Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of asymmetry and energy cost generated from predictive simulations of hemiparetic gait

Hemiparesis, defined as unilateral muscle weakness, often occurs in people post-stroke or people with cerebral palsy, however it is difficult to understand how this hemiparesis affects movement patterns as it often presents alongside a variety of other neuromuscular impairments. Predictive musculoskeletal modeling presents an opportunity to investigate how impairments affect gait performance assuming a particular cost function. Here, we use predictive simulation to quantify the spatiotemporal asymmetries and changes to metabolic cost that emerge when muscle strength is unilaterally reduced and how reducing spatiotemporal symmetry affects metabolic cost. We modified a 2-D musculoskeletal model by uniformly reducing the peak isometric muscle force unilaterally. We then solved optimal control simulations of walking across a range of speeds by minimizing the sum of the cubed muscle excitations. Lastly, we ran additional optimizations to test if reducing spatiotemporal asymmetry would result in an increase in metabolic cost. Our results showed that the magnitude and direction of effort-optimal spatiotemporal asymmetries depends on both the gait speed and level of weakness. Also, the optimal speed was 1.25 m/s for the symmetrical and 20% weakness models but slower (1.00 m/s) for the 40% and 60% weakness models, suggesting that hemiparesis can account for a portion of the slower gait speed seen in people with hemiparesis. Modifying the cost function to minimize spatiotemporal asymmetry resulted in small increases (~4%) in metabolic cost. Overall, our results indicate that spatiotemporal asymmetry may be optimal for people with hemiparesis. Additionally, the effect of speed and the level of weakness on spatiotemporal asymmetry may help explain the well-known heterogenous distribution of spatiotemporal asymmetries observed in the clinic. Future work could extend our results by testing the effects of other neuromuscular impairments on optimal gait strategies, and therefore build a more comprehensive understanding of the gait patterns observed in clinical populations.
Methodological reflections on health system-oriented assessment of maternity care in 16 hospitals in sub-Saharan Africa: an embedded case study

Abstract Health facility assessments (HFAs) assessing facilities’ readiness to provide services are well-established. However, HFA questionnaires are typically quantitative and lack depth to understand systems in which health facilities operate—crucial to designing context-oriented interventions. We report lessons from a multiple embedded case study exploring the experiences of HFA data collectors in implementing a novel HFA tool developed using systems thinking approach. We assessed 16 hospitals in four countries (Benin, Malawi, Tanzania and Uganda) as part of a quality improvement implementation research. Our tool was organized in 17 sections and included dimensions of hospital governance, leadership and financing; maternity care standards and procedures; ongoing quality improvement practices; interactions with communities and mapping of the areas related to maternal care. Data for this study were collected using in-depth interviews with senior experts who conducted the HFA in the countries 1–3 months after completion of the HFAs. Data were analysed using the inductive thematic analysis approach. Our HFA faced challenges in logistics (accessing key hospital-based respondents, high turnover of managerial staff and difficulty accessing information considered sensitive in the context) and methodology (response bias, lack of data quality and data entry into an electronic platform). Data elements of governance, leadership and financing were the most affected. Opportunities and strategies adopted aimed at enhancing data collection (building on prior partnerships and understanding local and institutional bureaucracies) and enhancing data richness (identifying respondents with institutional memory, learning from experience and conducting observations at various times). Moreover, HFA data collectors conducted abstraction of records and interviews in a flexible and adaptive way to enhance data quality. Lessons and new skills learned from our HFA could be used as inputs to respond to the growing need of integrating the systems thinking approach in HFA to improve the contextual understanding of operations and structure.
Dual-function DEFENSIN 8 mediates phloem cadmium unloading and accumulation in rice grains

Abstract Grain cadmium (Cd) is translocated from source to sink tissues exclusively via phloem, though the phloem Cd unloading transporter has not been identified yet. Here, we isolated and functionally characterized a defensin-like gene DEFENSIN 8 (DEF8) highly expressed in rice (Oryza sativa) grains and induced by Cd exposure in seedling roots. Histochemical analysis and subcellular localization detected DEF8 expression preferentially in pericycle cells and phloem of seedling roots, as well as in phloem of grain vasculatures. Further analysis demonstrated that DEF8 is secreted into extracellular spaces possibly by vesicle trafficking. DEF8 bound to Cd in vitro, and Cd efflux from protoplasts as well as loading into xylem vessels decreased in the def8 mutant seedlings compared with the wild type. At maturity, significantly less Cd accumulation was observed in the mutant grains. These results suggest that DEF8 is a dual function protein that facilitates Cd loading into xylem and unloading from phloem, thus mediating Cd translocation from roots to shoots and further allocation to grains, representing a phloem Cd unloading regulator. Moreover, essential mineral nutrient accumulation as well as important agronomic traits were not affected in the def8 mutants, suggesting DEF8 is an ideal target for breeding low grain Cd rice.
Advances in the management of liver and biliary tumors

Over the past 50 years, the management of liver and biliary tumors has evolved significantly. Initially considered highly morbid and lethal, resection is now the treatment of choice for a significant proportion of patients with malignant and benign hepatobiliary disease. Improved operative/anesthetic techniques, use of parenchymal‐sparing approaches, better patient selection for surgery, effective liver‐directed therapies, and new insights into tumor biology are significant contributors to our transformed approach to hepatobiliary neoplasms.
MicroRNA in the diagnosis of lung cancer: An overview of ten systematic reviews

Objective To provide theoretical support for clinical diagnosis of lung cancer through an overview of systematic reviews (SRs) of the diagnostic value of miRNA. Methods We searched PubMed, Embase, and the Cochrane Library to collect SRs of the diagnostic value of microRNA for lung cancer until April 2021. A comprehensive database search was carried out, screened, and extracted information independently by two researchers, to compare and analyze the sensitivity and specificity of relevant literatures. The ROBIS tool was applied to assess the risk of bias of included SRs and meta-analysis. Results A total of 10 SRs were included the results of risk of bias assessment by ROBIS tool showed: 10 SRs completely matched the four questions of phase one. In phase two, nine SRs were low risk of bias in the including criteria field; one study was uncertain; nine SRs were low risk of bias, one study was uncertain in the literature search and screening field; nine SRs were low risk of bias in the data abstraction and quality assessment field, one SR was high; and 10 SRs were low risk of bias in the data synthesis field. In the phase three of comprehensive risk of bias results, 8 studies were low risk, one was high risk, and one study was uncertain. MiRNA had a pooled sensitivity of 0.77 (95% CI: 0.73–0.81) and specificity of 0.81 (95% CI: 0.79–0.84). The summarized area under the SROC curve was 0.86 (95% CI: 0.83–0.89), and combined diagnostic odds ratio was 14.68 (10.87–19.81). The sensitivity and specificity of multiple MicroRNA was 0.80 (0.73–0.85) and 0.80 (0.76–0.83); the sensitivity and specificity of single MicroRNA was 0.74 (0.69–0.79) and 0.83 (0.80–0.88). Conclusion MiRNA is a promising biomarker for the diagnosis of lung cancer in Chinese population, with advanced sensitivity and specificity. It provides a faster and less invasive assessment of lung cancer than other markers that require histopathological analysis. We should improve the reliability of the conclusion. The construction of diagnosis for lung cancer provides reliable evidence support.
Comparative genomics reveals putative evidence for high-elevation adaptation in the American pika (Ochotona princeps)

Abstract High-elevation environments have lower atmospheric oxygen content, reduced temperatures, and higher levels of UV radiation than found at lower elevations. As such, species living at high elevations must overcome these challenges to survive, grow, and reproduce. American pikas (Ochotona princeps) are alpine lagomorphs that are habitat specialists typically found at elevations >2,000 m. Previous research has shown putative evidence for high-elevation adaptation; however, investigations to date have been limited to a fraction of the genome. Here, we took a comparative genomics approach to identify putative regions under selection using a chromosomal reference genome assembly for the American pika relative to 8 other mammalian species targeted based on phylogenetic relatedness and (dis)similarity in ecology. We first identified orthologous gene groups across species and then extracted groups containing only American pika genes as well as unclustered pika genes to inform functional enrichment analyses; among these, we found 141 enriched terms with many related to hypoxia, metabolism, mitochondrial function/development, and DNA repair. We identified 15 significantly expanded gene families within the American pika across all orthologous gene groups that displayed functionally enriched terms associated with hypoxia adaptation. We further detected 196 positively selected genes, 41 of which have been associated with putative adaptation to hypoxia, cold tolerance, and response to UV following a literature review. In particular, OXNAD1, NRDC, and those genes critical in DNA repair represent important targets for future research to examine their functional implications in the American pika, especially as they may relate to adaptation to rapidly changing environments.
Racial/ethnic differences in fibrosis prevalence and progression in biopsy‐proven steatosis: A focus on the Asian American population

Fatty liver disease (FLD) is a leading cause of chronic liver disease (CLD) globally, and vulnerable populations are disproportionately affected. Prior studies have suggested racial/ethnic differences in FLD prevalence and severity; however, these studies often excluded Asian Americans. This study aims to evaluate racial/ethnic differences in the prevalence of, and predictors associated with steatohepatitis, advanced fibrosis, and fibrosis progression over time within a diverse population. Using descriptive analyses and multivariable modeling, we performed a longitudinal evaluation of 648 patients with histologic evidence of FLD (steatosis or steatohepatitis) from August 2009 to February 2020 within San Francisco's safety‐net health care system. Overall demographics were median age of 53 years, 54% male, and 38% Asian (40% Hispanic, 14% White). On histology, 61% had steatohepatitis and 30% had advanced fibrosis (≥F3). The comparison between steatosis and steatohepatitis groups showed differences in sex, race/ethnicity, metabolic risk factors, and co‐existing CLD (predominantly viral hepatitis); patients with steatosis were more likely to be Asian (50%), and those with steatohepatitis were more likely to be Hispanic (51%). On multivariable modeling, while Asian race (vs. non‐Asian) was not associated with steatohepatitis or advanced fibrosis when models included all relevant clinical predictors, Asian race was associated with higher relative risk of fibrosis progression as defined by change in Fibrosis‐4 category over time (relative risk ratio = 1.9; p = 0.047). Conclusion: In this vulnerable population with a large proportion of Asian Americans, Asian race was associated with progression of fibrosis. Given the relative paucity of data in this high‐risk group, future studies should confirm these findings.
Consensus Clustering With Co-Association Matrix Optimization

Consensus clustering can derive a more promising and robust clustering result by integrating multiple partitions strategically. However, there are several limitations in the existing approaches: 1) most of the methods compute the ensemble-information matrix heuristically and lack of sufficient optimization; 2) the information from the original dataset is rarely considered; and 3) the noise in both label space and feature space is ignored. To address these issues, we proposed a novel consensus clustering method with co-association matrix optimization (CC-CMO), which aims at improving the co-association matrix by taking abundant information from both label space and feature space into consideration. In label space, CC-CMO derives a weighted partition matrix capturing the intercluster correlation and further designs a least squares regression (LSR) model to explore the global structure of data. In feature space, CC-CMO minimizes the reconstruction error with doubly stochastic normalization in the projective subspace to eliminate noise features as well as learn the local affinity of data. To improve the co-association matrix by jointly considering the subspace representation, global structure, and local affinity of data, we explicitly propose a unified optimization framework and design an alternating optimization algorithm for the optimal co-association matrix. Extensive experiments on a variety of real-world datasets demonstrate the superior performance of CC-CMO to the state-of-the-art consensus clustering approaches.
A randomized dietary intervention to increase colonic and peripheral blood SCFAs modulates the blood B- and T-cell compartments in healthy humans

ABSTRACT Background SCFAs have immune-modulating effects in animal models of disease. However, there is limited evidence that this may occur in humans. Objectives This study aimed to determine the effects of increased exposure to SCFAs via dietary manipulation on colonic fermentation and adaptive immune cells. Methods Twenty healthy young adults (18–45 y of age) underwent a blinded randomized crossover dietary intervention, consuming a high-SCFA diet and a matched low-SCFA diet for 21-d with a 21-d washout in between. SCFAs were provided through resistant starch, inulin, and apple cider vinegar. Blood and 3-d total fecal output were collected at baseline and at the end of each diet. GC was used to measure fecal and plasma SCFA. Flow cytometry was used for peripheral blood immunophenotyping. Results According to a paired samples Wilcoxon test, the high-SCFA diet was associated with significantly higher fecal SCFA concentrations [median (IQR); 86.6 (59.0) compared with 75.4 (56.2) µmol/g, P = 0.02] and lower fecal ammonia concentrations [26.2 (14.7) compared with 33.4 (18.5) µmol/g, P = 0.04] than the low-SCFA diet. Plasma propionate [9.87 (12.3) compared with 4.72 (7.6) µmol/L, P = 0.049] and butyrate [2.85 (1.35) compared with 2.02 (1.29) µmol/L, P = 0.03] were significantly higher after the high-SCFA diet than after the low-SCFA diet. Blood total B cells [184 (112) compared with 199 (143) cells/µL, P = 0.04], naive B cells [83 (66) compared with 95 (89) cells/µL, P = 0.02], Th1 cells [22 (19) compared with 29 (16) cells/µL, P = 0.03], and mucosal-associated invariant T cells [62 (83) compared with 69 (114) cells/µL, P = 0.02] were significantly lower after the high-SCFA diet than the low-SCFA diet. Conclusions Increasing colonic and peripheral blood SCFA has discrete effects on circulating immune cells in healthy humans following 3-wk intervention. Further studies (e.g., in patients with inflammatory disease) are necessary to determine whether 1) these changes have immunomodulatory effects, 2) they are therapeutically beneficial, and 3) prolonged intake might be required. This trial is registered at the Australian New Zealand Clinical Trials Registry as ACTRN12618001054202.
Do Weightbearing Restrictions Cause Excess Weight Gain in Children With LEGG-Calvé-Perthes Disease?

Background: Restricted weight bearing is commonly prescribed in Legg-Calvé-Perthes Disease (LCPD), raising concerns of causing overweight or obesity. This study utilizes prospectively collected data to address the following questions: (1) does body mass index (BMI) Z-score increase over the course of LCPD follow-up; (2) is having a BMI category of normal, overweight, or obese at baseline associated with BMI Z-score changes over the course of follow-up; and (3) is the duration of weight bearing restrictions (no restrictions, <3, 3 to <6, 6 to 9, or >9 mo) associated with BMI Z-score changes. Methods: Data of 130 children aged 5 to 12 years with unilateral early-stage LCPD were extracted from an international database. Nation-specific BMI Z-scores and percentile-based weight categories were determined, and the duration of follow-up and weight bearing restrictions were calculated. Longitudinal changes in BMI Z-scores were evaluated for the 3 study questions using mixed effects linear regression models with surgery as a covariate. Sensitivity analyses were used to determine the influence of socio-cultural background (USA vs. India) for each study question. Results: During the 35.5±15.9 months of follow-up, no statistically significant increase in BMI Z-scores was observed across the entire cohort, or following stratification by baseline weight categories or the duration of the weight bearing restriction. Sensitivity analyses indicated that patients in the USA had no change in their BMI Z-score. When stratified by weight categories, the normal weight of US children had a small increase in their BMI Z-score (0.005 per mo, 95% confidence interval: 0.0002, 0.009), but this was not seen in other BMI categories. The cohort of Indian children had a small but significant decrease in their BMI Z-score (−0.005/mo, 95% CI: −0.009, −0.0002). After stratification by weight categories, a small decrease of the BMI Z-score was observed only in the Indian overweight children (−0.016 per mo, 95% CI: −0.027, −0.005) and no other BMI category. Conclusions: Weightbearing restrictions over the course of follow-up for our cohort of children with early-stage LCPD were not associated with clinically meaningful increases of BMI Z-scores. Weight gain is multi-factorial and probably not caused by weight bearing restrictions alone. Level of Evidence: III Diagnostic Study.
A Deep Convolutional Autoencoder for Automatic Motion Artifact Removal in Electrodermal Activity Signals: A Preliminary Study

Automatic motion artifact (MA) removal in electrodermal activity (EDA) signals is a major challenge because of the aperiodic and irregular characteristics of EDA. Given the lack of a suitable MA removal algorithm, a substantial amount of EDA data is typically discarded, especially during ambulatory monitoring. Current methods for MA removal in EDA are feasible when data are corrupted with low magnitude artifacts. In this study, we propose a more data-driven deep convolutional autoencoder (DCAE) for automated motion artifact removal in EDA signals. The DCAE was trained using several publicly available datasets. We used both Gaussian white noise (GWN) and real-life induced MA data records collected in a laboratory setting to corrupt the clean EDA signals. We compared the performance of our DCAE network with three state-of-the-art methods using the performance metrics the signal-to-noise ratio (SNR) improvement (SNRimp), and the mean squared error (MSE). The proposed DCAE provided significantly higher SNRimpand lower MSE compared to three other methods for both synthetically and real-life induced MA. While the work is preliminary, this work illustrates a promising approach which can potentially be used to remove many different types of MA.
Action‐project method: An approach to describing and studying goal‐oriented joint actions

Practicing health professionals and educators frequently act together in an interdependent or joint capacity to reach goals. Teaching or learning a new skill or engaging with patients in shared decision‐making exemplifies this joint and goal‐directed nature of Health Professions Education (HPE) and practice. However, building a robust understanding of the complexity of action, and joint action in particular, in HPE or patient care remains a challenge because of a limited number of methodologies available within HPE research.
Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding

Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant–pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high‐throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant–pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant–pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high‐throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.
Bayesian Analysis of Nested Logit Model by Markov Chain Monte Carlo

We develop a Markov Chain Monte Carlo (MCMC) algorithm for estimating nested logit models in a Bayesian framework. Appropriate "heating target" and reparameterization techniques are adopted for fast mixing. For illustrative purposes, we have implemented the algorithm on two real-life examples involving 3-level structures. The first example involves Social Security's disability determination process, Lahiri et al. (1995). The second one is taken from Amemiya and Shimono's (1989) model of labor supply behavior of the aged. We applied a combination of various convergence criteria to ensure that the chain has converged to its target distribution.
Simplicial Bernstein form and positivity certificates for solutions obtained in a stationary digital twin by Bernstein Bubnov-Galerkin method

In this article, using the simplicial Bernstein form of polynomials on a simplex, we provide positivity certificates for the approximate solution of a linear elliptic PDE obtained by simplicial Bernstein Bubnov-Galerkin method. Particularly, we show how to obtain a simplicial Bernstein certificate of positivity for the approximate solution, although the discretized system does not satisfy a discrete weak maximum principle.