Tag: pubmed

Neurosurgery. 2021 May 14:nyab164. doi: 10.1093/neuros/nyab164. Online ahead of print.

ABSTRACT

BACKGROUND: Currently, different postoperative predictors of chordoma recurrence have been identified. Tumor growth rate (TGR) is an image-based calculation that provides quantitative information of tumor’s volume changing over time and has been shown to predict progression-free survival (PFS) in other tumor types.

OBJECTIVE: To explore the usefulness of TGR as a new preoperative radiological marker for chordoma recurrence.

METHODS: A retrospective single-institution study was carried out including patients reflecting these criteria: confirmed diagnosis of chordoma on pathological analysis, no history of previous radiation, and at least 2 preoperative thin-slice magnetic resonance images available to measure TGR. TGR was calculated for all patients, showing the percentage change in tumor size over 1 mo.

RESULTS: A total of 32 patients were retained for analysis. Patients with a TGR ≥ 10.12%/m had a statistically significantly lower mean PFS (P < .0001). TGR ≥ 10.12%/m (odds ratio = 26, P = .001) was observed more frequently in recurrent chordoma. In a subgroup analysis, we found that the association of Ki-67 labeling index ≥ 6% and TGR ≥ 10.12%/m was correlated with recurrence (P = .0008).

CONCLUSION: TGR may be considered as a preoperative radiological indicator of tumor proliferation and seems to preoperatively identify more aggressive tumors with a higher tendency to recur. Our findings suggest that the therapeutic strategy and clinical-radiological follow-up of patients with chordoma can be adapted also according to this new parameter.

PMID:33989415 | DOI:10.1093/neuros/nyab164

Bioinformatics. 2021 May 14:btab378. doi: 10.1093/bioinformatics/btab378. Online ahead of print.

ABSTRACT

SUMMARY: The sparse allele vectors (SAV) file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been developed to complement the storage format and supports basic features like importing, exporting and subsetting. Additionally, a C ++ programming API is available allowing for easy integration into analysis software.

AVAILABILITY AND IMPLEMENTATION: https://github.com/statgen/savvy.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:33989384 | DOI:10.1093/bioinformatics/btab378

PLoS One. 2021 May 14;16(5):e0251621. doi: 10.1371/journal.pone.0251621. eCollection 2021.

ABSTRACT

BACKGROUND: Acute respiratory infections are rising in developing countries including Ethiopia. Lack of evidence for the prevalence and associated factors of acute respiratory infection among street sweepers and door-to-door waste collectors in Dessie City, Ethiopia is a challenge for the implementation of appropriate measures to control acute respiratory infection. Thus, this study was designed to address the gaps.

METHODS: A comparative cross-sectional study was conducted among 84 door-to-door waste collectors and 84 street sweepers from March to May 2018. A simple random sampling technique was used to select study participants. Data were collected by trained data collectors using a pretested structured questionnaire and on-the-spot direct observation checklist. Data were analyzed using three different binary logistic regression models at 95% confidence interval (CI): the first model (Model I) was used to identify factors associated with acute respiratory infection among street sweepers, whereas the second model (Model II) was used to identify factors associated with acute respiratory infection among door-to-door waste collectors, and the third model (Model III) was used for pooled analysis to identify factors associated with acute respiratory infection among both street sweepers and door-to-door waste collectors. From each model multivariable logistic regression, variables with a p-value <0.05 were taken as factors significantly associated with acute respiratory infection.

RESULTS: The overall prevalence of acute respiratory infection among studied population was 42.85% with 95% CI (35.1, 50.0%). The prevalence of acute respiratory infection among street sweepers was 48.80% (95% CI: 37.3, 64.8%) and among door-to-door waste collectors was 36.90% (95% CI: 27.4, 46.4%). There was no statistically significant difference between the prevalence of acute respiratory infection among the two groups due to the overlapping of the 95% CI. Among the street sweepers, we found that factors significantly associated with acute respiratory infection were not cleaning personal protective equipment after use (adjusted odds ratio [AOR]: 2.40; 95% CI: 1.15, 5.51) and use of coal/wood for cooking (AOR: 3.95; 95% CI: 1.52, 7.89), whereas among door-to-door waste collectors, were not using a nose/mouth mask while on duty (AOR: 5.57; 95% CI: 1.39, 9.32) and not receiving health and safety training (AOR: 3.82; 95% CI: 1.14-7.03) were factors significantly associated with acute respiratory infection among door-to-door-waste collectors. From the pooled analysis, we found that not using a nose/mouth mask while on duty (AOR: 2.19; 95% CI: 1.16, 4.53) and using coal/wood for cooking (AOR: 2.74; 95% CI: 1.18, 6.95) were factors significantly associated with acute respiratory infection for both street sweepers and door-to-door waste collectors.

CONCLUSION: The prevalence of acute respiratory infection among street sweepers and door-to-door waste collectors has no statistically significant difference. For both groups, not using a nose/mouth mask while on duty and using coal/wood for cooking fuel factors associated with acute respiratory infection. The municipality should motivate and monitor workers use of personal protective equipment including masks and gloves. Workers should use a nose/mouth mask while on duty and should choose a clean energy source for cooking at home.

PMID:33989364 | DOI:10.1371/journal.pone.0251621

Phys Chem Chem Phys. 2021 May 14. doi: 10.1039/d1cp00418b. Online ahead of print.

ABSTRACT

We report the electronic, magnetic, structural, vibrational, and X-ray absorption spectroscopy of the inverse full-Heusler Fe2IrSi alloy. We employed state-of-the-art first-principles computational techniques. Our ab initio calculations revealed a ferromagnetic half-metallicity with a magnetic moment of ∼5.01 μB, which follows the Slater Pauling rule. We show rich magnetic behavior due to spin-orbit coupling through the entanglement of the Fe-3d/Ir-5d orbitals. The large extension of the Ir-5d orbital and the itinerant Fe-3d states enhanced spin-orbit and electron-electron interactions, respectively. The analyses of our results reveal that electron-electron interactions are essential for the proper description of the electronic properties while spin-orbit coupling effects are vital to accurately characterize the X-ray absorption and X-ray magnetic circular dichroism spectra. We estimate the strength of the spin-orbit coupling by comparing the intensity of the white-line features at the L3 and L2 absorption edges. This led to a branching ratio that deviates strongly from the statistical ratio of 2, indicative of strong spin-orbit coupling effects in the inverse full-Heusler Fe2IrSi alloy.

PMID:33989367 | DOI:10.1039/d1cp00418b

PLoS One. 2021 May 14;16(5):e0251624. doi: 10.1371/journal.pone.0251624. eCollection 2021.

ABSTRACT

BACKGROUND: Access to major services, often located in urban centres, is key to the realisation of numerous Sustainable Development Goals (SDGs). In Kenya, there are no up-to-date and localised estimates of spatial access to urban centres. We estimate the travel time to urban centres and identify marginalised populations for prioritisation and targeting.

METHODS: Urban centres were mapped from the 2019 Kenya population census and combined with spatial databases of road networks, elevation, land use and travel barriers within a cost-friction algorithm to compute travel time. Seven travel scenarios were considered: i) walking only (least optimistic), ii) bicycle only, iii) motorcycle only, iv) vehicle only (most optimistic), v) walking followed by motorcycle transport, vi) walking followed by vehicle transport, and vii) walking followed by motorcycle and then vehicle transport (most pragmatic). Mean travel time, and proportion of the population within 1-hour and 2-hours of the urban centres were summarized at sub-national units (counties) used for devolved planning. Inequities were explored and correlations between the proportion of the population within 1-hour of an urban centre and ten SDG indicators were computed.

RESULTS: A total of 307 urban centres were digitised. Nationally, the mean travel time was 4.5-hours for the walking-only scenario, 1.0-hours for the vehicle only (most optimistic) scenario and 1.5-hours for the walking-motorcycle-vehicle (most pragmatic) scenario. Forty-five per cent (21.3 million people) and 87% (41.6 million people) of Kenya’s population resided within 1-hour of the nearest urban centre for the least optimistic and most pragmatic scenarios respectively. Over 3.2 million people were considered marginalised or living outside the 2-hour threshold in the pragmatic scenario, 16.0 million Kenyans for walking only, and 2.2 million for the most optimistic scenario. County-level spatial access was highly heterogeneous ranging between 8%-100% and 32%-100% of people within the 1-hour threshold for the least and most optimistic scenarios, respectively. Counties in northern and eastern parts of Kenya were generally most marginalised. The correlation coefficients for nine SDG indicators ranged between 0.45 to 0.78 and were statistically significant.

CONCLUSION: Travel time to urban centres in Kenya is heterogeneous. Therefore, marginalised populations should be prioritised during resource allocation and policies should be formulated to enhance equitable access to public services and opportunities in urban areas.

PMID:33989356 | DOI:10.1371/journal.pone.0251624

PLoS One. 2021 May 14;16(5):e0251818. doi: 10.1371/journal.pone.0251818. eCollection 2021.

ABSTRACT

As species distribution models, and similar techniques, have emerged in marine ecology, a vast array of predictor variables have been created and diverse methodologies have been applied. Marine fish are vital food resources worldwide, yet identifying the most suitable methodology and predictors to characterize spatial habitat associations, and the subsequent distributions, often remains ambiguous. Our objectives were to identify knowledge gaps in fish guilds, identify research themes, and to determine how data sources, statistics, and predictor variables differ among fish guilds. Data were obtained from an international literature search of peer-reviewed articles (2007-2018; n = 225) and research themes were determined based on abstracts. We tested for differences in data sources and modeling techniques using multinomial regressions and used a linear discriminant analysis to distinguish differences in predictors among fish guilds. Our results show predictive studies increased over time, but studies of forage fish, sharks, coral reef fish, and other fish guilds remain sparse. Research themes emphasized habitat suitability and distribution shifts, but also addressed abundance, occurrence, stock assessment, and biomass. Methodologies differed by fish guilds based on data limitations and research theme. The most frequent predictors overall were depth and temperature, but most fish guilds were distinguished by their own set of predictors that focused on their specific life history and ecology. A one-size-fits-all approach is not suitable for predicting marine fish distributions. However, given the paucity of studies for some fish guilds, researchers would benefit from utilizing predictors and methods derived from more commonly studied fish when similar habitat requirements are expected. Overall, the findings provide a guide for determining predictor variables to test and identifies novel opportunities to apply non-spatial knowledge and mechanisms to models.

PMID:33989361 | DOI:10.1371/journal.pone.0251818

PLoS One. 2021 May 14;16(5):e0251609. doi: 10.1371/journal.pone.0251609. eCollection 2021.

ABSTRACT

BACKGROUND: Neonates with severe complications at birth or during the neonatal period who nearly died but survived constitute neonatal near miss (NNM) cases. Identifying NNM cases and correcting contributing factors are of the utmost importance to get relevant controls for neonatal deaths. However, limited studies are assessing the prevalence of NNM and associated factors with NNM cases in Ethiopia. So, this study is aimed at assessing the magnitude of neonatal near miss and associated factors among live births in public hospitals of Jimma zone, southwest Ethiopia, 2020.

METHODS: A facility-based cross-sectional study was conducted among 260 neonates from April 1-30 / 2020. Face to face interviewer-administered structured questionnaire was used to collect data from the mothers and a standard checklist was used for their neonates. The data was encoded and entered into Epi-Data version 4.2 and exported to SPSS version 23 for analysis. Independent variables with marginal associations (p-value <0.25) in the bivariable analysis were eligible for multivariable logistic regression analysis to detect an association with outcome variables. Finally, adjusted odds ratios (AOR) with 95% CI were used to estimate the strength of associations, and statistical significance was declared at a p-value < 0.05.

RESULT: The magnitude of NNM was 26.7% with [95%CI: 21.6-32.5]. Hypertension during pregnancy [AOR: 3.4; 95%CI: 1.32-8.88], mode of delivery [AOR: 3.32; 95%CI: 1.48-7.45], Obstructed labor [AOR: 2.95; 95%CI: 1.32-6.45] and non-vertex fetal presentation during delivery [AOR: 4.61; 95%CI: 2.16-9.84] were identified as significantly predictors of NNM.

CONCLUSION AND RECOMMENDATION: Over a quarter of the neonates were with NNM cases, which is relatively higher than the report of studies done in other countries. Hypertension during pregnancy, cesarean delivery, prolonged labor, and non-vertex fetal presentation were all found to increase the likelihood of NNM. Therefore, concerted efforts are needed from local health planners and health care providers to improve maternal health care services especially in early identification of the complications and taking appropriate management.

PMID:33989319 | DOI:10.1371/journal.pone.0251609

PLoS One. 2021 May 14;16(5):e0251131. doi: 10.1371/journal.pone.0251131. eCollection 2021.

ABSTRACT

BACKGROUND: Idiopathic membranous nephropathy (IMN) is one of the most common causes of nephrotic syndrome in adults involving multiple targets and factors. The effect of conservative nonimmunosuppressive or immunosuppressive therapies is unsatisfactory and with many side effects. Traditional Chinese medicine (TCM) can regulate immune function and improve kidney function.

PURPOSE: To evaluate the total effective rate, curative rate, recurrence rate and adverse events of TCM alone or TCM as an adjunctive therapy for IMN.

METHODS: Randomized controlled trials (RCT) comparing either TCM alone or the combination of TCM to western medicine (WM) therapies for patients with IMN were retrieved by searching English and Chinese database. Risk of bias summary was used to assess the methodological quality of eligible studies. Dichotomous data were presented using odds ratios (OR). The primary outcome measure was the total effective rate. Secondary outcomes included curative rate, recurrence rate and adverse events.

RESULTS: 29 RCTs involving 1883 participants met the inclusion criteria. There was no statistically significant difference between the therapy of TCM alone and WM on the total effective rates (OR: 2.00; 95% CI: 0.80-4.98; P = 0.14) and curative rate (OR: 1.66; 95%CI: 0.66-4.22; p = 0.28). However, compared to basic treatment or immunosuppressive therapies alone, results showed that TCM as an adjunctive therapy had beneficial effects on the total effective rate (OR: 2.59; 95% CI: 1.38-4.86; P = 0.003 and OR: 3.01; 95% CI: 2.25-4.04; P < 0.00001) and curative rate (OR: 3.01; 95%CI: 1.24-7.28; p = 0.01 and OR: 1.73; 95%CI: 1.10-2.71; p = 0.02). In addition, the combination of TCM treatment could reduce the recurrence rate (OR: 0.28; 95% CI: 0.12-0.68; P = 0.004) and adverse reactions (OR: 0.38; 95% CI: 0.27-0.54; p < 0.00001).

CONCLUSION: The results indicate that TCM is well-tolerated for the treatment of IMN. However, there remains a need for large-scale and high-quality trials.

PMID:33989325 | DOI:10.1371/journal.pone.0251131

PLoS One. 2021 May 14;16(5):e0251842. doi: 10.1371/journal.pone.0251842. eCollection 2021.

ABSTRACT

Electroencephalography (EEG) microstate analysis is a method wherein spontaneous EEG activity is segmented at sub-second levels to analyze quasi-stable states. In particular, four archetype microstates and their features are known to reflect changes in brain state in neuropsychiatric diseases. However, previous studies have only reported differences in each microstate feature and have not determined whether microstate features are suitable for schizophrenia classification. Therefore, it is necessary to validate microstate features for schizophrenia classification. Nineteen microstate features, including duration, occurrence, and coverage as well as thirty-one conventional EEG features, including statistical, frequency, and temporal characteristics were obtained from resting-state EEG recordings of 14 patients diagnosed with schizophrenia and from 14 healthy (control) subjects. Machine-learning based multivariate analysis was used to evaluate classification performance. EEG recordings of patients and controls showed different microstate features. More importantly, when differentiating among patients and controls, EEG microstate features outperformed conventional EEG ones. The performance of the microstate features exceeded that of conventional EEG, even after optimization using recursive feature elimination. EEG microstate features applied with conventional EEG features also showed better classification performance than conventional EEG features alone. The current study is the first to validate the use of microstate features to discriminate schizophrenia, suggesting that EEG microstate features are useful for schizophrenia classification.

PMID:33989352 | DOI:10.1371/journal.pone.0251842

PLoS One. 2021 May 14;16(5):e0251177. doi: 10.1371/journal.pone.0251177. eCollection 2021.

ABSTRACT

BACKGROUND: Significant progress has been made addressing adolescent health needs in New Zealand, but some areas, such as mental health issues remain, particularly for rangatahi Māori (indigenous Māori young people). Little is known about how contemporary Māori whānau (families) and communities influence health outcomes, health literacy and access to services. Previous nationally representative secondary school surveys were conducted in New Zealand in 2001, 2007 and 2012, as part of the Youth2000 survey series. This paper focuses on a fourth survey conducted in 2019 (https://www.youth19.ac.nz/). In 2019, the survey also included kura kaupapa Māori schools (Māori language immersion schools), and questions exploring the role of family connections in health and wellbeing. This paper presents the overall study methodology, and a weighting and calibration framework in order to provide estimates that reflect the national student population, and enable comparisons with the previous surveys to monitor trends.

METHODS: Youth19 was a cross sectional, self-administered health and wellbeing survey of New Zealand high school students. The target population was the adolescent population of New Zealand (school years 9-13). The study population was drawn from three education regions: Auckland, Tai Tokerau (Northland) and Waikato. These are the most ethnically diverse regions in New Zealand. The sampling design was two-stage clustered stratified, where schools were the clusters, and strata were defined by kura schools and educational regions. There were four strata, formed as follows: kura schools (Tai Tokerau, Auckland and Waikato regions combined), mainstream-Auckland, mainstream-Tai Tokerau and mainstream-Waikato. From each stratum, 50% of the schools were randomly sampled and then 30% of students from the selected schools were invited to participate. All students in the kura kaupapa schools were invited to participate. In order to make more precise estimates and adjust for differential non-response, as well as to make nationally relevant estimates and allow comparisons with the previous national surveys, we calibrated the sampling weights to reflect the national secondary school student population.

RESULTS: There were 45 mainstream and 4 kura schools included in the final sample, and 7,374 mainstream and 347 kura students participated in the survey. There were differences between the sampled population and the national secondary school student population, particularly in terms of sex and ethnicity, with a higher proportion of females and Asian students in the study sample than in the national student population. We calculated estimates of the totals and proportions for key variables that describe risk and protective factors or health and wellbeing factors. Rates of risk-taking behaviours were lower in the sampled population than what would be expected nationally, based on the demographic profile of the national student population. For the regional estimates, calibrated weights yield standard errors lower than those obtained with the unadjusted sampling weights. This leads to significantly narrower confidence intervals for all the variables in the analysis. The calibrated estimates of national quantities provide similar results. Additionally, the national estimates for 2019 serve as a tool to compare to previous surveys, where the sampling population was national.

CONCLUSIONS: One of the main goals of this paper is to improve the estimates at the regional level using calibrated weights to adjust for oversampling of some groups, or non-response bias. Additionally, we also recommend the use of calibrated estimators as they provide nationally adjusted estimates, which allow inferences about the whole adolescent population of New Zealand. They also yield confidence intervals that are significantly narrower than those obtained using the original sampling weights.

PMID:33989300 | DOI:10.1371/journal.pone.0251177