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Nevin Manimala Statistics

Correction for Shen and Feldman, Genetic nurturing, missing heritability, and causal analysis in genetic statistics

Proc Natl Acad Sci U S A. 2021 Sep 7;118(36):e2113732118. doi: 10.1073/pnas.2113732118.

NO ABSTRACT

PMID:34470827 | DOI:10.1073/pnas.2113732118

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Nevin Manimala Statistics

What represents treatment efficacy in long-term studies of gout flare prevention? An interview study of people with gout

J Rheumatol. 2021 Sep 1:jrheum.210476. doi: 10.3899/jrheum.210476. Online ahead of print.

ABSTRACT

OBJECTIVE: The patient experience of gout flares is multidimensional with several contributing factors, including pain intensity, duration and frequency. There is currently no consistent method for reporting gout flare burden in long-term studies. This study aimed to determine which factors contribute to patient perceptions of treatment efficacy in long-term studies of gout flare prevention.

METHODS: This study involved face-to-face interviews with people with gout using visual representations of gout flare patterns. Participants were shown different flare scenarios over a hypothetical 6-month treatment period portraying varying flare frequency, pain intensity and flare duration. The participants were asked to indicate and discuss which scenario they believed was most indicative of successful treatment over time. Quantitative data relating to the proportion of participants selecting each scenario were reported using descriptive statistics. A qualitative descriptive approach was used to code and categorize the data from the interview transcripts.

RESULTS: Twenty-two people with gout participated in the semi-structured interviews. All three factors of pain intensity, flare duration and flare frequency influenced participants’ perception of treatment efficacy. However, a shorter flare duration was the most common indicator of successful treatment, with half of participants (n = 11, 50%) selecting the scenario with a shorter flare duration over those with less painful flares.

CONCLUSION: Flare duration, flare frequency, and pain severity are all considered by patients with gout when considering treatment efficacy over time. Long term studies of gout should ideally capture all of these factors to better represent patients’ experience of treatment success.

PMID:34470799 | DOI:10.3899/jrheum.210476

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Nevin Manimala Statistics

Lifestyle Factors and Disease Activity over Time in Early Axial Spondyloarthritis – The SPondyloArthritis Caught Early (SPACE) Cohort

J Rheumatol. 2021 Sep 1:jrheum.210046. doi: 10.3899/jrheum.210046. Online ahead of print.

ABSTRACT

OBJECTIVE: Our aim was to study the importance of baseline Body Mass Index (BMI), smoking and alcohol consumption (AC) for disease activity (DA) over one year in early axial spondyloarthritis (axSpA), stratified by sex.

METHODS: In the SPondyloArthritis Caught Early cohort (patients with chronic back pain for ≥3 months, ≤2 years and onset <45 years), ASDAS was recorded at inclusion, 3 and 12 months. All patients included in the analysis had axSpA based on a high physician’s level of confidence at baseline. Differences in ASDAS over 1 year by BMI (normal <25, overweight 25-29.9, obese ≥30 kg/m2), smoking history (never/previous/current) and AC (none, 0.1-2, 3-5, ≥6 units/week) at baseline were estimated using mixed linear regression models.

RESULTS: There were 344 subjects (mean age 30 years; 49% men). In women, obesity was associated with 0.60 (95% CL 0.28, 0.91) higher ASDAS compared to normal BMI. In both sexes, AC tended to be associated with lower DA over one year, with a significant association only in women with the highest AC (mean difference -0.55 (96% CL-1.05, -0.04). Smoking was associated with higher ASDAS over one year compared to never smoking in both sexes, albeit the difference reached statistical significance only in female former smokers. Results were similar in multivariable analysis, adjusted for all lifestyle factors and other confounders.

CONCLUSION: In early axSpA, BMI and smoking are associated with higher DA over one year, and AC with lower DA. The magnitude of the modest associations may differ between men and women.

PMID:34470793 | DOI:10.3899/jrheum.210046

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Nevin Manimala Statistics

Long term exposure to low level air pollution and mortality in eight European cohorts within the ELAPSE project: pooled analysis

BMJ. 2021 Sep 1;374:n1904. doi: 10.1136/bmj.n1904.

ABSTRACT

OBJECTIVE: To investigate the associations between air pollution and mortality, focusing on associations below current European Union, United States, and World Health Organization standards and guidelines.

DESIGN: Pooled analysis of eight cohorts.

SETTING: Multicentre project Effects of Low-Level Air Pollution: A Study in Europe (ELAPSE) in six European countries.

PARTICIPANTS: 325 367 adults from the general population recruited mostly in the 1990s or 2000s with detailed lifestyle data. Stratified Cox proportional hazard models were used to analyse the associations between air pollution and mortality. Western Europe-wide land use regression models were used to characterise residential air pollution concentrations of ambient fine particulate matter (PM2.5), nitrogen dioxide, ozone, and black carbon.

MAIN OUTCOME MEASURES: Deaths due to natural causes and cause specific mortality.

RESULTS: Of 325 367 adults followed-up for an average of 19.5 years, 47 131 deaths were observed. Higher exposure to PM2.5, nitrogen dioxide, and black carbon was associated with significantly increased risk of almost all outcomes. An increase of 5 µg/m3 in PM2.5 was associated with 13% (95% confidence interval 10.6% to 15.5%) increase in natural deaths; the corresponding figure for a 10 µg/m3 increase in nitrogen dioxide was 8.6% (7% to 10.2%). Associations with PM2.5, nitrogen dioxide, and black carbon remained significant at low concentrations. For participants with exposures below the US standard of 12 µg/m3 an increase of 5 µg/m3 in PM2.5 was associated with 29.6% (14% to 47.4%) increase in natural deaths.

CONCLUSIONS: Our study contributes to the evidence that outdoor air pollution is associated with mortality even at low pollution levels below the current European and North American standards and WHO guideline values. These findings are therefore an important contribution to the debate about revision of air quality limits, guidelines, and standards, and future assessments by the Global Burden of Disease.

PMID:34470785 | DOI:10.1136/bmj.n1904

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Nevin Manimala Statistics

Risk of hospital admission with covid-19 among teachers compared with healthcare workers and other adults of working age in Scotland, March 2020 to July 2021: population based case-control study

BMJ. 2021 Sep 1;374:n2060. doi: 10.1136/bmj.n2060.

ABSTRACT

OBJECTIVE: To determine the risk of hospital admission with covid-19 and severe covid-19 among teachers and their household members, overall and compared with healthcare workers and adults of working age in the general population.

DESIGN: Population based nested case-control study.

SETTING: Scotland, March 2020 to July 2021, during defined periods of school closures and full openings in response to covid-19.

PARTICIPANTS: All cases of covid-19 in adults aged 21 to 65 (n=132 420) and a random sample of controls matched on age, sex, and general practice (n=1 306 566). Adults were identified as actively teaching in a Scottish school by the General Teaching Council for Scotland, and their household members were identified through the unique property reference number. The comparator groups were adults identified as healthcare workers in Scotland, their household members, and the remaining general population of working age.

MAIN OUTCOME MEASURES: The primary outcome was hospital admission with covid-19, defined as having a positive test result for SARS-CoV-2 during hospital admission, being admitted to hospital within 28 days of a positive test result, or receiving a diagnosis of covid-19 on discharge from hospital. Severe covid-19 was defined as being admitted to intensive care or dying within 28 days of a positive test result or assigned covid-19 as a cause of death.

RESULTS: Most teachers were young (mean age 42), were women (80%), and had no comorbidities (84%). The risk (cumulative incidence) of hospital admission with covid-19 was <1% for all adults of working age in the general population. Over the study period, in conditional logistic regression models adjusted for age, sex, general practice, race/ethnicity, deprivation, number of comorbidities, and number of adults in the household, teachers showed a lower risk of hospital admission with covid-19 (rate ratio 0.77, 95% confidence interval 0.64 to 0.92) and of severe covid-19 (0.56, 0.33 to 0.97) than the general population. In the first period when schools in Scotland reopened, in autumn 2020, the rate ratio for hospital admission in teachers was 1.20 (0.89 to 1.61) and for severe covid-19 was 0.45 (0.13 to 1.55). The corresponding findings for household members of teachers were 0.91 (0.67 to 1.23) and 0.73 (0.37 to 1.44), and for patient facing healthcare workers were 2.08 (1.73 to 2.50) and 2.26 (1.43 to 3.59). Similar risks were seen for teachers in the second period, when schools reopened in summer 2021. These values were higher than those seen in spring/summer 2020, when schools were mostly closed.

CONCLUSION: Compared with adults of working age who are otherwise similar, teachers and their household members were not found to be at increased risk of hospital admission with covid-19 and were found to be at lower risk of severe covid-19. These findings should reassure those who are engaged in face-to-face teaching.

PMID:34470747 | DOI:10.1136/bmj.n2060

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Nevin Manimala Statistics

Differences in the behaviour of trace and rare-earth elements in oxidizing and reducing soil environments: Case study of Terra Rossa soils and Cretaceous palaeosols from the Istrian peninsula, Croatia

Chemosphere. 2021 Jun 19;283:131286. doi: 10.1016/j.chemosphere.2021.131286. Online ahead of print.

ABSTRACT

This study compares the differences between the distribution of trace elements and rare-earth elements (REEs) formed under reducing and oxidizing soil conditions during pedogenesis on carbonate bedrock. Terra rossa (TR) soils, representing pedogenesis under oxic conditions, and Cretaceous palaeosols (CP), representing pedogenesis under reducing conditions, were sampled on the Istrian peninsula. They were studied by ICP-MS, ICP-OES, XRF, XRD, sequential extraction and statistical analyses. The differences in trace-element behaviour between the TR and CP stem from different redox conditions, but the most remarkable difference was observed in the behaviour of the REEs. Statistical analyses revealed that in TR soils all the REEs showed a very positive correlation, while in CPs the light REEs and heavy REEs showed an internal, very positive correlation. TR soils have almost twice as much REEs as CPs. This difference is pedogenetic, as both materials have a very similar amount of REEs in the residual fraction. While TR soils have the same amount of REEs in fractions other than the residual fraction, CPs have almost no REEs in these fractions. Different REE patterns obtained from sequential extraction, such as a middle-REE enrichment and a positive Ce anomaly in TR soils and light-REE depletion, heavy-REE enrichment, positive Ce and Eu anomalies in CPs, contributed to an understanding of the redox and pedogenetic processes. This study successfully emphasized the influence of different redox conditions on the behaviour of trace and rare-earth elements during pedogenesis on a carbonate bedrock and the ability of the REEs to track pedogenetic processes.

PMID:34470733 | DOI:10.1016/j.chemosphere.2021.131286

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Nevin Manimala Statistics

Avoiding bias in self-controlled case series studies of coronavirus disease 2019

Stat Med. 2021 Sep 1. doi: 10.1002/sim.9179. Online ahead of print.

ABSTRACT

Many studies, including self-controlled case series (SCCS) studies, are being undertaken to quantify the risks of complications following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19). One such SCCS study, based on all COVID-19 cases arising in Sweden over an 8-month period, has shown that SARS-CoV-2 infection increases the risks of AMI and ischemic stroke. Some features of SARS-CoV-2 infection and COVID-19, present in this study and likely in others, complicate the analysis and may introduce bias. In the present paper we describe these features, and explore the biases they may generate. Motivated by data-based simulations, we propose methods to reduce or remove these biases.

PMID:34470078 | DOI:10.1002/sim.9179

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Nevin Manimala Statistics

Real-time channel conditional distribution tracking for intelligent decoding of optical IMDD signals

Opt Lett. 2021 Sep 1;46(17):4426-4429. doi: 10.1364/OL.437740.

ABSTRACT

In this Letter, we propose a real-time machine learning scheme of a tracking optical intensity-modulation and direct-detection (IMDD) system’s conditional distribution using linear optical sampling and inline Gaussian mixer modeling (GMM) programming. End-to-end conditional distribution tracking enables an adaptive decoding of optical IMDD signals, with robustness to the bias point shift of the optical intensity modulator. Experimental demonstration is conducted over a 20-Gbits/s optical pulse amplitude modulation-4 (PAM-4) modulation system. Optical PAM-4 signals are optically down-sampled by short pulses to 250 Msa/s. Then, statistical characters of signal distribution can be estimated using inline GMM processing. Due to the real-time learned distribution, intelligent decoding of received signals exhibits a perfect adaptation to the changing bias point of a Mach-Zendner intensity modulator, enhancing the communication reliability with bit error rate (BER) below 3.8⋅10-3. In addition, the proposed scheme also provides the possibility of practical implementation to other machine learning signal decoding methods.

PMID:34470032 | DOI:10.1364/OL.437740

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Nevin Manimala Statistics

Simulation of statistically accurate time-integrated dynamic speckle patterns in biomedical optics

Opt Lett. 2021 Sep 1;46(17):4390-4393. doi: 10.1364/OL.435812.

ABSTRACT

The simulation of statistically accurate time-integrated dynamic speckle patterns using a physics-based model that accounts for spatially varying sample properties is yet to be presented in biomedical optics. In this Letter, we propose a solution to this important problem based on the Karhunen-Loève expansion of the electric field and apply our method to the formalisms of both laser speckle contrast imaging and diffuse correlation spectroscopy. We validate our technique against solutions for speckle contrast for different forms of homogeneous field and also show that our method can readily be extended to cases with spatially varying sample properties.

PMID:34470023 | DOI:10.1364/OL.435812

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Nevin Manimala Statistics

Deep diamond single-photon sources prepared by a femtosecond laser

Opt Lett. 2021 Sep 1;46(17):4386-4389. doi: 10.1364/OL.435799.

ABSTRACT

Nitrogen-vacancy color centers (NVs) in diamond have several potential applications ranging from quantum computing to data storage. However, artificial NVs are often close to the surface, which limits their spatial density and applicability. Here we demonstrate an effective and precise method for preparing deep single NVs in diamond. The method is based on a spatial-shaped femtosecond laser to overcome laser defocus in high-refractive materials, and realizes the preparation of single NVs at 95 µm. In addition, owing to the good energy distribution of the shaped laser focus, the single NVs exhibit a statistic yield of 56%±11% with excellent qualities. This processing method will contribute to the integration of color centers with emerging optical elements and high-density data storage.

PMID:34470022 | DOI:10.1364/OL.435799