Miracle-dz/UniFAR-FTUs huggingface dataset:
An isolated image inpainting approach based on the Poisson equation

Image inpainting is a technique used to recover damaged portions of an image and has a variety of applications.The exemplar based inpainting algorithm has a good performance on texture inpainting, but it may produce block effects and lead to artificial inpainting results when processing structure images.In this paper, we propose an isolated inpainting algorithm based on the Poisson equation.First the image to be repaired is decomposed into two components:the structure and texture images;then the two components are repaired separately by different methods according to their image characteristics;finally, the repaired components are combined back.For the structure image, the Laplacian operator is employed to enhance the structure information, and the Laplacian field is inpainted by the exemplar based algorithm, followed by a reconstruction based on the Poisson equation.In this way, the repaired structure image maintains both sharp edges and smooth interiors.Experiments show the proposed algorithm can improve the visual effect significantly and it has a good performance on large area inpainting.
Ultrafast laser ablation of transparent materials

The present work investigates the influence of the pulse duration and the temporal spacing between pulses on the ablation of aluminosilicate glass by comparing the results obtained with pulse durations of 0.4 ps and 6 ps. We found that surface modifications occur already at fluences below the single pulse ablation threshold and that laser-induced periodic surface structures (LIPSS) emerge as a result of those surface modifications. For 0.4 ps the ablation threshold fluences is lower than for 6 ps. Scanning electron micrographs of LIPSS generated with 0.4 ps exhibit a more periodic and less coarse structure as compared to structures generated with 6 ps. Furthermore we report on the influence of temporal spacing between the pulses on the occurrence of LIPSS and the impact on the quality of the cutting edge. Keywords: LIPSS,
State-space models for count time series with excess zeros

Count time series are frequently encountered in biomedical, epidemiological and public health applications. In principle, such series may exhibit three distinctive features: overdispersion, zero-inflation and temporal correlation. Developing a modelling framework that is sufficiently general to accommodate all three of these characteristics poses a challenge. To address this challenge, we propose a flexible class of dynamic models in the state-space framework. Certain models that have been previously introduced in the literature may be viewed as special cases of this model class. For parameter estimation, we devise a Monte Carlo Expectation-Maximization (MCEM) algorithm, where particle filtering and particle smoothing methods are employed to approximate the high-dimensional integrals in the E-step of the algorithm. To illustrate the proposed methodology, we consider an application based on the evaluation of a participatory ergonomics intervention, which is designed to reduce the incidence of workplace injuries among a group of hospital cleaners. The data consists of aggregated monthly counts of work-related injuries that were reported before and after the intervention.
Cost components of school-based oral health-promoting programs: A systematic review protocol

Introduction Oral health-promoting school programs play a crucial role in achieving universal coverage of oral health care by addressing oral diseases and promoting the well-being and quality of life of children and adolescents. However, a lack of studies has evaluated the costs associated with implementing these programs, which hinders decision-makers in adopting them on a large scale. This review aims to assess the cost components involved in school-based oral health-promoting programs. Methods This review will include studies that have conducted either partial or full economic evaluations, focusing on describing the cost components of oral health-promoting programs implemented in primary schools involving students aged 6 to 14. A systematic search was conducted across multiple databases: MEDLINE, The Cochrane Library, the Virtual Health Library, the NHS Economic Evaluation Database, Web of Science, Scopus, and EMBASE. Additionally, gray literature was searched using the Health Technology Assessment Database. Two independent reviewers will screen the titles and abstracts, followed by a full-text review based on predefined inclusion criteria. Data extraction and critical appraisal evaluation will also be carried out independently by two reviewers. In case of disagreements, the reviewer team will resolve them through discussion. Discussion The systematic review resulting from this protocol aims to provide evidence regarding the cost components and necessary resources for implementing and maintaining oral health-promoting school programs. This information can assist decision-makers in adopting these programs on a larger scale and effectively addressing oral diseases among children and adolescents.
Comparing neural language models for medical concept representation and patient trajectory prediction

Effective representation of medical concepts is crucial for secondary analyses of electronic health records. Neural language models have shown promise in automatically deriving medical concept representations from clinical data. However, the comparative performance of different language models for creating these empirical representations, and the extent to which they encode medical semantics, has not been extensively studied. This study aims to address this gap by evaluating the effectiveness of three popular language models - word2vec, fastText, and GloVe - in creating medical concept embeddings. By using a large dataset of digital health records, we created patient trajectories and used them to train the language models. We then assessed the ability of the learned embeddings to encode semantics through an explicit comparison with biomedical terminologies, and implicitly by predicting patient outcomes and trajectories with different degrees of information. Our qualitative analysis shows that empirical clusters of embeddings learned by fastText exhibit the highest similarity with theoretical clustering patterns obtained from biomedical terminologies, with a similarity score between empirical and theoretical clusters of 0.88, 0.80, and 0.92 for diagnosis, procedures, and medication codes, respectively. Conversely, for outcome prediction, word2vec and GloVe tend to outperform fastText, with the former achieving AUROC as high as 0.80, 0.63, and 0.88 for length-of-stay, readmission, and mortality prediction, respectively. In predicting the next steps in patient trajectories, GloVe achieves the highest performance for diagnostic and medication codes (AUPRC of 0.46 and of 0.82, respectively) at the highest level of the semantic hierarchy, while fastText outperforms the other models for procedure codes (AUPRC of 0.67). Our study demonstrates that subword information is crucial for learning medical concept representations, but global embedding vectors are better suited for downstream tasks, such as trajectory prediction. Thus, these models can be harnessed to learn representations that convey clinical meaning, and our insights highlight the potential of using machine learning techniques to semantically encode medical data.
Environment-Wide Association Studies of Anemia in the National Health and Nutrition Examination Surveys

Background: Anemia is a global health problem that can lead to chronic illness in adults and may be fatal in children and the elderly. While some dietary factors and heavy metals are known risk factors for anemia, there are no environment-wide studies of anemia. Objectives: Our goal was to identify environment-wide risk factors for anemia. Methods: We evaluated general anemia in children and adults and further classified anemia as a) iron, vitamin B12, or folate deficiency anemia; b) anemia in general chronic diseases; and c) anemia in chronic kidney disease. As well as quantitative measures including level of hemoglobin, serum vitamin B12, red blood cell (RBC) folate, and serum iron. Environment-wide association studies (EWAS) were performed to identify novel environmental risk factors of anemia in discovery and replication subsets of the National Health and Nutrition Examination Surveys (NHANES). Results: We identified and replicated 106 potential environmental risk factors for anemia. As expected, serum iron was the top exposure associated with general anemia for adults. Cadmium was associated with adult hemoglobin levels, as were vitamin Bs, micronutrients, smoking, and alcohol consumption. Further, decreased levels of multiple vitamins, including vitamin A, vitamin Es and multiple vitamin Bs, were associated with general anemia in adults. Use of tobacco and alcohol was also found to be associated with red blood cell folate and serum iron levels. In children, serum iron level was associated with folic acid supplements and vitamin A supplements. Discussion: This is the first EWAS of anemia, providing insights into the environmental etiology of anemia risk in children and adults. These results may lead to the development of public health recommendations to mitigate anemia risk factors.
The periaqueductal grey in chronic low back pain: dysregulated metabolites and function

Mechanisms underlying chronic pain are insufficiently understood. Preclinical evidence suggests a potential contribution of excitatory glutamatergic and inhibitory GABAergic imbalances in pain-relevant brain areas, such as a lower excitatory/inhibitory tone in the brainstem periaqueductal grey (PAG). This cross-sectional magnetic resonance spectroscopy (MRS) study investigated whether a lower excitatory/inhibitory tone is also observed in the PAG of patients with non-specific chronic low back pain (CLBP) and whether this would relate to altered psychophysical measures of descending pain modulation and experimental pressure pain sensitivity. Specifically, the ratio between pooled glutamate and glutamine and GABA levels (Glx/GABA), Glx and GABA in the PAG were compared between CLBP patients and pain-free controls. Further, associations of Glx/GABA with conditioned pain modulation (CPM) effects and pressure pain thresholds (PPTs) were assessed. MRS was acquired on a 3T Philipps MR system using a point-resolved spectroscopy sequence optimized with very selective saturation pulses (OVERPRESS) and voxel-based flip angle calibration in a 1.1 mL volume of interest. Data from 41 CLBP patients (median [interquartile range]: 54 years [41 - 65], 22 females) and 29 age- and sex-matched controls (47 years [34 - 67], 17 females) fulfilled MRS quality criteria. CPM and PPTs were assessed at the lower back as most painful area and the non-dominant hand as pain-free control area. The CPM paradigm consisted of PPTs applied before, during (parallel CPM effect) and after a cold water bath and an ambient temperature water bath as control paradigm to identify 'true' CPM effects. In the PAG of CLBP patients, a lower Glx/GABA ratio, i.e. a lower excitatory/inhibitory tone, was observed (P = 0.002, partial {eta}2 = 0.14) driven by decreased Glx (P = 0.012, partial {eta}2 = 0.11) and increased GABA (P = 0.038, d = 0.46). CLBP patients showed disrupted associations between Glx/GABA and PPTs compared to controls in both areas (lower back: P = 0.004, partial {eta}2 = 0.12; hand: P = 0.002, partial {eta}2 = 0.16). In controls, lower Glx/GABA was associated with lower PPTs (lower back: r = 0.48, P = 0.009, hand: r = 0.53, P = 0.003), but this link was missing in CLBP patients (r's > -0.23, P's > 0.150). Additionally, CLBP patients with more severe clinical pain showed smaller CPM effects at the hand (rho = 0.54, P = 0.003). These findings suggest a dysfunction of the PAG in patients with CLBP and might indicate altered descending inhibition of deep tissue afferents.
Searching and visualizing genetic associations of pregnancy traits by using GnuMoM2b

Adverse pregnancy outcomes (APOs) are major risk factors for women's health during pregnancy and even in the years after pregnancy. Due to the heterogeneity of APOs, only few genetic associations have been identified. In this report, we conducted genome-wide association studies (GWAS) of 479 traits that are possibly related to APOs using a large and racially diverse study, Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-Be (nuMoM2b). To display the extensive results, we developed a web-based tool GnuMoM2b (https://gnumom2b.cumcobgyn.org/) for searching, visualizing, and sharing results from GWAS of 479 pregnancy traits as well as phenome-wide association studies (PheWAS) of more than 17 million single nucleotide polymorphisms (SNPs). The genetic results from three ancestries (Europeans, Africans, and Admixed Americans) and meta-analyses are populated in GnuMoM2b. In conclusion, GnuMoM2b is a valuable resource for extraction of pregnancy-related genetic results and shows the potential to facilitate meaningful discoveries.
3D surface reconstruction based on image stitching from gastric endoscopic video sequence

This paper proposes a method for reconstructing 3D detailed structures of internal organs such as gastric wall from endoscopic video sequences. The proposed method consists of the four major steps: Feature-point-based 3D reconstruction, 3D point cloud stitching, dense point cloud creation and Poisson surface reconstruction. Before the first step, we partition one video sequence into groups, where each group consists of two successive frames (image pairs), and each pair in each group contains one overlapping part, which is used as a stitching region. Fist, the 3D point cloud of each group is reconstructed by utilizing structure from motion (SFM). Secondly, a scheme based on SIFT features registers and stitches the obtained 3D point clouds, by estimating the transformation matrix of the overlapping part between different groups with high accuracy and efficiency. Thirdly, we select the most robust SIFT feature points as the seed points, and then obtain the dense point cloud from sparse point cloud via a depth testing method presented by Furukawa. Finally, by utilizing Poisson surface reconstruction, polygonal patches for the internal organs are obtained. Experimental results demonstrate that the proposed method achieves a high accuracy and efficiency for 3D reconstruction of gastric surface from an endoscopic video sequence.
Towards Longitudinal Glioma Segmentation: Evaluating combined pre- and post-treatment MRI training data for automated tumor segmentation using nnU-Net

Identification of key phenotypic regions such as necrosis, contrast enhancement, and edema on magnetic resonance imaging (MRI) is important for understanding disease evolution and treatment response in patients with glioma. Manual delineation is time intensive and not feasible for a clinical workflow. Automating phenotypic region segmentation overcomes many issues with manual segmentation, however, current glioma segmentation datasets focus on pre-treatment, diagnostic scans, where treat-ment effects and surgical cavities are not present. Thus, existing automatic segmenta-tion models are not applicable to post-treatment imaging that is used for longitudinal evaluation of care. Here, we present a comparison of three-dimensional convolutional neural networks (nnU-Net architecture) trained on large temporally defined pre-treatment, post-treatment, and mixed cohorts. We used a total of 1563 imaging timepoints from 854 patients curated from 13 different institutions as well as diverse public data sets to understand the capabilities and limitations of automatic segmenta-tion on glioma images with different phenotypic and treatment appearance. We as-sessed the performance of models using Dice coefficients on test cases from each group comparing predictions with manual segmentations generated by trained techni-cians. We demonstrate that training a combined model can be as effective as models trained on just one temporal group. The results highlight the importance of a diverse training set, that includes images from the course of disease and with effects from treatment, in the creation of a model that can accurately segment glioma MRIs at multiple treatment time points.
Predictors of decline in kidney function in the general population: a decade of follow-up from the Tehran Lipid and Glucose Study

Abstract Background and aims We aimed to assess the potential socio-demographic, clinical, and lifestyle-related risk factors for kidney function decline (KFD), defined as ≥30% estimated glomerular filtration rate (eGFR) decline, in an Iranian cohort study. Methods 7190 participants (4049 women) aged 20–90 years with 2–5 eGFR data from examinations (2001–2005 to 2015–2018) were included. Cox proportional hazard models were used to examine the association between potential risk factors and eGFR decline. Results During 11.5 years of follow-up, 1471 (889 women) participants had incident KFD with a crude incidence rate of 192.1 (182.6–202.2) per 10,000 person-year. Among the total population, older age, female gender, prehypertension, hypertension, diabetes, widowed/divorced states, higher triglycerides (TG), prevalent cardiovascular diseases (CVD), and higher baseline eGFR were significantly associated with higher, while moderate physical activity and a positive family history of diabetes were associated with lower risk of KFD (all p values <.05). Prevalent CVD in women but not men, diabetes, and hypertension among postmenopausal than premenopausal women were significant risk factors of KFD. According to the presence of chronic kidney disease (CKD) at baseline, higher eGFR decreased the risk of KFD in patients with CKD and increased KFD risk in those without CKD (all p for interactions <.05). Conclusion KFD is associated with multiple modifiable risk factors among the Iranian urban population that is affected by gender, menopausal status, and initial kidney function. Interventions targeting these factors might potentially help reduce the burden of KFD. Key messages: Menopausal status may influence the relationship between cardiometabolic risk factors and KFD; The impact of higher baseline eGFR on the risk of KFD differed between subjects with preserved kidney function and CKD patients. The interaction between gender, menopausal status, and baseline kidney function with different risk factors on KFD may help to make renal risk prediction scores to identify those in the general population at risk who may benefit from early prevention.
The Application of Genetic Algorithm in the Bi-criteria Layout Problem with Aisles

According to the idea of Systematic Layout Planning,this paper proposes a bi-criteria mathematic model concerning the material handling costs and nonmaterial relation requirements for a layout problem with fixed lengthways and transverse passageways between sections.Since this problem is NP-hard,we develop a new multi-objective genetic algorithm approach hybridized with local search to obtain the set of its Pareto solutions.In this paper,we adapt a random weight approach to combine the normalized value of two objectives.The numerical experiments show the great effectiveness of the proposed method in dealing with layout problems in moderate scales.
Mistreatment in paediatric residency programs in Thailand: a national survey

ABSTRACT Background and Aims Mistreatment in the learning environment is associated with adverse outcomes for residents. Most studies with that regard have been performed in western countries which may have different socio-cultural background and educational and training systems than the non-Western Asian countries. This study aimed (1) to determine the national prevalence of mistreatment in Thai paediatric residents and a correlation with the risk for burnout and other factors and (2) to launch a mistreatment awareness program (MAP) in our training program. Methods The study was divided into two phases. Phase 1, an online survey of mistreatment-related questions, was sent to current paediatric residents across the country. Burnout and depression were also self-evaluated by formal screening questions. The results were categorized by the Negative Acts Questionnaire-Revised into five domains of mistreatment: workplace learning–related bullying (WLRB), person-related bullying (PRB), physically intimidating bullying, sexual harassment, and ethnic harassment. Frequent mistreated exposure was defined as if mistreatment occurred >1/week. Phase 2, MAP was conducted by distributing the results of the first phase with some examples of mistreatment events and mistreatment-related videos. After 3 months, at our centre, the survey was resent to evaluate mistreatment. Results The response rate was 27% (n = 140). We found that 91% experienced ≥1 mistreated situation in the prior 6 months. Most mistreatment domains were WLRB and PRB, and residents were commonly instigated by clinical faculty and nurses. Most (84%) mistreated residents did not report the events. An association between frequent mistreated exposure and burnout was also found (P < 0.001). For Phase 2, the mistreated situations especially the WLRB and PRB domains dropped after the launch of MAP. Conclusions Thai paediatric residents frequently perceive mistreatment in their learning environment. Specific aspects of mistreatment, such as WLRB and PRB, should be carefully explored and managed through particular groups of instigators.
DV-Hop Localization Algorithm Based on Estimate of Average Hop Distance and Correction in Position

Conventional DV-Hop localization algorithm considers only the average hop distance estimated by the closest anchor node.so it will lead to larger error in position.In response to this problem,an improved DV-Hop localization algorithm based on estimate of average hop distance and correction in position is brought forward.When computing distances between an unknown node and all anchor nodes,it can obtain different distances taking into account the difference in distance and hops between the closest anchor node and other anchor nodes.The average hop distance estimated in this way is closer to the actual distance.In addition,it corrects the results of the initial positioning in circle.The simulation results show that the improved algorithm can improve the positioning accuracy effectively without increasing hardware consumption in nodes comparing with conventional DV-Hop algorithm.Furthermore,it is simple and needs small amount of calculation.So it is a practical program for nodes localization in wireless sensor networks.