Miracle-dz/UniFAR-FTUs huggingface dataset:
Maximum likelihood parameter estimation in time series models using sequential Monte Carlo

Publications Journal papers: { L. Jiang, S. S. Singh, S. Yıldırım (2015), Bayesian tracking and parameter learning for non-linear multiple target tracking models IEEE Transactions on Signal Processing { S. Yıldırım, S. Singh, T. Dean, A. Jasra (2015), Parameter Estimation in Hidden Markov Models with Intractable Likelihoods Using Sequential Monte Carlo, Journal of Computational and Graphical Statistics { S. Yıldırım, L. Jiang, S. S. Singh, and T. Dean (2014), Calibrating the Gaussian Multi-target Tracking Model, Statistics and Computing { S. Yıldırım, S. S. Singh, and A. Doucet (2013), An Online Expectation-Maximisation Algorithm for Changepoint Models, Journal of Computational and Graphical Statistics { S. Yıldırım, A. T. Cemgil, M. Aktar, Y. Özakın, and A. Ertüzün (2010), A Bayesian Deconvolution Approach for Receiver Function Analysis, IEEE Transactions in Geoscience and Remote Sensing. { D. Gençaǧa, E. E. Kuruoǧlu, A. Ertüzün, and S. Yıldırım (2008), Estimation of Time Varying AR SαS Processes using Gibbs Sampling, Signal Processing.
Cooperate or not with knowledge-advantaged ENGO: Motivating supplier environmental responsibility of competitive core enterprises

Recently, core enterprises are compelled to invest in the environmental responsibility of upstream suppliers, since their brand image and market share will be significantly impacted when suppliers fail to comply with environmental regulations. However, the effectiveness of the core enterprises’ investment efficiency is limited by insufficient environmental knowledge. Although cooperating with the knowledge-advantaged environmental non-governmental organization (ENGO) may be an effective solution, we observe from the recent examples that not all core enterprises are willing to cooperate in a competitive market. Within this context, we develop a theoretical model to investigate whether competitive core enterprises can benefit from cooperating with the knowledge-advantaged ENGO to motivate the supplier’s environmental responsibility. Our results show that cooperation incentivizes core enterprises’ investments in the supplier’s environmental responsibility, which in turn motivates better environmental responsibility of the supplier. However, we illustrate that cooperation is not necessarily the optimal strategy for core enterprises in the duopoly scenario. Specifically, as the knowledge absorption ability increases, a core enterprise may free-ride on another’s investment, shifting its strategic preference from cooperating to not cooperating. In addition, competition may stimulate the core enterprises’ investments and cooperation motivation, thus improving the total environmental effort and supply chain members’ profits. Our findings provide insights into the competitive core enterprises’ strategic choice regarding suppliers’ environmental responsibility management.
Stroke and Emerging Blood Biomarkers: A Clinical Prospective

Stroke constitutes the primary source of adult functional disability, exhibiting a paramount socioeconomic burden. Thus, it is of great importance that the prediction of stroke outcome be both prompt and accurate. Although modern neuroimaging and neurophysiological techniques are accessible, easily available blood biomarkers reflecting underlying stroke-related pathophysiological processes, including glial and/or neuronal death, neuroendocrine responses, inflammation, increased oxidative stress, blood–brain barrier disruption, endothelial dysfunction, and hemostasis, are required in order to facilitate stroke prognosis. A literature search of two databases (MEDLINE and Science Direct) was conducted in order to trace all relevant studies published between 1 January 2010 and 31 December 2021 that focused on the clinical utility of brain natriuretic peptide, glial fibrillary acidic protein, the red cell distribution width, the neutrophil-to-lymphocyte ratio, matrix metalloproteinase-9, and aquaporin-4 as prognostic tools in stroke survivors. Only full-text articles published in English were included. Twenty-eight articles were identified and are included in this review. All studied blood-derived biomarkers proved to be valuable prognostic tools poststroke, the clinical implementation of which may accurately predict the survivors’ functional outcomes, thus significantly enhancing the rehabilitation efficiency of stroke patients. Along with already utilized clinical, neurophysiological, and neuroimaging biomarkers, a blood-derived multi-biomarker panel is proposed as a reasonable approach to enhance the predictive power of stroke prognostic models.
Assessing Height Variations in Qinghai-Tibet Plateau from Time-Varying Gravity Data and Hydrological Model

Height variations caused by mass change make an important contribution to the tectonic uplift of the Qinghai-Tibet Plateau (QTP). To study the deformation attributable to hydrological loading and real potential tectonic vertical motion, satellite gravity data from the Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow-On (GRACE-FO) with data from the Global Land Data Assimilation System (GLDAS) and Global Positioning System (GPS) are adopted to estimate height variations in QTP. Based on spherical harmonic function (SHF) and Green’s function (GF), the results show the trend of height variations is unevenly distributed in the spatial domain. The SHF indicated that the rate in the southwest of the QTP is ~1 mm/year, while the northern and eastern show a subtle decreasing trend, which indicates hydrological loading is not the main cause of the uplift observed with GRACE. The maximum annual amplitude of height variations is ~12 mm, reaching the annual maximum around February to March. The average correlation coefficients of SHF, and GF height variations with GPS heights are 0.70 and 0.82, respectively. Based on cross wavelet transform, it is concluded that there are annual signals between the height variations derived from GPS with GRACE (-FO) and GLDAS. Finally, the tectonic vertical motion in the QTP is given by removing the effect of hydrological loading, which shows most GPS stations are uplifted at a rate of 0.06 mm/year–1.97 mm/year.
Econometrics by Example

PART I: THE LINEAR REGRESSION MODEL CHAPTER 1: The Linear Regression Model: An Overview CHAPTER 2: Functional Forms of Regression Models CHAPTER 3: Qualitative Explanatory Variables Regression Models PART II: CRITICAL EVALUATION OF THE CLASSICAL LINEAR REGRESSION MODEL CHAPTER 4: Regression Diagnostic I: Multicollinearity CHAPTER 5: Regression Diagnostic II: Heteroscedasticity CHAPTER 6: Regression Diagnostic III: Autocorrelation CHAPTER 7: Regression Diagnostic IV: Model Specification Errors PART III: REGRESSION MODELS WITH CROSS-SECTIONAL DATA CHAPTER 8: The Logit And Probit Models CHAPTER 9: Multinomial Regression Models CHAPTER 10: Oridinal Regression Models CHAPTER 11: Limited Dependent Variable Regression Models CHAPTER 12: Modeling Count Data: The Poisson and Negative Binomial Regression Models PART IV: TOPICS IN TIME SERIES ECONOMETRICS CHAPTER 13: Stationary and Nonstationary Time Series CHAPTER 14: Cointegration and Error Correction Models CHAPTER 15: Asset Price Volatility: The ARCH and GARCH Models CHAPTER 16: Economic Forecasting CHAPTER 17: Panel Data Regression Models CHAPTER 18: Survival Analysis CHAPTER 19: Stochastic Regressors and the Method of Instrumental Variables
Predictive Power of MIB-1 vs. Mitotic Count on Progression-Free Survival in Skull-Base Meningioma

Simple Summary Meningiomas are mainly benign intracranial tumors. Nevertheless, risk of recurrence exists in long-term follow-up, so new prognostic markers are still need to be identified. MIB-1 is no diagnostic criterion in WHO classification of meningiomas by now. This retrospective study shows that MIB-1 as well as mitotic count are good predictors for progression-free survival in skull-base meningiomas. The implantation of MIB-1 may enable an improved classification of meningiomas regarding progression-free survival. Moreover, this analysis of skull-base meningiomas shows that current cut-offs may have to be adjusted for meningioma location. Abstract Although meningiomas are mainly non-aggressive and slow-growing tumors, there is a remarkable recurrence rate in a long-term follow-up. Proliferative activity and progression-free survival (PFS) differs significantly among the anatomic location of meningiomas. The aim of the present study was to investigate the predictive power of MIB-1 labeling index and mitotic count (MC) regarding the probability of PFS in the subgroup of skull-base meningiomas. A total of 145 patients were included in this retrospective study. Histopathological examinations and follow-up data were collected. Ideal cut-off values for MIB-1 and MC were ≥4.75 and ≥6.5, respectively. MIB-1 as well as MC were good predictors for PFS in skull-base meningiomas. Time-dependent analysis of MIB-1 and MC in prediction of recurrence of skull-base meningioma showed that their prognostic values were comparable, but different cut-offs for MC should be considered regarding the meningioma’s location. As the achievement of a gross total resection can be more challenging in skull-base meningiomas and second surgery implies a higher risk profile, the recurrence risk could be stratified according to these findings and guide decision-making for follow-ups vs. adjuvant therapies.
A Numerical Study of the Impact of Vertical Shear on the Distribution of Rainfall in Hurricane Bonnie (1998)

Abstract Despite the significant impacts of torrential rainfall from tropical cyclones at landfall, quantitative precipitation forecasting (QPF) remains an unsolved problem. A key task in improving tropical cyclone QPF is understanding the factors that affect the intensity and distribution of rainfall around the storm. These include the storm motion, topography, and orientation of the coast, and interactions with the environmental flow. The combination of these effects can produce rainfall distributions that may be nearly axisymmetric or highly asymmetric and rainfall amounts that range from 1 or 2 cm to >30 cm. This study investigates the interactions between a storm and its environmental flow through a numerical simulation of Hurricane Bonnie (1998) that focuses on the role of vertical wind shear in governing azimuthal variations of rainfall. The simulation uses the high-resolution nonhydrostatic fifth-generation Pennsylvania State University–NCAR Mesoscale Model (MM5) to simulate the storm between 0000.
Analytical Validation of an Assay for Concurrent Measurement of Amino Acids in Dog Serum and Comparison of Amino Acid Concentrations between Whole Blood, Plasma, and Serum from Dogs

Amino acids play an important role in metabolism. Comprehensive analytical validation of an assay for the concurrent measurement of a large number of amino acids in dogs is lacking, which precludes its usefulness in a clinical setting. Amino acids are often measured in plasma or whole blood. However, serum is commonly used for gastrointestinal diagnostic testing in dogs and is therefore convenient to use. This study aimed to analytically validate an assay for the concurrent measurement of amino acids in dog serum and to evaluate differences in amino acid concentrations in whole blood, plasma, and serum in dogs. Analytical validation of the assay (Biochrom 30+ Amino Acid Analyzer) was performed on fresh or banked serum samples from dogs. Whole blood, plasma, and serum from 36 healthy dogs were analyzed, and concentrations of the three sample types were compared. The assay was demonstrated to be precise, reproducible, accurate, linear, and stable for the measurement of the majority of compounds detected in dog serum. Cystine, glutamic acid, and ethanolamine were shown to be unstable at conditions commonly encountered in clinical settings. Significant differences in concentrations were identified between whole blood, plasma, and serum for 33 of 42 compounds. Amino acid profiles in serum and plasma were more similar to each other than to those in whole blood. While some amino acids are present in similar concentrations in whole blood, plasma, and serum, others are highly dependent on the type of biofluid, and measurements warrant strict adherence to sample type-based reference intervals.
In Situ Regolith Seismic Velocity Measurement at the InSight Landing Site on Mars

Interior exploration using Seismic Investigations, Geodesy and Heat Transport's (InSight) seismometer package Seismic Experiment for Interior Structure (SEIS) was placed on the surface of Mars at about 1.2 m distance from the thermal properties instrument Heat flow and Physical Properties Package (HP3) that includes a self‐hammering probe. Recording the hammering noise with SEIS provided a unique opportunity to estimate the seismic wave velocities of the shallow regolith at the landing site. However, the value of studying the seismic signals of the hammering was only realized after critical hardware decisions were already taken. Furthermore, the design and nominal operation of both SEIS and HP3 are nonideal for such high‐resolution seismic measurements. Therefore, a series of adaptations had to be implemented to operate the self‐hammering probe as a controlled seismic source and SEIS as a high‐frequency seismic receiver including the design of a high‐precision timing and an innovative high‐frequency sampling workflow. By interpreting the first‐arriving seismic waves as a P‐wave and identifying first‐arriving S‐waves by polarization analysis, we determined effective P‐ and S‐wave velocities of vP=119−21+45 ${v}_{P}=11{9}_{-21}^{+45}$ m/s and vS=63−7+11 ${v}_{S}=6{3}_{-7}^{+11}$ m/s, respectively, from around 2,000 hammer stroke recordings. These velocities likely represent bulk estimates for the uppermost several 10s of cm of regolith. An analysis of the P‐wave incidence angles provided an independent vP/vS ratio estimate of 1.84−0.35+0.89 $1.8{4}_{-0.35}^{+0.89}$ that compares well with the traveltime based estimate of 1.86−0.25+0.42 $1.8{6}_{-0.25}^{+0.42}$ . The low seismic velocities are consistent with those observed for low‐density unconsolidated sands and are in agreement with estimates obtained by other methods.
Correlation analysis of four KRTAP gene polymorphisms and cashmere fiber diameters in two cashmere goat breeds

Abstract Fiber diameter, a quantitative trait, is controlled by minor effect polygenes. Keratin-associated proteins (KRTAPs) are an important part of hair, and their rich polymorphisms facilitate the mining of cashmere trait molecular markers. In this study, Jiangnan and Tibetan cashmere goats were taken as the research object; multiplex PCR and exome sequencing technology were used to identify the exon regional polymorphisms of cashmere goats KRTAP15-1, KRTAP13.1, KRTAP27-1, and KRTAP24-1. The effects of mutation sites on the fiber diameter of cashmere were analyzed by least square method. The results showed that there were 28 mutation sites in the four KRTAP genes in Jiangnan cashmere goats and Tibetan cashmere goat populations. Among them, the KRTAP13.1, KRTAP27-1, and KRTAP24-1 gene polymorphisms were found to be significantly related to the fiber diameter of Jiangnan cashmere goats. The exploration of molecular markers in this study will help to improve the fiber diameter of the down, while the identification of gene polymorphisms will provide original data for the utilization and protection of germplasm resources of cashmere goats. Le diamètre de la fibre, une caractéristique quantitative, est contrôlé par des polygènes à effet mineur. Les protéines associées à la kératine (KRTAPs — «keratin-associated proteins») sont parties importantes des poils, et leurs polymorphismes riches facilitent le minage des marqueurs moléculaires des caractéristiques du cachemire. Dans cette étude, les chèvres à cachemire de Jiangnan et du Tibet ont été utilisées comme objets de recherche. La PCR multiplexe et la technologie de séquençage d’exons ont été utilisées afin de déterminer les polymorphismes régionaux des exons des chèvres à cachemire KRTAP15-1, KRTAP13.1, KRTAP27-1, et KRTAP24-1. Les effets des sites de mutation sur le diamètre de la fibre du cachemire ont été analysés par la méthode des moindres carrés. Les résultats ont montré qu’il y avait 28 sites de mutation dans les quatre gènes KRTAP dans les populations de chèvres à cachemire de Jiangnan et du Tibet. Parmi ceux-ci, les polymorphismes de gènes KRTAP13.1, KRTAP27-1, et KRTAP24-1 se sont avérés reliés de façon significative au diamètre de la fibre des chèvres à cachemire de Jiangnan. L’exploration des marqueurs moléculaires dans cette étude aidera à améliorer le diamètre de la fibre du duvet, tandis que l’identification des polymorphismes des gènes offrira des données originales pour l’utilisation et la protection des ressources du patrimoine génétique des chèvres à cachemire. [Traduit par la Rédaction]
Identification of Candidate MicroRNA-mRNA Subnetwork for Predicting the Osteosarcoma Progression by Bioinformatics Analysis

Osteosarcoma (OS) is the pretty common primary cancer of the bone among the malignancies in adolescents. A single molecular component or a limited number of molecules is insufficient as a predictive biomarker of OS progression. Hence, it is necessary to find novel network biomarkers to improve the prediction and therapeutic effect for OS. Here, we identified 230 DE-miRNAs and 821 DE-mRNAs through two miRNA expression-profiling datasets and three mRNA expression-profiling datasets. We found that hsa-miR-494 is closely linked with the survival of OS patients. In addition, we analyzed GO and KEGG enrichment for targets of hsa-miR-494-5p and hsa-miR-494-3p through R programming. And five mRNAs were predicted as common targets of hsa-miR-494-5p and hsa-miR-494-3p. We further revealed that upregulated TRPS1 was strongly correlated with poor outcomes in OS patients through the survival analysis based on the TARGET database. The qRT-PCR study verified that the expression of hsa-miR-494-5p and hsa-miR-494-3p was declined considerably, while TRPS1 was notably raised in OS cells when compared to the osteoblasts. Thus, we generated a new regulatory subnetwork of key miRNAs and target mRNAs using Cytoscape software. These results indicate that the novel miRNA-mRNA subnetwork composed of hsa-miR-494-5p, hsa-miR-494-3p, and TRPS1 might be a characteristic molecule for assessing the prognostic value of OS patients.
Influence of seasonality on hematological parameters of farmed streaked prochilod (Prochilodus lineatus)

The objective of the present study was to evaluate the influence of seasonality on the hematological aspects of juvenile farmed Prochilodus lineatus, to highlight the changes caused by seasonal variations and to develop reference intervals appropriate for each season. The study of the hematological parameters of farmed species has showed the mechanisms of adaptation to environmental variations, both in the natural environment and in production systems, allowing discernment of the differences between physiological and pathological reactions. Among the environmental factors, temperature and day length are recognized as a key factor in promoting changes in fish physiology, which can be reflected in hematological parameters. The present study analyzed the hematological parameters of juveniles of farmed streaked prochilod (Prochilodus lineatus) considering seasonal features such as temperature and day length, to highlight the changes caused by seasonality and the mechanisms involved in adaptation, and thus, elaborate reference intervals for each season. We found that seasonality has a significant impact on the hematological parameters of juvenile specimens of farmed streaked prochilod (Prochilodus lineatus), as it promotes changes in hematimetry, hemoglobinometry, white blood cells count and in the prevalence of leukocyte types. These findings demonstrate the importance of establishing reference intervals for farmed species, considering the factors responsible for physiological modifications, especially seasonal features.
On the relevance of the MHD approach to study the Kelvin-Helmholtz instability of the terrestrial magnetopause

It is shown that the usual MHD approximation is not suitable for the description of the Kelvin-Helmholtz instability of the terrestrial magnetopause. Indeed such a description implies an ideal magnetopause with a smooth continuous variation of the plasma and field parameters occuring in an extended current sheet. However, the actual magnetopause and its adjacent plasma boundary layer are highly irregular, both spatially and temporally. Therefore, finite ion Larmor radius effects do not represent small corrections. It is argued that these small-scale inhomogeneities can change drastically the usual large-scale description of the magnetopause oscillations.
Spatially-resolved x-ray Scattering Experiments.

Spatially-resolved x-ray scattering experiments by Eliseo J. Gamboa Co-chairs: R Paul Drake, Paul A. Keiter In many laboratory astrophysics experiments, intense laser irradiation creates novel material conditions with large, one-dimensional gradients in the temperature, density, and ionization state. X-ray Thomson scattering (XRTS) is a powerful technique for measuring these parameters in dense plasmas. However, the scattered signal has previously been measured with little or no spatial resolution. This limits XRTS to characterizing homogenous plasmas like steady shocks or isochorically heated matter. This dissertation reports on the development of the imaging x-ray Thomson spectrometer diagnostic for the Omega laser facility, which extends XRTS to the general case of plasmas with one-dimensional structure. The di↵raction of x-rays from a toroidally-curved crystal creates high-resolution images that are simultaneously spectrally and spatially resolved along a one-dimensional profile. The technique of imaging x-ray Thomson scattering is applied to produce the first measurements of the spatial profiles of the temperature, ionization state, relative material density, and shock speed of a blast wave in a high-energy density system. A decaying shock is probed with 90 scattering of 7.8 keV helium-like nickel x-rays. The spatially-resolved scattering is used to infer the material conditions along the shock
Homogeneous links and closed homogeneous braids

Is any positive knot the closure of a positive braid? No. But if we consider positivity in terms of the generators of the braid group due to Birman, Ko and Lee, then the answer is yes. In this paper we prove that the same occurs when considering homogeneity. In the way we prove that the plumbing of two surfaces is a BKL-homogeneous surface if and only if both summands are BKL-homogeneous surfaces, a parallel result to that of Rudolph involving quasipositive surfaces. BKL-homogeneous surfaces are, in fact, a natural generalization of quasipositive surfaces.