Tag: nevin manimala

BMC Med Res Methodol. 2023 Apr 5;23(1):83. doi: 10.1186/s12874-023-01901-z.

ABSTRACT

BACKGROUND: National mortality statistics are based on a single underlying cause of death. This practice does not adequately represent the impact of the range of conditions experienced in an ageing population in which multimorbidity is common.

METHODS: We propose a new method for weighting the percentages of deaths attributed to different causes that takes account of the patterns of associations among underlying and contributing causes of death. It is driven by the data and unlike previously proposed methods does not rely on arbitrary choices of weights which can over-emphasise the contribution of some causes of death. The method is illustrated using Australian mortality data for people aged 60 years or more.

RESULTS: Compared to the usual method based only on the underlying cause of death the new method attributes higher percentages of deaths to conditions like diabetes and dementia that are frequently mentioned as contributing causes of death, rather than underlying causes, and lower percentages to conditions to which they are closely related such as ischaemic heart disease and cerebrovascular disease. For some causes, notably cancers, which are usually recorded as underlying causes with few if any contributing causes the new method produces similar percentages to the usual method. These different patterns among groups of related conditions are not apparent if arbitrary weights are used.

CONCLUSION: The new method could be used by national statistical agencies to produce additional mortality tables to complement the current tables based only on underlying causes of death.

PMID:37020203 | DOI:10.1186/s12874-023-01901-z

BMC Bioinformatics. 2023 Apr 5;24(1):135. doi: 10.1186/s12859-023-05169-4.

ABSTRACT

BACKGROUND: Population structure and cryptic relatedness between individuals (samples) are two major factors affecting false positives in genome-wide association studies (GWAS). In addition, population stratification and genetic relatedness in genomic selection in animal and plant breeding can affect prediction accuracy. The methods commonly used for solving these problems are principal component analysis (to adjust for population stratification) and marker-based kinship estimates (to correct for the confounding effects of genetic relatedness). Currently, many tools and software are available that analyze genetic variation among individuals to determine population structure and genetic relationships. However, none of these tools or pipelines perform such analyses in a single workflow and visualize all the various results in a single interactive web application.

RESULTS: We developed PSReliP, a standalone, freely available pipeline for the analysis and visualization of population structure and relatedness between individuals in a user-specified genetic variant dataset. The analysis stage of PSReliP is responsible for executing all steps of data filtering and analysis and contains an ordered sequence of commands from PLINK, a whole-genome association analysis toolset, along with in-house shell scripts and Perl programs that support data pipelining. The visualization stage is provided by Shiny apps, an R-based interactive web application. In this study, we describe the characteristics and features of PSReliP and demonstrate how it can be applied to real genome-wide genetic variant data.

CONCLUSIONS: The PSReliP pipeline allows users to quickly analyze genetic variants such as single nucleotide polymorphisms and small insertions or deletions at the genome level to estimate population structure and cryptic relatedness using PLINK software and to visualize the analysis results in interactive tables, plots, and charts using Shiny technology. The analysis and assessment of population stratification and genetic relatedness can aid in choosing an appropriate approach for the statistical analysis of GWAS data and predictions in genomic selection. The various outputs from PLINK can be used for further downstream analysis. The code and manual for PSReliP are available at https://github.com/solelena/PSReliP .

PMID:37020193 | DOI:10.1186/s12859-023-05169-4

BMC Infect Dis. 2023 Apr 5;23(1):201. doi: 10.1186/s12879-023-08203-1.

ABSTRACT

BACKGROUND: Both post-COVID-19 condition (long COVID) and the presence of persisting symptoms that do not meet formal definitions of post-COVID-19-condition may adversely affect quality of life and function. However, their prevalence among children and young people in England is unclear.

METHODS: We used data from repeated surveys in a large cohort of English schoolchildren from the COVID-19 Schools Infection Survey (SIS) for the school year 2021/22 to describe the weighted prevalence of post-COVID-19-condition and compare persisting symptoms between individuals with a positive SARS-CoV-2 test and those with neither a positive test history nor suspected infection.

RESULTS: Among 7797 children from 173 schools, 1.8% of primary school pupils (aged 4 to 11 years), 4.5% of secondary school pupils in years 7-11 (aged 11 to 16 years) and 6.9% of those in years 12-13 (aged 16 to 18 years) met a definition of post-COVID-19 condition in March 2022. Specific persisting symptoms such as anxiety or difficulty concentrating were frequently reported regardless of prior infection status and increased with age: 48.0% of primary school pupils, 52.9% of secondary school pupils in years 7-11 and 79.5% in years 12-13 reporting at least one symptom lasting more than 12 weeks. Persisting loss of smell and taste, cardiovascular and some systemic symptoms were more frequently reported by those with a previous positive test.

CONCLUSIONS: We showed that ongoing symptoms were frequently reported by English schoolchildren regardless of SARS-CoV-2 test results and some specific symptoms such as loss of smell and taste were more prevalent in those with a positive test history. Our study emphasises the wide-ranging impacts of the COVID-19 pandemic on the health and wellbeing of children and young people.

PMID:37020190 | DOI:10.1186/s12879-023-08203-1

Ann Biomed Eng. 2023 Apr 5. doi: 10.1007/s10439-023-03193-2. Online ahead of print.

ABSTRACT

Platelet adhesion to blood vessel walls is a key initial event in thrombus formation in both vascular disease processes and prosthetic cardiovascular devices. We extended a deformable multiscale model (MSM) of flowing platelets, incorporating Dissipative Particle Dynamics (DPD) and Coarse-Grained Molecular Dynamics (CGMD) describing molecular-scale intraplatelet constituents and their interaction with surrounding flow, to predict platelet adhesion dynamics under physiological flow shear stresses. Binding of platelet glycoprotein receptor Ibα (GPIbα) to von Willebrand factor (vWF) on the blood vessel wall was modeled by a molecular-level hybrid force field and validated with in vitro microchannel experiments of flowing platelets at 30 dyne/cm². High frame rate videos of flipping platelets were analyzed with a Semi-Unsupervised Learning System (SULS) machine learning-guided imaging approach to segment platelet geometries and quantify adhesion dynamics parameters. In silico flipping dynamics followed in vitro measurements at 15 and 45 dyne/cm² with high fidelity, predicting GPIbα-vWF bonding and debonding processes, distribution of bonds strength, and providing a biomechanical insight into initiation of the complex platelet adhesion process. The adhesion model and simulation framework can be further integrated with our established MSMs of platelet activation and aggregation to simulate initial mural thrombus formation on blood vessel walls.

PMID:37020171 | DOI:10.1007/s10439-023-03193-2

Eur Spine J. 2023 Apr 5. doi: 10.1007/s00586-023-07675-8. Online ahead of print.

ABSTRACT

BACKGROUND: The microsurgical anterior approach to the cervical spine is commonplace. Fewer surgeons perform posterior cervical microsurgical procedures on a routine basis for lack of indication, more bleeding, persistent postoperative neck pain, and risk of progressive misalignment. In comparison, the endoscopic technique is preferentially performed through the posterior approach. Many spine surgeons and even surgeons versed in lumbar endoscopy are often reluctant to consider endoscopic procedures in the cervical spine. We report the results of a surgeon survey to find out why.

METHODS: A questionnaire of 10 questions was sent to spine surgeons by email and chat groups in social media networks including Facebook, WeChat, WhatsApp, and LinkedIn to collect practice pattern data about microscopic and endoscopic spine surgery in the lumbar and cervical spine. The responses were cross-tabulated by surgeons’ demographic data. Pearson Chi-Square measures, Kappa statistics, and linear regression analysis of agreement or disagreement were performed by analyzing the distribution of variances using the statistical package SPSS Version 27.0.

RESULTS: The survey response rate was 39.7%, with 50 of the 126 surgeons who started the survey submitting a completed questionnaire. Of the 50 surgeons, 56.2% were orthopedic, and 42% neurological surgeons. Most surgeons worked in private practice (42%). Another 26% were university-employed, 18% were in private practice affiliated with a university, and the remaining 14% were hospital employed. The majority of surgeons (55.1%) were autodidacts. The largest responding surgeon groups were between 35-44 years (38%) and between 45-54 years of age (34%). Half of the responding surgeons were routinely performing endoscopic cervical spine surgery. The other half did not perform it for the main hurdle of fear of complications (50%). Lack of appropriate mentorship was listed as second most reason (25.4%). More concerns for not performing cervical endoscopic approaches were the perception of lack of technology (20.8%) and suitable surgical indication (12.5%). Only 4.2% considered cervical endoscopy too risky. Nearly a third (30.6%) of the spine surgeons treated over 80% of their cervical spine patients with endoscopic surgeries. Most commonly performed were posterior endoscopic cervical discectomy (PECD; 52%), posterior endoscopic cervical foraminotomy (PECF; 48%), anterior endoscopic cervical discectomy (AECD; 32%), cervical endoscopic unilateral laminotomy for bilateral decompression (CE-ULBD; 30%), respectively.

CONCLUSION: Cervical endoscopic spine surgery is gaining traction among spine surgeons. However, by far most surgeons performing cervical endoscopic spine surgery work in private practice and are autodidacts. This lack of a teacher to shorten the learning curve as well as fear of complications are two of the major impediments to the successful implementation of cervical endoscopic procedures.

PMID:37020150 | DOI:10.1007/s00586-023-07675-8

Biochem Genet. 2023 Apr 5. doi: 10.1007/s10528-023-10371-3. Online ahead of print.

ABSTRACT

The anti-inflammatory adipokine intelectin-1, which is encoded by the ITLN1 gene, is hypothesized to be linked to the pathogenesis of type 2 diabetes (T2DM) and obesity. The purpose of this study was to examine the effect of the ITLN1 gene polymorphism rs2274907 on obesity and T2DM in Turkish adults. The impact of genotype on lipid profiles and serum intelectin levels in the obese and diabetes groups was also investigated. Randomly selected 2266 adults (mean age, 55.0 ± 11.7 years; 51.2% women) participating in the population-based Turkish adult risk factor study were cross-sectionally analyzed. The genotyping of rs2274907 A > T polymorphism was performed by using the hybridization probe based LightSNiP assay in real-time PCR. T2DM were defined using the criteria of the American Diabetes Association. Obesity was described as Body mass index ≥ 30 kg/m². Statistical analyses were used to investigate the association of genotypes with clinical and biochemical measurements. According to findings, there was no vital connection between the rs2274907 polymorphism and obesity, T2DM, or serum intelectin-1 level. The TA+AA carriers had significantly higher triglyceride levels (p = 0.007) compared with the TT carriers in both obese and T2DM women when adjusted for relevant covariates. ITLN1 rs2274907 polymorphism is not correlated with the risk of obesity and T2DM and not affect serum ITLN1 levels in Turkish adults. However, this polymorphism appears to be important in regulating triglyceride levels in obese and diabetic women.

PMID:37020118 | DOI:10.1007/s10528-023-10371-3

Sci Rep. 2023 Apr 5;13(1):5562. doi: 10.1038/s41598-023-32781-4.

ABSTRACT

The control chart is the most valuable tool in the manufacturing process to track the output process in the industries. Quality specialists always want a visual framework that recognizes sustainable improvements in the monitoring processes. The efficiency of a control chart is increased by utilizing a memory-based estimator or by using any extra information relevant to the key variable. In this study, we present Extended EWMA (EEWMA) and EWMA based monitoring charts for observing the process location using moving average (MA) statistic under two different situations, i.e., when some extra information is known and unknown. We also propose an EEWMA control chart using Auxiliary Information. The output of these charts is evaluated and contrasted to the various existing charts on the basis of average run length (ARL). The comparison indicates that the proposed charts outperform rivals in identifying all types of shifts in the process location parameter. The implementation of these plans is also rendered to incorporate them in a practical situation.

PMID:37020111 | DOI:10.1038/s41598-023-32781-4

Breast Cancer Res Treat. 2023 Apr 5. doi: 10.1007/s10549-023-06903-5. Online ahead of print.

ABSTRACT

PURPOSE: Women with preeclampsia are more likely to deliver preterm. Reports of inverse associations between preeclampsia and breast cancer risk, and positive associations between preterm birth and breast cancer risk are difficult to reconcile. We investigated the co-occurrence of preeclampsia/gestational hypertension with preterm birth and breast cancer risk using data from the Premenopausal Breast Cancer Collaborative Group.

METHODS: Across 6 cohorts, 3096 premenopausal breast cancers were diagnosed among 184,866 parous women. We estimated multivariable hazard ratios (HR) and 95% confidence intervals (CI) for premenopausal breast cancer risk using Cox proportional hazards regression.

RESULTS: Overall, preterm birth was not associated (HR 1.02, 95% CI 0.92, 1.14), and preeclampsia was inversely associated (HR 0.86, 95% CI 0.76, 0.99), with premenopausal breast cancer risk. In stratified analyses using data from 3 cohorts, preterm birth associations with breast cancer risk were modified by hypertensive conditions in first pregnancies (P-interaction = 0.09). Preterm birth was positively associated with premenopausal breast cancer in strata of women with preeclampsia or gestational hypertension (HR 1.52, 95% CI: 1.06, 2.18), but not among women with normotensive pregnancy (HR = 1.09, 95% CI: 0.93, 1.28). When stratified by preterm birth, the inverse association with preeclampsia was more apparent, but not statistically different (P-interaction = 0.2), among women who did not deliver preterm (HR = 0.82, 95% CI 0.68, 1.00) than those who did (HR = 1.07, 95% CI 0.73, 1.56).

CONCLUSION: Findings support an overall inverse association of preeclampsia history with premenopausal breast cancer risk. Estimates for preterm birth and breast cancer may vary according to other conditions of pregnancy.

PMID:37020102 | DOI:10.1007/s10549-023-06903-5

ESMO Open. 2023 Apr 3;8(2):101205. doi: 10.1016/j.esmoop.2023.101205. Online ahead of print.

ABSTRACT

BACKGROUND: Both acute and chronic symptoms of oxaliplatin-induced peripheral neuropathy (OIPN) affect patients’ treatment dose and duration as well as quality-of-life. Hand/foot-cooling has been shown to reduce taxane-induced peripheral neuropathy but there is unclear evidence in the setting of oxaliplatin.

PATIENTS AND METHODS: In a monocentric, open-label phase II trial, patients with malignancies of the digestive system receiving oxaliplatin-based chemotherapy were randomly assigned to receive either continuous cooling of hands and feet using hilotherapy at 11°C during oxaliplatin infusion compared with usual care (no cooling). The primary endpoint was grade ≥2 neuropathy-free rate in 12 weeks after initiation of chemotherapy. Secondary endpoints included OIPN-related treatment alterations, acute OIPN symptoms and perceived comfort of the intervention.

RESULTS: The intention-to-treat population included 39 patients in the hilotherapy group and 38 in the control group. The grade ≥2 neuropathy-free rate at 12 weeks was 100% in the experimental group versus 80.5% in the control group (P = 0.006). This effect was persistent at 24 weeks (66.0% versus 49.2%, respectively) (P = 0.039). Next, treatment alterations-free rate at week 12 was 93.5% in the hilotherapy group compared with 83.3% in the control group (P = 0.131). Patients in the hilotherapy group experienced significantly less acute OIPN symptoms of numbness or tingling [odds ratio (OR) 0.05, 95% confidence interval (CI) 0.02-0.11, P < 0.0001], pain (OR 0.06, 95% CI 0.02-0.15, P < 0.0001) and/or cold sensitivity (OR 0.02, 95% CI 0.01-0.05, P < 0.0001) in fingers or toes as well as less pharyngeal cold sensitivity (OR 0.14, 95% CI 0.05-0.42, P = 0.0005). The majority of patients in the hilotherapy group rated the intervention as neutral, rather comfortable or very comfortable.

CONCLUSIONS: In this first study on hand/foot-cooling in oxaliplatin alone, hilotherapy significantly reduced the incidence of grade ≥2 OIPN at 12 and 24 weeks. Hilotherapy also reduced acute OIPN symptoms and was generally well tolerated.

PMID:37018872 | DOI:10.1016/j.esmoop.2023.101205

Eur J Obstet Gynecol Reprod Biol. 2023 Apr 1;285:1-6. doi: 10.1016/j.ejogrb.2023.03.044. Online ahead of print.

ABSTRACT

BACKGROUND: Medical practice relies on reliable research observations. Whether such observations are true is traditionally tested by hypotheses and expressed with P-values. A strict P-value driven interpretation could potentially deny benefits of treatment.

OBJECTIVE: A strict P-value driven interpretation was compared to a context driven causality interpretation using the Bradford Hill Criteria to determine the clinical benefit of an intervention.

METHODS: We searched all randomised controlled trials in Women’s Health, published in five leading medical journals since January 2014. These were then scored using the 10 Bradford Hill Criteria for causation. Each component of the Bradford Hill Criteria was given a score from zero to three, resulting in a total score between zero and 30 for each article, converted into a decimal value. These scores were then compared to conclusions based on the p-value and conclusions drawn by the authors. For results discordant between Bradford Hill Criteria and P-values, we compared results with meta-analysis.

RESULTS: We found 68 articles for extraction of data. Of these, 49 (72%) showed concordance between Bradford Hill criteria and p-value driven interpretation, 25 (37%) of the articles reporting effectiveness (true positive), and 24 (35%) reporting no effectiveness (true negative). In eight (12%) articles, Bradford Hill criteria scores suggested effetiveness while p-values driven interpretation did not. Seven of those eight articles had p-values between 0.05 and 0.10. Out of these eight articles, six had a subsequent meta-analysis’ published on the intervention being studied. All six meta-analysis demonstrated effetiveness of the intervention.

CONCLUSIONS: In the interpretation of clinical trials, a context driven interpretation of causality may be more clinically informative than a strict P-value driven approach.

PMID:37018860 | DOI:10.1016/j.ejogrb.2023.03.044