Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of Sarcopenia in Africa: A Systematic Review

Objective The world population gradually getting older, age-related sarcopenia is becoming more frequent. Known to be highly prevalent in high income countries, relative data in Africa are still scarce. This review aims to estimate the prevalence of sarcopenia in Africa and its characteristics. Study Design and Setting A literature search in PubMed, Web of Science, Google Scholar, and Scopus was conducted in October 2022. All studies reporting the prevalence of sarcopenia in Africa within 15 years were included, and we did an assessment of bias with Hoy et al's risk bias assessment tool. The estimated prevalence of sarcopenia was the outcome and we performed secondary analyses by age, gender, and diagnostic criteria. The random effect model was used for the prevalence estimation. The prevalence of sarcopenia and 95% confidence interval (95% CI) were calculated using the inverse-variance method. Results A total of 17 studies met our eligibility criteria, for a study population of 12,690 participants with 44.3% males and 55.7% females. The overall prevalence of sarcopenia was 25% (95% CI: 19–30%). The prevalence of sarcopenia among 50 years old and older was 23% (95% CI: 17–29%). We had a higher prevalence of sarcopenia among males (30%, %95 IC: 20–39%) than females (29%, %95 IC: 21–36%). The prevalence of sarcopenia was different depending on the diagnosis criteria used. Conclusion The prevalence of sarcopenia in Africa was relatively high. However, the fact that the majority of included studies were hospital-based studies shows the necessity of further community-based studies in order to have a more accurate representation of the situation in the general population.
CXCL12 and CXCR4 as Potential Early Biomarkers for Luminal A and Luminal B Subtypes of Breast Cancer

Purpose Breast cancer is the most common type of malignancy in women. Factors that increase the risk of occurrence include chronic inflammation, with chemokines as its mediators. Therefore, the purpose of the present study was to determine the diagnostic utility of CXCL12 and CXCR4 as modern tumor markers in patients with early-stage luminal A and luminal B subtype of breast cancer and also to compare the results with the routinely used marker – CA 15-3. Patients and Methods The study included 100 patients with early breast cancer of luminal A and B subtypes, 50 women with benign breast lesion and 50 healthy women. The levels of CXCL12 and CXCR4 concentrations were determined by enzyme-linked immunosorbent assay (ELISA), comparative marker CA 15-3 – by electrochemiluminescence method (ECLIA). Results Concentrations of CXCL12 were significantly lower, while CXCR4 and CA 15-3 – significantly higher among patients with early-stage breast cancer than healthy women. CXCL12 also showed lower concentrations among fibroadenoma patients in comparison to healthy women, while CXCR4 – lower concentrations among fibroadenoma patients than cancer group. CXCL12 showed significantly higher values of sensitivity (79%), specificity (82%), positive predictive value (89.72%), negative predictive value (80%), diagnostic accuracy (80%) and diagnostic power (AUC = 0.8196) in the whole breast cancer group compared to the CA 15-3 marker (58%; 72%; 80.56%; 46.15%, 62.67%, 0.6434, resp.). Analysis of combined parameters resulted in increased sensitivity, negative predictive value and power of the test with a slight decrease in positive predictive value and a more significant decrease in specificity, reaching the best values for the three-parameter test CXCL12+CXCR4+CA15-3 (96%; 85.71%; AUC = 0.8812; 78.69%; 48%, resp.). Conclusion The results indicate the preliminary usefulness of CXCL12 and CXCR4 as early biomarkers in the diagnosis of breast cancer, especially in the combined panel with CA 15-3.
Local Optima of Nonconvex Regularized M-Estimators

Local Optima of Nonconvex Regularized M -Estimators by Po-Ling Loh Master of Science in Computer Science University of California, Berkeley Professor Martin Wainwright, Chair We establish theoretical results concerning all local optima of various regularized M estimators, where both loss and penalty functions are allowed to be nonconvex. Our results show that as long as the loss function satisfies restricted strong convexity and the penalty function satisfies suitable regularity conditions, any local optimum of the composite objective function lies within statistical precision of the true parameter vector. Our theory covers a broad class of nonconvex objective functions, including corrected versions of the Lasso for error-in-variables linear models; regression in generalized linear models using nonconvex regularizers such as SCAD and MCP; and graph and inverse covariance matrix estimation. On the optimization side, we show that a simple adaptation of composite gradient descent may be used to compute a global optimum up to the statistical precision stat in log(1/ stat) iterations, which is the fastest possible rate of any first-order method. We provide a variety of simulations to illustrate the sharpness of our theoretical predictions.
An application of Dirichlet process in clustering subjects via variance shift models: A course-evaluation study

In this article, the Dirichlet process (DP) is applied to cluster subjects with longitudinal observations. The basis of clustering is the ability of subjects to adapt themselves to new circumstances. Indeed, the basis of clustering depends on the time of changing response variability. This is done by providing a random change-point time in the variance structure of mixed-effects models. The DP is assumed as a prior for the distribution of the random change point. The discrete nature of the DP is utilized to cluster subjects according to the time of adaption. The proposed model is useful to identify groups of subjects with distinctive time-based progressions or declines. Transition mixed-effects models are also used to account for the serial correlation among observations over time. A joint modelling approach is utilized to handle the bias created in these models. The Gibbs sampling technique is adopted to achieve parameter estimates. Performance of the proposed method is evaluated via conducting a simulation study. The usefulness of the proposed model is assessed on a course-evaluation dataset.
Population Pharmacokinetics of Oral Azacitidine, and Exposure–Response Analysis in Acute Myeloid Leukemia

Oral azacitidine (oral‐AZA) maintenance is approved for adults with acute myeloid leukemia (AML) in remission post‐intensive chemotherapy, not proceeding to hematopoietic stem cell transplantation. This study aimed to develop a population pharmacokinetic (PopPK) model to characterize oral‐AZA concentration–time profiles in patients with AML, myelodysplastic syndrome, or chronic myelomonocytic leukemia. PopPK‐estimated exposure parameters were used to evaluate exposure–response relationships in the phase III QUAZAR AML‐001 study. The PopPK dataset comprised 286 patients with 1,933 evaluable oral‐AZA concentration records. The final PopPK model was a one‐compartment model with first‐order absorption incorporating an absorption lag time and first‐order elimination. Regression analyses identified two oral‐AZA exposure parameters (area under the plasma concentration–time curve at steady state (AUCss); maximum plasma concentration (Cmax)) as statistically significant predictors for relapse‐free survival (hazard ratio (HR) = 0.521, P < 0.001; HR = 0.630, P = 0.013; respectively), and AUCss as a significant predictor for overall survival (HR = 0.673, P = 0.042). The probability of grade ≥ 3 neutropenia was significantly increased with increases in AUCss (odds ratio (OR) = 5.71, 95% confidence interval (CI) = 2.73–12.62, P < 0.001), cumulative AUC through cycles 1 to 6 (OR = 2.71, 95% CI = 1.76–4.44, P < 0.001), and Cmax at steady‐state (OR = 2.38, 95% CI = 1.23–4.76, P = 0.012). A decreasing trend was identified between AUCss and relapse‐related schedule extensions, vs. an increasing trend between AUCss and event‐related dose reductions. As the majority (56.8%) of patients required no dose modifications, and the proportions requiring schedule extension (19.4%) or dose reduction (22.9%) were almost equal, oral‐AZA 300 mg once daily for 14 days is the optimal dosing schedule balancing survival benefit and safety risk.
Isogeometric Analysis and Shape Optimization in Fluid Mechanics

This paper deals with isogeometric analysis of the 2-dimens ional, steady state, incompressible Navier-Stokes equation subjected to Dirichlet boundary conditions. We presen t a detailed description of the numerical method used to solve the boundary value problem. Numerical inf-sup stabil ity tests for the simplified Stokes problem confirm the existence of many stable discretizations of the velocity an d pressure spaces, and in particular show that stability may be achieved by means of knot refinement of the velocity space. Error convergence studies for the full Navier-Stokes problem show optimal convergence rates for this type of disc retizations. Finally, a comparison of the results of the method to data from the literature for the the lid-driven squ are cavity for Reynolds numbers up to 10,000 serves as benchmarking of the discretizations and confirms the robust nes of the method.
Simulating the dynamics of harmonically trapped Weyl particles with cold atoms

During my PhD, I contributed to the design and construction of the Fermix experiment, dedicated to the study of a 6Li-40K fermionic mixture at ultra low temperatures. Our main results are twofold. First, we developed a new sub-Doppler laser cooling scheme, taking advantage of the existence of dark states in the D1 line of alkali atoms. This so-called \emph{grey molasses} allows for a phase space density up to $10^{-4}$, the highest value reported for the simultaneous laser cooling of those two species. The improvement due to this cooling step enabled the production of a quantum degenerate 40K gas in a dipole trap, with 3x10^5 atoms in two spin states at 62 nK, corresponding to 17% of the Fermi temperature. Second, introducing a canonical mapping, we showed that non-interacting ultra-relativistic particles (Weyl fermions) in a harmonic trap can be simulated by cold fermions confined in a quadrupole potential. We study experimentally, numerically and theoretically the relaxation of these systems towards a steady state which can not be described by a Boltzman distribution, but rather presents strongly anisotropic effective temperatures. This analogy also allows us to translate fundamental properties of relativistic particles in the language of cold atoms. In particular, we demonstrate that the Klein paradox is equivalent to Majorana losses.Finally, we present a theoretical study of the long range interactions between particles confined in two 2D layers immersed in a 3D atomic cloud.
Temperature-Dependent Optical Properties of Single Crystalline and Polycrystalline Silver Thin Films

Silver holds a unique place in plasmonics compared to other noble metals owing to its low losses in the visible and near-IR wavelength ranges. With a growing interest in local heating and high temperature applications of plasmonics, it is becoming critical to characterize the dielectric function of nanometer-scale thin silver films at higher temperatures, especially near the breakdown temperature, which depends on the film thickness and crystallinity. So far, such a comprehensive study has been missing. Here we report the in situ high temperature ellipsometry measurements of ultrasmooth and epitaxial quality crystalline silver films, along with electron beam evaporated polycrystalline silver films at temperatures up to 700 °C, in the wavelength range of 330–2000 nm. Our findings show that the dielectric function of all the films changes remarkably at elevated temperatures with larger relative changes observed in polycrystalline films. In addition, low-loss epitaxial films were found to be thermally more s.
Examining Cases of Child Physical Abuse Evaluations to Identify Opportunities to Improve Intimate Partner Violence Screening in Pediatric Emergency Departments

The association between child maltreatment and intimate partner violence (IPV) is well supported. Universal IPV screening has been recommended by the American Academy of Pediatrics and the United States Preventative Task Force, and many children’s hospitals have established screening protocols. However, the yield and best screening method in families undergoing a child physical abuse (PA) evaluation have not been fully explored. To determine if there is a discrepancy in IPV disclosures between universal IPV screening completed during pediatric emergency department (PED) triage (“triage screening”) and IPV screening by a social worker (“social work screening”) in families of children who were evaluated for PA. Caregivers of children who presented to an urban tertiary PED and underwent an evaluation for PA via a child abuse pediatrics consult. A retrospective chart review was completed. Data collection included: caregiver responses to both triage screening and social work screening, interview setting details and participants, the child’s injuries, and details of the family’s reported IPV experiences. Our study (N = 329) revealed that social work screening produced significantly more positive IPV disclosures than triage screening (14.0% vs. 4.3%, p < .001). Additionally, non-IPV violence concerns were identified in 35.7% (n = 5) of the positive triage screens, whereas social work screens had none. These results highlight the benefits of IPV screening by social work in high-risk scenarios, such as child PA evaluations, regardless of universal IPV screening results. Exploring differences between the two screening methods can inform decisions about screening protocols to improve IPV identification in high-risk populations.
A Discrete Model for Nonlinear Vibration of Beams Resting on Various Types of Elastic Foundations

This paper presents a discrete physical model to approach the problem of nonlinear vibrations of beams resting on elastic foundations. The model consists of a beam made of several small bars, evenly spaced. The bending stiffness is modeled by spiral springs, and the Winkler soil stiffness is modeled using linear vertical springs. Concentrated masses, presenting the inertia of the beam, are located at the bar ends. Finally, the nonlinear effect is presented by the axial forces in the bars, assumed to behave as longitudinal springs, due to the change in their length induced by the Pythagorean Theorem. This model has the advantage of simplifying parametric studies, because of its discrete nature, allowing any modification in the mass matrix, the stiffness matrix, and the nonlinearity tensor to be made separately. Therefore, once the model is established, various practical applications may be performed without the need of going through all the formulation again. The study of the nonlinear behavior makes the solution of the movement equation rise in complexity. By considering this discrete model and using the linearization method, one can achieve an idealized approach to this nonlinear problem and obtain quite easily approximate solutions.
Dynamique algébrique des applications rationnelles de surfaces

Cette these se se compose de trois parties. La premiere partie est consacree a l'etude des points periodiques des applications birationnelles des surfaces projectives. Nous montrons que toute application birationnelle de surface dont la croissance des degres est exponentielle admet un ensemble de points periodiques Zariski dense. Dans la seconde partie, nous demontrons la conjecture de Mordell-Lang dynamique pour toute application polynomiale birationnelle du plan affine definie sur un corps de caracteristique nulle. Notre approche donne une nouvelle demonstration de cette conjecture pour les automorphismes polynomiaux du plan. Enfin la troisieme partie porte sur un probleme de geometrie affine inspire par la generalisation au cas de toutes les applications polynomiales du plan affine de la conjecture de Mordell-Lang dynamique. Etant donne un ensemble fini S de valuations sur l'anneau de polynomes k[x,y] sur un corps algebriquement clos k triviales sur k, nous donnons une condition necessaire et suffisante pour que le corps des fractions de l'intersection des anneaux de valuations de S avec k[x,y] soit de degre de transcendance 2 sur k.
Cardiac morbidity and the cause of death in elderly patients with prostate cancer and incidental cardiac uptake on bone scintigraphy

Cardiac transthyretin amyloidosis (ATTR) is a possible incidental finding on bone scintigraphy imaged due to prostate cancer. We investigated its significance in 1426 elderly prostate cancer patients (>70 years) who underwent bone scintigraphy in three nuclear medicine departments in Finland. Patients with Perugini grade two or three uptakes were considered positive for cardiac uptake. Heart failure diagnoses and pacemaker implantations were collected from the hospital's records. Mortality data were gathered from the Finnish national statistical service (Statistics Finland). The Median follow‐up time was 4 years (interquartile range: 2−5 years). Cardiac uptake was detected in 37 individuals (2.6%), and it was associated with an elevated risk of both overall and cardiovascular death in univariable analysis. However, cardiac uptake did not predict overall mortality in the multivariable analysis when adjusted to age, bone metastases or the diagnosis of heart failure (p > 0.05). The risk of heart failure was higher in patients with cardiac uptake (47% vs. 15%, p < 0.001), while the risk of pacemaker implantations was not elevated (5% vs. 5%, p = 0.89). In conclusion, cardiac uptake on bone scintigraphy imaged due to prostate cancer is associated with an elevated risk of heart failure and both overall and cardiovascular death. However, cardiac uptake was not independently associated with overall mortality when adjusted to age, bone metastasis or heart failure. Therefore, they are essential to consider when incidental cardiac uptake is detected on bone scintigraphy. The need for pacemaker implantation was not elevated in patients with cardiac uptake.
Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference

Abstract Human immunodeficiency virus 1 (HIV) proviruses archived in the persistent reservoir currently pose the greatest obstacle to HIV cure due to their evasion of combined antiretroviral therapy and ability to reseed HIV infection. Understanding the dynamics of the HIV persistent reservoir is imperative for discovering a durable HIV cure. Here, we explore Bayesian methods using the software BEAST2 to estimate HIV proviral integration dates. We started with within-host longitudinal HIV sequences collected prior to therapy, along with sequences collected from the persistent reservoir during suppressive therapy. We built a BEAST2 model to estimate integration dates of proviral sequences collected during suppressive therapy, implementing a tip date random walker to adjust the sequence tip dates and a latency-specific prior to inform the dates. To validate our method, we implemented it on both simulated and empirical data sets. Consistent with previous studies, we found that proviral integration dates were spread throughout active infection. Path sampling to select an alternative prior for date estimation in place of the latency-specific prior produced unrealistic results in one empirical data set, whereas on another data set, the latency-specific prior was selected as best fitting. Our Bayesian method outperforms current date estimation techniques with a root mean squared error of 0.89 years on simulated data relative to 1.23–1.89 years with previously developed methods. Bayesian methods offer an adaptable framework for inferring proviral integration dates.
Variational iteration and homotopy perturbation method for solving Lorenz system

In this paper, homotopy perturbation method and variational iteration method are implemented to give approximate and analytical solutions of nonlinear ordinary differential equation systems such as Lorenz system. Homotopy perturbation is compared the variational iteration method for Lorenz system. The variational iteration method is predominant than the other non-linear methods, such as perturbation method. The main property of the VIM method is in its flexibility and ability to solve nonlinear equations accurately and conveniently. In this method, in general Lagrange multipliers are constructed by correction functionals for the systems. Multipliers can be identified by the variational theory. Some plots are presented to compare of the VIM and HPM.
STG-MTL: Scalable Task Grouping for Multi-Task Learning Using Data Map

Multi-Task Learning (MTL) is a powerful technique that has gained popularity due to its performance improvement over traditional Single-Task Learning (STL). However, MTL is often challenging because there is an exponential number of possible task groupings, which can make it difficult to choose the best one, and some groupings might produce performance degradation due to negative interference between tasks. Furthermore, existing solutions are severely suffering from scalability issues, limiting any practical application. In our paper, we propose a new data-driven method that addresses these challenges and provides a scalable and modular solution for classification task grouping based on hand-crafted features, specifically Data Maps, which capture the training behavior for each classification task during the MTL training. We experiment with the method demonstrating its effectiveness, even on an unprecedented number of tasks (up to 100).
Degree growth of lattice equations defined on a 3x3 stencil

We study complexity in terms of degree growth of one-component lattice equations defined on a $3\times 3$ stencil. The equations include two in Hirota bilinear form and the Boussinesq equations of regular, modified and Schwarzian type. Initial values are given on a staircase or on a corner configuration and depend linearly or rationally on a special variable, for example $f_{n,m}=\alpha_{n,m}z+\beta_{n,m}$, in which case we count the degree in $z$ of the iterates. Known integrable cases have linear growth if only one initial values contains $z$, and quadratic growth if all initial values contain $z$. Even a small deformation of an integrable equation changes the degree growth from polynomial to exponential, because the deformation will change factorization properties and thereby prevent cancellations.
Fast and Optimal Inference for Change Points in Piecewise Polynomials via Differencing

We consider the problem of uncertainty quantification in change point regressions, where the signal can be piecewise polynomial of arbitrary but fixed degree. That is we seek disjoint intervals which, uniformly at a given confidence level, must each contain a change point location. We propose a procedure based on performing local tests at a number of scales and locations on a sparse grid, which adapts to the choice of grid in the sense that by choosing a sparser grid one explicitly pays a lower price for multiple testing. The procedure is fast as its computational complexity is always of the order $\mathcal{O} (n \log (n))$ where $n$ is the length of the data, and optimal in the sense that under certain mild conditions every change point is detected with high probability and the widths of the intervals returned match the mini-max localisation rates for the associated change point problem up to log factors. A detailed simulation study shows our procedure is competitive against state of the art algorithms for similar problems. Our procedure is implemented in the R package ChangePointInference which is available via https://github.com/gaviosha/ChangePointInference.