed to validate the Italian version of the Vaccination Attitudes Examination (VAX) scale and to describe nurses’ attitudes towards COVID-19 vaccination.

DESIGN: A cross-sectional study was carried out from May to June 2021. Descriptive statistics, Explorative and Confirmatory Factor Analyses have been performed.

METHODS: An online survey was carried out in Italy. The VAX scale referring to the COVID-19 vaccine was used.

FINDINGS: 430 nurses participated in the study, mainly female (73.2%). Mean age was 40.2 years. VAX scale revealed an optimal reliability; Exploratory Factor Analysis and Confirmatory Analysis supported a 4-factors model. VAX scale mean scores showed low mistrust about vaccine’s benefit (2.03±1.07), concerns about commercial profiteering (2.33±1.39) and preference for natural immunity (2.90±1.37). More worries concerning unexpected future effects were found (4.46±1.36). Gender, taking care of a frail person in family, having children or working in a COVID-19 setting are no significantly related to vaccination attitude. Participants from northern Italy expressed greater confidence in vaccine’s benefits, the younger had significant lower scores about commercial profiteering.

CONCLUSIONS: The Italian version of the VAX scale resulted a reliable tool to assess the nurses’ attitudes towards COVID-19 vaccination. An overall positive nurses’ attitude towards the COVID-19 vaccination was highlighted. The concern about unforeseen future effects suggested the need to increase the information on this issue.

CLINICAL RELEVANCE: The results provided a valid and reliable tool to measure vaccination attitudes in the Italian context. This study could strengthen the health policies with educational interventions of healthcare workers through specific vaccination pathways. The healthcare professionals’ vaccination attitudes play the key role also in promoting vaccination uptake in the population.

PMID:35142334 | DOI:10.7416/ai.2022.2502

Clin Nephrol. 2022 Feb 10. doi: 10.5414/CN110706. Online ahead of print.

ABSTRACT

AIMS: Investigate if kidney function markers predict posterior reversible encephalopathy syndrome (PRES) in children.

MATERIALS AND METHODS: In a case-control study of high-risk children with confirmed PRES (n = 35) compared to controls (n = 14), we recorded blood urea nitrogen (BUN), serum creatinine, serum albumin, hemoglobin concentrations, estimated glomerular filtration rate, and documentation of acute kidney injury (AKI). We applied multivariable regression models and determined receiver operating characteristic curves.

RESULTS: Mean age was 9.5 (SD 4.9) years, 51% were female, 29% had chronic kidney disease, 67% had nephrotoxic medication exposure, and 29% had AKI. A 1-mg/dL increase in BUN (adjusted OR 1.03, 95% CI 0.99 – 1.07) and AKI (adjusted OR 3.78, 0.68 – 21.13) were minimally, but not statistically significantly, associated with PRES. BUN = 21.6 mg/dL performed best but had low ability to predict PRES (area under the curve 0.664, 0.498 – 0.831), with 60.0% sensitivity, 71.4% specificity, and positive and negative predictive values of 84.0% and 41.7%, respectively.

CONCLUSION: Kidney function may be a relatively more minor risk factor for PRES than previously believed. Further prospective studies with larger sample sizes and better kidney function assessments are warranted to evaluate the role of kidney function in the development of PRES.

PMID:35142281 | DOI:10.5414/CN110706

Clin Nephrol. 2022 Feb 10. doi: 10.5414/CN110476. Online ahead of print.

ABSTRACT

Deletions involving the TSC2 and PKD1 genes lead to tuberous sclerosis complex (TSC) and autosomal dominant polycystic kidney disease (ADPKD), which is known as TSC2–PKD1 contiguous gene deletion syndrome (PKDTS). PKDTS leads to severe symptoms and death. There are few reported cases of PKDTS, the phenotypic descriptions are poor, and detailed statistics and descriptions of the time of onset and prognosis of PKDTS are lacking. This is the first study to report on the clinical data of PKDTS patients in China. We analyzed all cases including Chinese individuals and summarized the clinical manifestations and genetic characteristics. Our study was the first to use a combination of exome sequencing and multiplex ligation-dependent probe amplification (MLPA) to screen and diagnose PKDTS. We found that many PKDTS patients have the following: multiple renal cysts; angiofibromas (≥ 3) or fibrous cephalic plaque; subependymal nodules; seizures; intellectual disability. PKDTS develops into polycystic kidney disease from before birth to 17 years old and the time of occurrence of end-stage renal disease or dialysis was 21.62 ± 12.87 years of age, which was significantly earlier than in ADPKD caused by PKD1 mutation. Compared with non-Chinese individuals of diverse ancestry, Chinese people have significant differences in the clinical characteristics, including ungual fibromas (≥ 2), and shagreen patch. Five novel large deletions were identified in Chinese. We found no relationship between the clinical phenotype and the genotype. We combined exome sequencing with MLPA to develop a diagnostic method for PKDTS.

PMID:35142283 | DOI:10.5414/CN110476

Curr HIV Res. 2022 Feb 10. doi: 10.2174/1570162X20666220210142209. Online ahead of print.

ABSTRACT

BACKGROUND: Effective global antiretroviral vaccines and therapeutic strategies depend on the diversity, evolution, and epidemiology of their various strains as well as their transmission and pathogenesis. Most viral disease-causing particles are clustered into a taxonomy of subtypes to suggest pointers toward nucleotide-specific vaccines or therapeutic applications of clinical significance sufficient for sequence-specific diagnosis and homologous viral studies. These are very useful to formulate predictors to induce cross-resistance to some retroviral control drugs being used across study areas.

OBJECTIVE: This research proposed a collaborative framework of hybridized (Machine Learning and Natural Language Processing) techniques to discover hidden genome patterns and feature predictors, for HIV-1 genome sequences mining.

METHOD: 630 human HIV-1 genome sequences above 8500 bps were excavated from the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov) for 21 countries across different continents, Antarctica exempt. These sequences were transformed and learned using a self-organizing map (SOM). To discriminate emerging/new sub-strain(s), the HIV-1 reference genome was included as part of the input isolates/samples during the training. After training the SOM, component planes defining pattern clusters of the input datasets were generated, for cognitive knowledge mining and subsequent labelling of the datasets. Additional genome features including dinucleotide transmission recurrences, codon recurrences, and mutation recurrences, were finally extracted from the raw genomes to construct output classification targets for supervised learning.

RESULTS: SOM training explains the inherent pattern diversity of HIV-1 genomes as well as inter- and intra-country transmissions in which mobility might play an active role, as corroborated by literature. Nine sub-strains were discovered after disassembling the SOM correlation hunting matrix space attributed to disparate clusters. Cognitive knowledge mining separated similar pattern clusters bounded by a certain degree of correlation range, discovered by the SOM. A Kruskal-Wallis rank-sum test and Wilcoxon rank-sum test showed statistically significant variations in dinucleotide, codon, and mutation patterns.

CONCLUSION: Results of the discovered sub-strains and response clusters visualizations corroborate existing literature, with significant haplotype variations. The proposed framework would assist in the development of decision support systems for easy contact tracing, infectious disease surveillance, and studying the progressive evolution of the reference HIV-1 genome.

PMID:35142269 | DOI:10.2174/1570162X20666220210142209

Neuropsychol Rehabil. 2022 Feb 10:1-31. doi: 10.1080/09602011.2022.2030761. Online ahead of print.

ABSTRACT

This exploratory sub-study aimed to develop a framework to conceptualize boredom in stroke survivors during inpatient rehabilitation, establish the effect of an activity promotion intervention on boredom, and to investigate factors that are associated with boredom. A framework was developed and explored within a cluster non-randomised controlled trial. Self-reported boredom was measured in 160 stroke survivors 13 (±5) days after rehabilitation admission; 91 participants received usual-care (control) and 69 had access to a patient-driven model of activity promotion (intervention). Individuals with pre-existing dementia or unable to participate in standard rehabilitation were excluded. Hierarchical logistic regression analysis was used to identify demographic, health and activity measures associated with boredom. Results indicated 39% of participants were highly bored. There was no statistically significant difference in boredom levels between treatment groups (difference -11%, 95% CI -26% to 4%). The presence of depression (OR 6.17, 95% CI 2.57-14.79) and lower levels of socialization (OR 0.96, 95% CI 0.92-0.99) predicted high boredom levels. This comprehensive framework provides a foundation for understanding the many interacting factors associated with boredom. Results suggest managing depression and improving opportunities for socialization may support meaningful engagement in rehabilitation to optimize recovery following stroke.

PMID:35142257 | DOI:10.1080/09602011.2022.2030761

Eur J Sport Sci. 2022 Feb 10:1-10. doi: 10.1080/17461391.2021.2023658. Online ahead of print.

ABSTRACT

Interpreting the physical qualities of youth athletes is complex due to the effects of growth, maturation and development. This study aimed to evaluate the effect of position, chronological age, relative age and maturation on the physical qualities of elite male academy rugby union players. 1,424 participants (n = 2,381 observations) from nine Rugby Football Union regional academies prospectively completed a physical testing battery at three time points, across three playing seasons. Anthropometrics, body composition, muscular power, muscular strength, speed, aerobic capacity and running momentum were assessed. Positional differences were identified for all physical qualities. The largest effect sizes were observed for the associations between chronological age (d = 0.65-0.73) and maturation (d = -0.77 to -0.69) and body mass related variables (i.e. body mass and running momentum). Relative strength, maximum velocity and aerobic capacity were the only models to include two fixed effects with all other models including at least three fixed effects (i.e. position and a combination of chronological age, relative age and maturation). These findings suggest a multidimensional approach considering position, chronological age, relative age and maturation is required to effectively assess the physical qualities of male age grade rugby union players. Therefore practitioners should use regression equations rather than traditional descriptive statistic tables to provide individualised normative comparisons thus enhancing the application of testing results for talent identification and player development.Highlights Practitioners should record and incorporate position, chronological age, relative age and maturation into the physical evaluation of elite academy rugby union players.The regression equations provided within this study offer highly generalisable comparative values that are specific to a players chronological and biological development.Through the use of enhanced player evaluation practitioners will be able to make more informed decisions surrounding talent identification and athlete development.

PMID:35142263 | DOI:10.1080/17461391.2021.2023658

Nurs Ethics. 2022 Feb 10:9697330211043271. doi: 10.1177/09697330211043271. Online ahead of print.

ABSTRACT

BACKGROUND: A large number of nurse researchers do not adhere to ethical standards while performing the research. Moreover, there is far less data on knowledge of existing national ethical guidelines. This study was, therefore, done to assess awareness and adherence to current national ethical guidelines among nursing students and faculty members.

METHODS: A cross-sectional descriptive study was done among nursing faculty members and theses carried out by postgraduate nursing students between 2012 and 2017. Using the convenience sampling technique, seven states of North India were selected. In each of the selected seven states, one government and one private nursing college was selected. Thus, a sample of 14 nursing colleges was selected. Then, using simple random sampling, a total of 140 nursing faculty members and 280 postgraduate nursing theses were selected from all the chosen institutes to be part of the study. Data analysis was done using descriptive statistics.

ETHICAL CONSIDERATIONS: The study has been approved by the institutional ethical committee (ECR/737/Inst/UK/2018/RR-18). In addition, written permission from the head of each nursing institute was obtained before conducting the study. After participants read the Participation Information Sheet, they were asked for written informed consent before data collection. Confidentiality of the information and anonymity of the participants were maintained throughout the study.

RESULTS: The majority (81.8%) of the participants were females. It was found that compared to private nurses, government college nurses were more adhered to the research guidelines on research project approval (68.6% vs 22.1%), informed consent guidelines (74.3% vs 25%), providing patient information sheets (55.7% vs 10%), maintaining information confidentiality (82.9% vs 72.1%), maintaining anonymity (76.4% vs 22.9%) and obtaining custodian permission (97.8 vs 89.3%). It was also shown that nurses were more aware of the informed consent process domain (4.3 ± 0.3) followed by the general ethical principles domain (3.8 ± 0.8).

CONCLUSION: Government college nurses adhered more to the research guidelines as compared to those employed in private settings. Most of the faculty members were not part of any clinical trials and had no research ethics training at all. Therefore, it is needed to provide an instructional programme to raise awareness of the research ethical standards.

PMID:35142244 | DOI:10.1177/09697330211043271

Cancer Commun (Lond). 2022 Feb 10. doi: 10.1002/cac2.12256. Online ahead of print.

ABSTRACT

BACKGROUND: Primary human papillomavirus (HPV) screening is recommended for the detection of cervical intraepithelial neoplasia (CIN) in the general population; however, the triage for HPV-positive women remains a challenge. This study aimed to evaluate the age-specific effectiveness of primary HPV screening versus primary cytology screening for identifying optimal strategies for women of different ages.

METHODS: The dataset of the prevalence round screening was derived from the National Cervical Cancer Screening Program in China. Primary cervical screening protocols included cytology only, HPV testing with cytology triage, and HPV testing with HPV-16/18 genotyping plus cytology triage. The primary outcomes were age-specific detection rate, colposcopy referral rate and positive predictive value (PPV) for CIN2+. Multivariate Poisson regression was used to evaluate the relative effectiveness of HPV testing and cytology according to age groups. The I² statistic with a random-effect model was used to test the heterogeneity in relative effectiveness of HPV testing versus cytology between age groups.

RESULTS: This study included 1,160,981 women. HPV testing with HPV-16/18 genotyping plus cytology triage significantly increased the CIN2+ detection by 36% (rate ratio [RR]: 1.36, 95% confidential interval [CI] 1.21-1.54) for women aged 35-44 years and by 34% (RR: 1.34, 95% CI 1.20-1.51) for women aged 45-54 years compared with cytology only. HPV testing with cytology triage had similar CIN2+ detection rate compared with cytology only. The PPVs were substantially increased for both HPV testing groups. Among women aged 55-64 years old, HPV testing with HPV-16/18 genotyping plus cytology triage increased the colposcopy referral rate by 19% (RR 1.19, 95% CI 1.10-1.29) compared with cytology only, but did not increase the CIN2+ detection (1.09, 0.91-1.30). The effectiveness of HPV testing with cytology triage did not change in older women. The between-age-group heterogeneity in the effectiveness was statistically significant for HPV testing with HPV-16/18 genotyping plus cytology triage versus cytology only.

CONCLUSIONS: Our results suggested that the effectiveness of primary HPV screening with different triage strategies differed among age groups. HPV testing with HPV-16/18 genotyping plus cytology triage could be used for women aged 35-54 years to detect more lesions, and HPV testing with cytology triage could balance the CIN2+ detection and the number of colposcopies for women aged 55-64 years. Longitudinal data including both prevalence and incidence screening rounds are warranted to assess age-specific triage strategies.

PMID:35142100 | DOI:10.1002/cac2.12256

ESC Heart Fail. 2022 Feb 9. doi: 10.1002/ehf2.13838. Online ahead of print.

ABSTRACT

AIMS: Although comprehensive cardiac rehabilitation (CCR) is recommended for patients with heart failure (HF), participants often show low adherence. The aim of this study was to evaluate the association of CCR completion and response with long-term clinical outcomes.

METHODS AND RESULTS: We screened 824 HF patients who participated in a 3 month CCR programme and underwent baseline assessment, including cardiopulmonary exercise testing (CPX). After excluding 52 participants who experienced all-cause death or HF hospitalization within 180 days, long-term outcomes were compared between those who attended 3 month follow-up assessment including CPX (completers) and those who did not (non-completers). We also compared the prognostic value of the changes in peak oxygen uptake (VO₂ ) vs. quadriceps muscle strength (QMS) during the 3 month CCR programme. Among the 772 study patients, there were no significant differences in baseline characteristics, including left ventricular ejection fraction, B-type natriuretic peptide levels, and peak VO₂ , between the completers (n = 561) and non-completers (n = 211), except for a higher age (63.2 ± 14.2 vs. 59.4 ± 16.2 years; P = 0.0015) and proportion of females (27% vs. 17%; P = 0.0030) among the completers. During a median follow-up of 55.4 months, the completers had lower rates of the composite of all-cause death or HF hospitalization (34.4% vs. 44.6%; P = 0.0015) and all-cause death (16.9% vs. 24.6%; P = 0.0037) than the non-completers. After adjustment for prognostic baseline characteristics, including age and sex, CCR completion was associated with 34% and 44% reductions in the composite outcome and all-cause death, respectively. Among the completers, peak VO₂ and QMS increased significantly (8.9 ± 15.8% and 10.5 ± 17.9%, respectively) over 3 months. Patients who had an increase in peak VO₂ ≥ 6.3% (median value) during the CCR programme had significantly lower rates of the composite outcome (27.0% vs. 33.8%; P = 0.048) and all-cause mortality (10.0% vs. 17.4%; P = 0.0069) than those who did not. No statistically significant difference was observed in the composite outcome (30.5% vs. 30.4%; P = 0.76) or all-cause mortality (13.0% vs. 14.4%; P = 0.39) between those with and without an increase in QMS ≥8.3% (median value).

CONCLUSIONS: In HF patients who participated in a 3 month CCR programme, its completion was associated with lower risks of subsequent HF hospitalization and death. Within the group of patients who completed the programme, the improvement in exercise capacity, but not in skeletal muscle strength, over the 3-month period was associated with better outcomes. These findings highlight the importance of the post-CCR follow-up assessment, including CPX, to identify a patient’s adherence and response to the CCR programme.

PMID:35142087 | DOI:10.1002/ehf2.13838