Miracle-dz/UniFAR-FTUs huggingface dataset:
Some recent advances in model-based small area estimation

Small area estimation has received a lot of attention in recent years due to growing demand for reliable small area estimators. Traditional area-specific direct estimators do not provide adequate precision because sample sizes in small areas are seldom large enough. This makes it necessary to employ indirect estimators that borrow strength from related areas; in particular, model-based indirect estimators. Ghosh and Rao (1994) provided a comprehensive review and appraisal of methods for small area estimation, covering the literature to 1992-1993. This paper supplements Ghosh and Rao (1994) by covering the literature over the past five years or so on model-based estimation. In particular, we cover several small area models and empirical best linear unbiased prediction (EBLUP), empirical Bayes (EB) and hierarchical Bayes (HB) methods applied to these models. We also present several recent applications of small area estimation. 1. J.N. K. Rao, School of Mathematics and Statistics, Carleton University, Ottawa, Ontario, K1S 5B6.
Higher Order MSE of Jackknife 2SLS

In this paper we consider parameter estimation in a simple linear simultaneous equations model. It is well known that two stage least squares (2SLS) estimators perform poorly when the instruments are weak. In this case 2SLS tends to suffer from substantial small sample biases. It is also known that LIML and Nagar-type estimators are less biased than 2SLS but suffer from large small sample variability. We construct a bias corrected version of 2SLS based on the Jackknife principle. Using higher order expansions we show that the MSE of our Jackknife 2SLS estimator is approximately the same as the MSE of the Nagar-type estimator. Monte Carlo simulations show that even in relatively large samples the MSE of LIML and Nagar can be substantially larger than for Jackknife 2SLS.
A Biscuit Containing Fucoxanthin Prevents Colorectal Carcinogenesis in Mice

ABSTRACT Fucoxanthin (Fx) is a critical pigment required for photosynthesis in brown algae and microalgae. Fx is also a dietary marine carotenoid that with potent anticancer activity in vitro and in vivo. Some popular light meals for increased satiety, such as biscuits, cereals, and crackers, are frequently fortified with micronutrients for human health benefits. However, data on the anticancer potential of Fx-supplemented light meals in humans and animal models remain limited. In the present study, we investigated the anticancer effects of a Fx-supplemented biscuit using a carcinogenic murine azoxymethane/dextran sodium sulfate (AOM/DSS) model. We observed that periodic administration of biscuits containing 0.3% Fx (Fx-biscuit) at an interval of 3 days (each 15 h) per week for 15 weeks significantly inhibited colorectal carcinogenesis in AOM/DSS mice. Comprehensive gene analysis demonstrated that the Fx-biscuit significantly altered the expression of 138 genes in the colorectal mucosal tissue of the mice. In particular, the expression of heat shock protein 70 (HSP70) genes, Hspa1b (–35.7-fold) and Hspa1a (–34.9-fold), was markedly downregulated. HSP70 is a polyfunctional chaperone protein that is involved in cancer development. Compared to the control-biscuit group, the number of cells with markedly high fluorescence for HSP70 protein (HSP70high) in colorectal mucosal crypts and adenocarcinomas significantly reduced by 0.3- and 0.2-fold, respectively, in the Fx-biscuit group. Our results suggested that Fx-biscuit possesses chemopreventive potential in the colorectal cancer of AOM/DSS mice via the downregulation of HSP70.
Skeletal Disease Acquisition in Fibrous Dysplasia: Natural History and Indicators of Lesion Progression in Children

Fibrous dysplasia (FD) is a rare mosaic disorder resulting in fractures, pain, and disability. Bone lesions appear during childhood and expand during skeletal growth. The rate at which FD lesions progress and the biochemical determinants of FD lesion formation have not been established, making it difficult to investigate and implement preventative therapies. The purpose of this study was to characterize FD lesion progression in children, and to identify clinical variables associated with progressive disease. Clinical data and imaging from an ongoing natural history study at the National Institutes of Health (NIH) were reviewed. 99m‐Technetium methylene diphosphonate (99Tc‐MDP) scans were used to determine Skeletal Burden Score (SBS), a validated quantitative scoring system. FD progression rate was determined by the change in the SBS in each patient per year. Thirty‐one children had serial 99Tc‐MDP scans, with a median age at first scan of 6 years (interquartile range [IQR] 4–8, range 2–10), and median follow‐up 1.1 years (IQR 1.1–2.1, range 0.7–11.2). The median FD progression rate for the total group was 2.12 SBS units/year (IQR 0.81–2.94, range 0.05–7.81). FD progression rates were highest in children under age 8 years and declined with age (p = 0.03). Baseline disease severity was associated with subsequent disease progression (p = 0.009), with the highest FD progression rates in patients with moderate disease (baseline SBS 16–30), and lowest progression rates in those with severe disease (SBS ≥50). Serum levels of the bone formation marker osteocalcin were positively correlated with subsequent FD progression rate (p = 0.01, R = 0.58). There was no association between FD progression and baseline endocrinopathies, fractures, or surgery rates. FD lesions progress during childhood, particularly in younger children and those with moderate involvement. Osteocalcin may potentially serve as a biomarker for progressive disease. These findings may allow clinicians to investigate preventative therapies, and to identify children with FD who are candidates for early interventions. Published 2022. This article is a U.S. Government work and is in the public domain in the USA.
MiR-21 participates in the neuroprotection of diazoxide against hypoxic-ischemia encephalopathy by targeting PDCD4

ABSTRACT Background Hypoxic-ischemic encephalopathy (HIE) is one of the leading causes of neonatal death and permanent neurological disability. Here, we designed to quest therapeutic effects of diazoxide (DZ) on HIE and its mechanism. Methods The cell model of HIE was established. CCK8 and flow cytometry were applied to test cell viability and apoptosis. RT-qPCR and western blotting was evaluated to the expression of miR-21, PDCD4, PI3K, and p-AKT/AKT. Commercial kits were employed to detect SOD, MDA, LDH. DCFH-DA was used to measure intracellular ROS. ELISA was performed to estimate IL-1β, IL-6 and TNF-α. Dual-luciferase reporter gene and RIP assay were applied to confirm the binding relationships between miR-21 and PDCD4. Results In H19-7 cells and PC12 cells stimulated by OGD, with low cell viability, high apoptosis, miR-21 high expression and PDCD4 low expression. However, the functions were all reversed by DZ administration. Furthermore, miR-21 inhibitor could abolish the beneficial effects of DZ on OGD-induced cells. Besides, miR-21 could interact with PDCD4. In addition, PDCD4 involved with the regulation of DZ to OGD-induced cells via PI3K/AKT pathway. Conclusion DZ enhanced miR-21 level and inhibited PDCD4 level via PI3K/AKT pathway to resisted HIE.
Gut microbiota in mucosa and feces of newly diagnosed, treatment-naïve adult inflammatory bowel disease and irritable bowel syndrome patients

ABSTRACT The knowledge on how gut microbes contribute to the inflammatory bowel disease (IBD) at the onset of disease is still scarce. We compared gut microbiota in newly diagnosed, treatment-naïve adult IBD (Crohn’s disease (CD) and ulcerative colitis (UC)) to irritable bowel syndrome (IBS) patients and healthy group. Mucosal and fecal microbiota of 49 patients (13 UC, 10 CD, and 26 IBS) before treatment initiation, and fecal microbiota of 12 healthy subjects was characterized by 16S rRNA gene sequencing. Mucosa was sampled at six positions, from terminal ileum to rectum. We demonstrate that mucosal microbiota is spatially homogeneous, cannot be differentiated based on the local inflammation status and yet provides bacterial footprints superior to fecal in discriminating disease phenotypes. IBD groups showed decreased bacterial diversity in mucosa at all taxonomic levels compared to IBS. In CD and UC, Dialister was significantly increased, and expansion of Haemophilus and Propionibacterium characterized UC. Compared to healthy individuals, fecal microbiota of IBD and IBS patients had increased abundance of Proteobacteria, Enterobacteriaceae, in particular. Shift toward reduction of Adlercreutzia and butyrate-producing taxa was found in feces of IBD patients. Microbiota alterations detected in newly diagnosed treatment-naïve adult patients indicate that the microbiota changes are set and detectable at the disease onset and likely have a discerning role in IBD pathophysiology. Our results justify further investigation of the taxa discriminating between disease groups, such as H. parainfluenzae, R. gnavus, Turicibacteriaceae, Dialister, and Adlercreutzia as potential biomarkers of the disease.
Evaluation of the Amharic version of the London measure of unplanned pregnancy in Ethiopia

Background Unplanned pregnancy is an important public health problem in both the developing and developed world, as it may cause adverse social and health outcomes for mothers, children, and families as a whole. London Measure of Unplanned Pregnancy (LMUP) has been formally and informally validated in multiple and diverse settings. However, there is a dearth of literature on the validation of LMUP in Ethiopia either in the Amharic version or other languages. Objective The general objective of this study was to translate the LMUP into Amharic and evaluate its psychometric properties in a sample of Amharic-speaking women receiving antenatal care (ANC) service at public health facilities in Arbaminch and Birbir towns. Methods A cross-sectional study design was used for the study. Forward and backward translation of original English LMUP to Amharic was done. A cognitive interview using a pretested structured questionnaire was used to collect the data from respondents. The collected data was analyzed using SPSS version 25. Reliability was assessed using Cronbach’s alpha, inter-item correlations, and corrected item-total correlations while construct validity was assessed using principal components analysis and hypothesis testing. Results Data was collected from 320 women attending antennal care services at selected public health care facilities. LMUP range of 1to 11 was captured. The prevalence of unplanned pregnancies was 19(5.9%), while 136(42.5 were ambivalent and 165(51.6%) were planned pregnancies. The reliability testing demonstrated acceptable internal consistency (Cronbach’s alpha = 0.799) and the validity testing confirmed the unidimensional structure of the scale. In addition, all hypotheses were confirmed. Conclusions Amharic version of LMUP is a valid and reliable tool to measure pregnancy intention so that it can be used by Amharic speaking population in Ethiopia. It can also be used in research studies among Amharic-speaking women to measure unplanned pregnancy.
The role of external beam radiation therapy in the management of thyroid carcinomas: A retrospective study in Iran Cancer Institute

Thyroid cancers are histologically classified into three types; differentiated thyroid carcinoma (DTC), medullary thyroid carcinoma (MTC), and anaplastic thyroid carcinoma (ATC). Among the several therapeutic strategies for treatment and management of thyroid cancer, surgical resection in combination with radioactive iodine therapy (RAI) is indicated for moderate to high‐risk differentiated thyroid cancer (DTC) patients‐ according to current guidelines. However, external radiation therapy (EBRT) can be a viable alternative treatment option for these patients and scarce evidence is available regarding the efficacy and effectiveness of EBRT on thyroid cancer.
Feasibility of a Clinical-Radiomics Model to Predict the Outcomes of Acute Ischemic Stroke

Objective To develop a model incorporating radiomic features and clinical factors to accurately predict acute ischemic stroke (AIS) outcomes. Materials and Methods Data from 522 AIS patients (382 male [73.2%]; mean age ± standard deviation, 58.9 ± 11.5 years) were randomly divided into the training (n = 311) and validation cohorts (n = 211). According to the modified Rankin Scale (mRS) at 6 months after hospital discharge, prognosis was dichotomized into good (mRS ≤ 2) and poor (mRS > 2); 1310 radiomics features were extracted from diffusion-weighted imaging and apparent diffusion coefficient maps. The minimum redundancy maximum relevance algorithm and the least absolute shrinkage and selection operator logistic regression method were implemented to select the features and establish a radiomics model. Univariable and multivariable logistic regression analyses were performed to identify the clinical factors and construct a clinical model. Ultimately, a multivariable logistic regression analysis incorporating independent clinical factors and radiomics score was implemented to establish the final combined prediction model using a backward step-down selection procedure, and a clinical-radiomics nomogram was developed. The models were evaluated using calibration, receiver operating characteristic (ROC), and decision curve analyses. Results Age, sex, stroke history, diabetes, baseline mRS, baseline National Institutes of Health Stroke Scale score, and radiomics score were independent predictors of AIS outcomes. The area under the ROC curve of the clinical-radiomics model was 0.868 (95% confidence interval, 0.825–0.910) in the training cohort and 0.890 (0.844–0.936) in the validation cohort, which was significantly larger than that of the clinical or radiomics models. The clinical radiomics nomogram was well calibrated (p > 0.05). The decision curve analysis indicated its clinical usefulness. Conclusion The clinical-radiomics model outperformed individual clinical or radiomics models and achieved satisfactory performance in predicting AIS outcomes.
merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models

Abstract Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms’ metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models’ reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.
Competitive performance of Pinus massoniana is related to scaling relationships at the individual plant and branch levels

Abstract Premise Competition is an important driver of tree mortality and thus affects forest structure and dynamics. Tree architectural traits, such as height‐to‐diameter (H‐D) and branch length‐to‐diameter (L‐d) relationships are thought to influence species competitiveness by affecting light capture. Unfortunately, little is known about how the H vs. D and L vs. d scaling exponents are related to tree performance (defined in the context of growth vigor) in competition. Methods Using data from field surveys of 1547 individuals and destructive sampling of 51 trees with 1086 first‐order branches from a high‐density Pinus massoniana forest, we explored whether the H vs. D and the L vs. d scaling exponents respectively differed numerically across tree performance and branch vertical position in crowns. Results The results indicated that (1) the H vs. D scaling exponent decreased as tree performance declined; (2) the L vs. d scaling exponent differed across tree performance classes (i.e., the scaling exponent of “inferior” trees was significantly larger than that of “moderate” and “superior” trees); (3) the L vs. d scaling exponent decreased as branch position approached ground level; and (4) overall, the branch scaling exponent decreased as tree performance improved in each crown layer, but decreased significantly in the intermediate layer. Conclusions This study highlights the variation within (and linkage among) length‐to‐diameter scaling relationships across tree performance at the individual and branch levels. This linkage provides new insights into potential mechanisms of tree growth variation (and even further mortality) under competition in subtropical forests.
Multi-scale analysis of habitat fragmentation on small-mammal abundance and tick-borne pathogen infection prevalence in Essex County, MA

Habitat fragmentation and heterogeneity transform otherwise contiguous tracks of forest into smaller patches in the northeastern U.S. and likely impact abundances, movement patterns, and disease transmission pathways for small-mammal communities at multiple scales. We sought to determine the structure of a small-mammal community in terms of mammal abundance and infection prevalence of Borrelia burgdorferi sensu stricto (s.s.), Anaplasma phagocytophilum, and Babesia microti within a fragmented landscape in Essex County, Massachusetts, USA. We studied communities at multiple spatial scales, including vegetation, edge type, and landscape (including 200-m, 500-m, and 1000-m radii) scales. A total of 16 study sites were chosen to represent four edge types: interior forest, pasture edge, natural edge, and residential edge. At each site, we trapped small mammals and conducted vegetation surveys and GIS analysis. Upon capture, a tissue sample was collected to analyze for presence of pathogens. Northern short-tailed shrew (Blarina brevicauda) abundance did not differ based on edge type, whereas abundance of the white-footed mouse (Peromyscus leucopus) was greatest at pasture edges, although the relationship was relatively weak. White-footed mouse abundance was negatively associated with amount of forested area within a 500-m radius, whereas northern short-tailed shrew abundance demonstrated a positive relationship with fragmentation indices at the 200-m radius. White-footed mice captured at interior-forest habitat were more likely be infected with B. burgdorferi (s.s.) than individuals from edge habitat. Greater prevalence of B. burgdorferi infection of white-footed mice in forest interiors compared to edge habitats counters previous studies. Reasons for this and implications are discussed.
Evaluating data quality in the Australian and New Zealand dialysis and transplant registry using administrative hospital admission datasets and data-linkage

Background: Clinical quality registries provide rich and useful data for clinical quality monitoring and research purposes but are susceptible to data quality issues that can impact their usage. Objective: This study assessed the concordance between comorbidities recorded in the Australia and New Zealand Dialysis and Transplant (ANZDATA) Registry and those in state-based hospital admission datasets. Method: All patients in New South Wales, South Australia, Tasmania, Victoria and Western Australia recorded in ANZDATA as requiring chronic kidney replacement therapy (KRT) between 01/07/2000 and 31/12/2015 were linked with state-based hospital admission datasets. Coronary artery disease, diabetes mellitus, cerebrovascular disease, chronic lung disease and peripheral vascular disease recorded in ANZDATA at each annual census date were compared overall, over time and between different KRT modalities to comorbidities recorded in hospital admission datasets, as defined by the International Classification of Diseases (ICD-10-AM), using both the kappa statistic and logistic regression analysis. Results: 29, 334 patients with 207,369 hospital admissions were identified. Comparison was made at census date for every patient comparison. Overall agreement was “very good” for diabetes mellitus (92%, k = 0.84) and “poor” to “fair” (21–61%, k = 0.02–0.22) for others. Diabetes mellitus recording had the highest accuracy (sensitivity 93% (±SE 0.2) and specificity 93% (±SE 0.2)), and cerebrovascular disease had the lowest (sensitivity 54% (±SE 0.2) and specificity 21% (±SE 0.3)). The false positive rates for cerebrovascular disease, peripheral vascular disease and chronic airway disease ranged between 18 and 33%. The probability of a false positive was lowest for kidney transplant patients for all comorbidities and highest for patients on haemodialysis. Conclusions and Implications: Agreement between the clinical quality registry and hospital admission datasets was variable, with the prevalence of comorbidities being higher in ANZDATA.
Capsule endoscopy - a non-invasive modality to investigate the GI tract: out with the old and in with the new?

ABSTRACT Introduction Capsule endoscopy has had significant development since it was introduced into the field of medicine in 2000. It is non-invasive, well tolerated, does not require sedation and is a first-line small bowel investigative modality. As it transits through the entire gastrointestinal (GI) tract, it has the potential to provide a pan-enteric examination. Areas covered In this review we will discuss the new diagnostic modalities along with traditional methods which have been used for examination of the gastro intestinal (GI) tract. The main focus of this review will be on the use of capsule endoscopy for pan-enteric examination. Expert opinion Capsule endoscopy is an accepted first-line investigation for the small bowel. Diagnostic sensitivity of the colon capsule is comparable to colonoscopy in controlled trials and is being evaluated in high-risk patients in routine clinical practice in national programs. Preliminary data suggest that a magnetic-controlled examination of the upper GI tract could be developed to enable a complete upper GI examination.