Tag: statistics

BMC Bioinformatics. 2022 Nov 19;23(1):499. doi: 10.1186/s12859-022-05045-7.

ABSTRACT

BACKGROUND: Genotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and more complex. Moreover, the size of segregating populations remains constrained by cost issues and is less and less commensurate with the numbers of SNPs available. Thus, guaranteeing a statistically robust marker order requires that maps include only a carefully selected subset of SNPs.

RESULTS: In this context, the SeSAM software allows automatic genetic map construction using seriation and placement approaches, to produce (1) a high-robustness framework map which includes as many markers as possible while keeping the order robustness beyond a given statistical threshold, and (2) a high-density total map including the framework plus almost all polymorphic markers. During this process, care is taken to limit the impact of genotyping errors and of missing data on mapping quality. SeSAM can be used with a wide range of biparental populations including from outcrossing species for which phases are inferred on-the-fly by maximum-likelihood during map elongation. The package also includes functions to simulate data sets, convert data formats, detect putative genotyping errors, visualize data and map quality (including graphical genotypes), and merge several maps into a consensus. SeSAM is also suitable for interactive map construction, by providing lower-level functions for 2-point and multipoint EM analyses. The software is implemented in a R package including functions in C++.

CONCLUSIONS: SeSAM is a fully automatic linkage mapping software designed to (1) produce a framework map as robust as desired by optimizing the selection of a subset of markers, and (2) produce a high-density map including almost all polymorphic markers. The software can be used with a wide range of biparental mapping populations including cases from outcrossing. SeSAM is freely available under a GNU GPL v3 license and works on Linux, Windows, and macOS platforms. It can be downloaded together with its user-manual and quick-start tutorial from ForgeMIA (SeSAM project) at https://forgemia.inra.fr/gqe-acep/sesam/-/releases.

PMID:36402957 | DOI:10.1186/s12859-022-05045-7

Bone Marrow Transplant. 2022 Nov 19. doi: 10.1038/s41409-022-01870-9. Online ahead of print.

NO ABSTRACT

PMID:36402922 | DOI:10.1038/s41409-022-01870-9

Sci Rep. 2022 Nov 19;12(1):19932. doi: 10.1038/s41598-022-24457-2.

ABSTRACT

This paper is devoted to the synthesis of new signal processing algorithms based on the methodology of complete sufficient statistics and the possibility of using the Lehmann-Scheffe theorem. Using the example of a sequence of quasi-rectangular pulses, an approach to estimating their period was illustrated, taking into account the duty-off factor and the pulse squareness coefficient. A mathematical model was developed, on the basis of which, estimates of the potential accuracy of the methods were carried out. It is established that for the sample size value (n > 8), the relative root-mean-square error of estimating the repetition period using the methodology of complete sufficient statistics is lower than that of the traditional estimate. In addition to theoretical calculations, simulation results confirming the achieved effect are presented. The results obtained have a wide range of applicability and can be used in the design of control and measuring equipment in the oil and gas industry, in the development of medical equipment, in the field of telecommunications, in the design of pulse-Doppler radars, etc.

PMID:36402901 | DOI:10.1038/s41598-022-24457-2

Pacing Clin Electrophysiol. 2022 Nov 19. doi: 10.1111/pace.14625. Online ahead of print.

ABSTRACT

BACKGROUND: The percutaneous extraction of endovascular cardiostimulation and defibrillation leads is the most frequent technique nowadays. The tools used today must guarantee the success of the procedure, with the minimum of complications. Our objective was to analyze the safety and efficacy of lead extraction using the Evolution® mechanical dissection tool (Cook Medical, United States).

METHODS: A retrospective study was carried out in a total of 826 consecutive patients from October 2009 to December 2018 who underwent the procedure with the Evolution® mechanical dissection tool.Preoperative study included complete blood tests, echocardiogram, and chest X-ray. The procedures were performed in the operating room, under general anesthesia and echocardiographic control.

RESULTS: A total of 1227 leads were extracted with a mean chronicity of 10.3±5.1 years. Clinical success rate was 99.7%. A total of 16 (1.9%) complications occurred, 2 (0.24%) were major complications and 14 (1.7%) were minor complications. There was no operative mortality. There was no statistically significant relationship between implant chamber and complete efficacy. The complete extraction was achieved in all left ventricular leads, in 762 of 774 (98.45%) of right ventricular lead removal, and in 330 of 334 (98.8%) of right atrial leads (p = 0.31).

CONCLUSION: In our experience, percutaneous extraction of intravenous leads via the use of the Evolution® tool (Cook Medical, United States), is a very effective and safe technique that offers low morbidity and mortality. This article is protected by copyright. All rights reserved.

PMID:36401870 | DOI:10.1111/pace.14625

Adv Gerontol. 2022;35(4):485-491.

ABSTRACT

According to the Russian Society of Urologists, the frequency of infertility in marriage in the Russian Federation is 8-17,2%; half of the cases are associated with the male factor. Among the risk factors for the development of male infertility, there are mainly medical reasons, lifestyle factors and negative environmental factors. Despite the fact that the problem of infertility is addressed by men of different ages, from youth to the elderly, the correction of risk factors is usually carried out without taking into account the age of the patient, which makes it difficult to develop a personalized strategy for the treatment or prevention of infertility. The aim of the study was to study the structure of the leading risk factors for the development of infertility in men from infertile couples, to identify and characterize their age-associated features. The analysis of the medical histories of 1 198 men from infertile couples and the collection of information on all available risk factors for infertility were carried out. The analysis of age features was performed by dividing the sample into 5 age groups: 1st (n=271) – men ≤29,9 years; 2nd (n=415) – 30-34,9 years; 3rd (n=291) – 35-39,9 years; 4th (n=141) – 40-44,9 years; 5th (n=80) – ≥45 years. It was shown that in the general sample of medical causes, factors associated with chronic inflammation predominate: sexually transmitted infections (STIs) – 54%; prostatitis – 32%; obesity – 27%; from non-medical: alcohol – 73%; stress – 47%; smoking – 41%. With increasing age, the frequency of obesity, STIs, prostatitis, hepatitis B/C, mumps increases statistically significantly, while the most unfavorable group of men is 40-45 years old for factors such as STIs, hepatitis B/C and mumps, and the group of men over 45 years old for factors such as obesity and prostatitis.

PMID:36401856

Adv Gerontol. 2022;35(4):458-465.

ABSTRACT

The demographic situation of the Russian Federation is characterized by an aging population, which is a new challenge to achieve active and healthy longevity. The purpose of the study is to identify the factors influencing the increase in active longevity based on the results of the analysis of statistical data on the proportion of people over 60 years of age and life expectancy and sociological studies. On the basis of official statistics, the analysis of life expectancy, the proportion of people over 60 years old was carried out. The obtained data of the sociological study revealed that in order for the Russian Federation to follow the course of increasing active and healthy longevity, it must focus on the determinants of socio-economic character. On the basis of the age-shifting method, the forecast of the proportion of people over 60 years old was carried out (using the example of one of the regions of the Russian Federation). The Center for Family and Demography of the Academy of Sciences of the Republic of Tatarstan has developed recommendations for achieving active and healthy longevity, which are presented in the annual Demographic report of the Republic of Tatarstan, by improving health and reducing mortality.

PMID:36401852

J Bone Miner Res. 2022 Nov 19. doi: 10.1002/jbmr.4740. Online ahead of print.

ABSTRACT

Osteoporosis has traditionally been characterized by underlying endocrine mechanisms though evidence indicates a role of inflammation in its pathophysiology. Lipopolysaccharide (LPS), a component of gram-negative bacteria that reside in the intestines, can be released into circulation and stimulate the immune system, upregulating bone resorption. Exogenous LPS is used in rodent models to study the effect of systemic inflammation on bone and to date a variety of different doses, routes, and durations of LPS administration have been used. The study objective was to assess if systemic administration of LPS induces inflammatory bone loss in rodent models. A systematic search of Medline and 4 other databases resulted in a total of 110 studies that met the inclusion criteria. Pooled standardized mean differences (SMD) and corresponding 95% confidence intervals (CI) with a random-effects meta-analyses was used for bone volume fraction (BV/TV) and volumetric bone mineral density (vBMD). Heterogeneity was quantified using the I² statistic. Shorter-term (<2 weeks) and longer-term (>2 weeks) LPS interventions were analyzed separately because of intractable study design differences. BV/TV was significantly reduced in both shorter- (SMD = -3.79%, 95% CI [-4.20, -3.38], I² 62%; p < 0.01) and longer-term (SMD = -1.50%, 95% CI [-2.00, -1.00], I² 78%; p < 0.01) studies. vBMD was also reduced in both shorter- (SMD = -3.11%, 95% CI [-3.78, -2.44]; I² 72%; p < 0.01) and longer-term (SMD = -3.49%, 95% CI [-4.94, -2.04], I² 82%; p < 0.01) studies. In both groups, regardless of duration LPS negatively impacted trabecular bone structure, but not cortical bone structure, and an upregulation in bone resorption demonstrated by bone cell staining and serum biomarkers was reported. This suggests systemically delivered exogenous LPS in rodents is a viable model for studying inflammatory bone loss, particularly in trabecular bone. This article is protected by copyright. All rights reserved.

PMID:36401814 | DOI:10.1002/jbmr.4740

J Hepatobiliary Pancreat Sci. 2022 Nov 19. doi: 10.1002/jhbp.1279. Online ahead of print.

ABSTRACT

INTRODUCTION: Tumor size(TS) represents a critical parameter in the risk assessment of laparoscopic liver resections(LLR). Moreover, TS has been rarely related to the extent of liver resection. The aim of this study was to study the relationship between tumor size and difficulty of laparoscopic left lateral sectionectomy( L-LLS).

METHODS: The impact of TS cutoffs was investigated by stratifying tumor size at each 10mm-interval. The optimal cut-offs were chosen taking into consideration the number of endpoints which show a statistically significant split around the cut-points of interest and the magnitude of relative risk after correction for multiple risk factors.

RESULTS: 1910 L-LLS were included. Overall, open conversion and intraoperative blood transfusion were 3.1% and 3.3%, respectively. The major morbidity rate was 2.7% and 90-days mortality 0.6%. Three optimal TS cut-offs were identified: 40-mm, 70-mm, and 100-mm. All the selected cut-offs showed a significant discriminative power for the prediction of open conversion, operative time, blood transfusion and need of Pringle manoeuvre. Moreover, 70-mm and 100-mm cut-offs were both discriminative for estimated blood loss and major complications. A stepwise increase in rates of open conversion rate (Z=3.90,p<0.001), operative time (Z=3.84,p<0.001), blood loss (Z=6.50,p<0.001), intraoperative blood transfusion rate (Z=5.15,p<0.001), Pringle manoeuvre use (Z=6.48,p<0.001), major morbidity(Z=2.17,p=0.030) and 30-days readmission (Z=1.99, p=0.047) was registered as the size increased.

CONCLUSIONS: L-LLS for tumours of increasing size was associated with poorer intraoperative and early postoperative outcomes suggesting increasing difficulty of the procedure. We determined 3 optimal TS cutoffs(40-mm, 70-mm and 100-mm) to accurately stratify surgical difficulty after L-LLS.

PMID:36401813 | DOI:10.1002/jhbp.1279

Liver Int. 2022 Nov 19. doi: 10.1111/liv.15480. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: Non-alcoholic fatty liver disease (NAFLD) is associated with a high risk of cardiovascular disease. Whether risk scores developed in the general population accurately assess cardiovascular risk in the NAFLD population is unknown. This study aimed to evaluate the performance of the Pooled Cohort Equations (PCE) in NAFLD.

METHODS: Individuals in the Multi-Ethnic Study of Atherosclerosis with baseline non-contrast cardiac computed tomography scans with sufficient data to determine the presence of hepatic steatosis were identified and assessed for the development of incident 10-year atherosclerotic cardiovascular disease. The discrimination and calibration of the PCE were evaluated, and the observed and expected events by risk category (<5%, 5-<7.5%, 7.5-<20%, ≥20%) were determined. Risk reclassification with addition of NAFLD to the PCE was assessed.

RESULTS: Of 4,014 participants included, 698 (17.4%) with NAFLD were identified, including 247 (35.3%) with moderate-to-severe steatosis. Discrimination of the PCE was suboptimal in NAFLD (c-statistic 0.69), particularly moderate-to-severe steatosis (0.65), and calibration was overall poor. While risk was overestimated in non-NAFLD, it was underestimated in NAFLD in lower/intermediate risk categories, predominantly in women (5-<7.5% observed/expected ratio = 1.67). Addition of NAFLD to the PCE improved risk classification in women.

CONCLUSIONS: The PCE overall performed suboptimally in cardiovascular risk assessment in NAFLD, particularly in women and individuals with moderate-to-severe steatosis in clinically relevant risk categories. Primary prevention may need to be considered at a lower risk threshold in these groups, and further work is needed to improve risk stratification in this growing high-risk population.

PMID:36401810 | DOI:10.1111/liv.15480

Epilepsia. 2022 Nov 19. doi: 10.1111/epi.17471. Online ahead of print.

ABSTRACT

OBJECTIVE: A realistic seizure diary simulator is currently unavailable for many research needs, including clinical trial analysis, and evaluation of seizure detection and seizure forecasting tools. In recent years, important statistical features of seizure diaries have been characterized. These include: (1) heterogeneity of individual seizure frequencies, (2) the relation between average seizure rate and standard deviation, (3) multiple risk cycles, (4) seizure clusters, and (5) limitations on inter-seizure intervals. The present study unifies these features into a single model.

METHODS: Our approach, Cyclic Heterogeneous Overdispersed Clustered Open-source L-relationship Adjustable Temporally limited E-diary Simulator (CHOCOLATES) is based on a hierarchical model centered on a Gamma Poisson generator with several modifiers. This model accounts for the aforementioned statistical properties. The model was validated by simulating 10,000 randomized clinical trials (RCTs) of medication to compare with 23 historical RCTs. Metrics of 50% responder rate (RR50) and median percent change (MPC) were evaluated. We also used CHOCOLATES as input to a seizure forecasting tool to test the flexibility of the model. We examined the area under the ROC curve (AUC) for test data with and without cycles and clusters.

RESULTS: The model recapitulated typical findings in 23 historical RCTs without the necessity of introducing an additional “placebo effect”. The model produced the following RR50 values: placebo: 17±4%; drug 38±5%; and the following MPC values: placebo: 13±6%; drug 40±4%. These values are similar to historical data: for RR50: placebo, 21±10%, drug: 43±13%; and for MPC: placebo: 17±10%, drug: 41±11%. The seizure forecasts achieved AUC of 0.68 with cycles and clusters, whereas without them the AUC was 0.51.

SIGNIFICANCE: CHOCOLATESrepresents the most realistic seizure occurrence simulator to date, based on observations from thousands of patients in different contexts. This tool is open-source and flexible, and can be used for many applications, including clinical trial simulation and testing of seizure forecasting tools.

PMID:36401798 | DOI:10.1111/epi.17471