Miracle-dz/UniFAR-FTUs huggingface dataset:
Artificial intelligence-based measurements of PET/CT imaging biomarkers are associated with disease-specific survival of high-risk prostate cancer patients

Abstract Objective Artificial intelligence (AI) offers new opportunities for objective quantitative measurements of imaging biomarkers from positron-emission tomography/computed tomography (PET/CT). Clinical image reporting relies predominantly on observer-dependent visual assessment and easily accessible measures like SUVmax, representing lesion uptake in a relatively small amount of tissue. Our hypothesis is that measurements of total volume and lesion uptake of the entire tumour would better reflect the disease`s activity with prognostic significance, compared with conventional measurements. Methods An AI-based algorithm was trained to automatically measure the prostate and its tumour content in PET/CT of 145 patients. The algorithm was then tested retrospectively on 285 high-risk patients, who were examined using 18F-choline PET/CT for primary staging between April 2008 and July 2015. Prostate tumour volume, tumour fraction of the prostate gland, lesion uptake of the entire tumour, and SUVmax were obtained automatically. Associations between these measurements, age, PSA, Gleason score and prostate cancer-specific survival were studied, using a Cox proportional-hazards regression model. Results Twenty-three patients died of prostate cancer during follow-up (median survival 3.8 years). Total tumour volume of the prostate (p = 0.008), tumour fraction of the gland (p = 0.005), total lesion uptake of the prostate (p = 0.02), and age (p = 0.01) were significantly associated with disease-specific survival, whereas SUVmax (p = 0.2), PSA (p = 0.2), and Gleason score (p = 0.8) were not. Conclusion AI-based assessments of total tumour volume and lesion uptake were significantly associated with disease-specific survival in this patient cohort, whereas SUVmax and Gleason scores were not. The AI-based approach appears well-suited for clinically relevant patient stratification and monitoring of individual therapy.
Anthropometric and Leg Power Factors Affect Offensive Kinetic Patterns in Fencing.

This study aimed to identify potential factors that may influence specific fencing offensive kinetic patterns in a large group of well-trained fencers having different ages, gender level, and training specialization. One-hundred-thirty fencers (males: n = 72) and (females: n = 58), participating in three different fencing weapons (epee, foil, and sabre), having considerable experience of national and international competitions. All members of seven national fencing teams were measured for basic anthropometric parameters, leg power performance and velocity values for three specific kinetic offensive patterns during an International Fencing camp. A multivariate analysis of variance (MANOVA) revealed a significant velocity multivariate effect in age competitive categories (Wilks Λ = 0.129, F = 2.112, p <0.01, n 2 = 0.060) gender (Wilks Λ = 0.103, F = 3.743, p < 0.05, n 2 = 0.103), competition levels (Wilks Λ = 0.863, F = 5.198, p <0.01, n 2 = 0.137) and discipline practiced (Wilks Λ = 0.239, F = 4.305, p < 0.001, n 2 = 0.119) respectively. Significant correlations were observed between lunge and step lunge velocity and long jump (LJ), countermovement jump (CMJ), drop jump (DJ), and reaction strength index (RSI). Age, gender, level of participants, and the choice of the weapon practiced, influenced fencing performance. Different leg power abilities could be decisive factors in training schedules design and monitoring training adaptations.
Ciguatoxin-Producing Dinoflagellate Gambierdiscus in the Beibu Gulf: First Report of Toxic Gambierdiscus in Chinese Waters

Ciguatera poisoning is mainly caused by the consumption of reef fish that have accumulated ciguatoxins (CTXs) produced by the benthic dinoflagellates Gambierdiscus and Fukuyoa. China has a long history of problems with ciguatera, but research on ciguatera causative organisms is very limited, especially in the Beibu Gulf, where coral reefs have been degraded significantly and CTXs in reef fish have exceeded food safety guidelines. Here, five strains of Gambierdiscus spp. were collected from Weizhou Island, a ciguatera hotspot in the Beibu Gulf, and identified by light and scanning electron microscopy and phylogenetic analyses based on large and small subunit rDNA sequences. Strains showed typical morphological characteristics of Gambierdiscus caribaeus, exhibiting a smooth thecal surface, rectangular-shaped 2′, almost symmetric 4″, and a large and broad posterior intercalary plate. They clustered in the phylogenetic tree with G. caribaeus from other locations. Therefore, these five strains belonged to G. caribaeus, a globally distributed Gambierdiscus species. Toxicity was determined through the mouse neuroblastoma assay and ranged from 0 to 5.40 fg CTX3C eq cell−1. The low level of toxicity of G. caribaeus in Weizhou Island, with CTX-contaminated fish above the regulatory level in the previous study, suggests that the long-term presence of low toxicity G. caribaeus might lead to the bioaccumulation of CTXs in fish, which can reach dangerous CTX levels. Alternatively, other highly-toxic, non-sampled strains could be present in these waters. This is the first report on toxic Gambierdiscus from the Beibu Gulf and Chinese waters and will provide a basis for further research determining effective strategies for ciguatera management in the area.
Comparison of the sensitivity of patient-reported outcomes for detecting the benefit of biologics in severe asthma

Background The sensitivity of patient-reported outcomes (PROs) to detect the effects of treatment change depends on the match between the change in items of the PRO and the change that takes place in a sample of people. The aim of this study is to compare the sensitivity of different PROs in detecting changes following the initiation of biologic treatment in asthma. Methods: Patients starting a biologic treatment as part of clinical care completed the Asthma Control Questionnaire (ACQ-6), the Severe Asthma Questionnaire (SAQ and SAQ-global scores) and the EQ5D (EQ-5D-5L and EQ5D-VAS) at baseline. They completed the ACQ-6, SAQ, SAQ-global and a retrospective global rating of change (GRoC) scale at weeks 4, 8 and 16 and completed the EQ-5D-5L and EQ5D-VAS at week 16. The SAQ-global and EQ5D-VAS differ but both are single item 100-point questions. Sensitivity was measured by Cohen’s D effect size at each of the three time points. Results: 110 patients were recruited. Depending on the time of assessment, effect size varied between 0.45 and 0.64 for the SAQ, between 0.50 and 0.77 for the SAQ-global; between 0.45 and 0.69 for ACQ-6; between 0.91 and 1.22 for GRoC; 0.32 for EQ-5D-5L and 0.49 for EQ5D-VAS. Conclusion: The sensitivity to change of a questionnaire varies with the time of measurement. The three asthma-specific prospective measures (SAQ, SAQ-global and ACQ-6) have similar sensitivity to change. The single-item EQ5D-VAS was less sensitive than the asthma specific measures and less sensitive than the single-item SAQ-global. The EQ-5D-5L was least sensitive.
Revision of hip flexor anatomy and function in modern humans, and implications for the evolution of hominin bipedalism

Hip flexor musculature was instrumental in the evolution of hominin bipedal gait and in endurance running for hunting in the genus Homo. The iliacus and psoas major muscles were historically considered to have separate tendons with different insertions on the lesser trochanter. However, in the early 20th century, it became “common knowledge” that the two muscles insert together on the lesser trochanter as the “iliopsoas” tendon. We revisited the findings of early anatomists and tested the more recent paradigm of a common “iliopsoas” tendon based on dissections of hips and their associated musculature (n = 17). We rediscovered that the tendon of the psoas muscle inserts only into a crest running from the superior to anterior aspect of the lesser trochanter, separate from the iliacus. The iliacus inserts fleshly into the anterior portion of the lesser trochanter and into an inferior crest extending from it. We developed 3D multibody dynamics biomechanical models for: (a) the conjoint “iliopsoas” tendon hypothesis and (b) the separate insertion hypothesis. We show that the conjoint model underestimates the iliacus' capacity to generate hip flexion relative to the separate insertion model. Further work reevaluating the primate lower limb (including human) through dissection, needs to be performed to develop those datasets for reconstructing anatomy in fossil hominins using the extant phylogenetic bracket approach, which is frequently used for tetrapods clades outside of paleoanthropology.
Systematic Review of Recent Lipidomics Approaches Toward Inflammatory Bowel Disease

Researchers have endeavored to identify the etiology of inflammatory bowel diseases, including Crohn’s disease and ulcerative colitis. Though the pathogenesis of inflammatory bowel diseases remains unknown, dysregulation of the immune system in the host gastrointestinal tract is believed to be the major causative factor. Omics is a powerful methodological tool that can reveal biochemical information stored in clinical samples. Lipidomics is a subset of omics that explores the lipid classes associated with inflammation. One objective of the present systematic review was to facilitate the identification of biochemical targets for use in future lipidomic studies on inflammatory bowel diseases. The use of high-resolution mass spectrometry to observe alterations in global lipidomics might help elucidate the immunoregulatory mechanisms involved in inflammatory bowel diseases and discover novel biomarkers for them. Assessment of the characteristics of previous clinical trials on inflammatory bowel diseases could help researchers design and establish patient selection and analytical method criteria for future studies on these conditions. In this study, we curated literature exclusively from four databases and extracted lipidomics-related data from literature, considering criteria. This paper suggests that the lipidomics approach toward research in inflammatory bowel diseases can clarify their pathogenesis and identify clinically valuable biomarkers to predict and monitor their progression.
Longitudinal Body Weight Change, Visit-To-Visit Body Weight Fluctuation, and Cognitive Decline Among Older Adults.

BACKGROUND The evidence regarding dementia and late-life weight change is inconsistent, and data on body weight fluctuation and dementia are limited. OBJECTIVE To test the hypothesis that weight loss and substantial weight fluctuation predict cognitive decline independent of body weight and traditional risk factors of dementia. METHODS This study utilized longitudinal data from the National Alzheimer's Coordinating Center for 10,639 stroke- and dementia-free older adults (60.9%female, mean age 71.6 years, median follow-up 5.5 years). Trends in weight change and weight fluctuation were estimated for each individual by regressing repeated body weight measurements on time. Cognitive decline was examined as diagnostic progression from normal to mild cognitive impairment (MCI) or dementia and from MCI to dementia. RESULTS Compared to participants with stable weight, those with weight loss had increased odds of diagnostic progression (adjusted OR = 1.35, 95%CI [1.21, 1.51]). Also, large weight fluctuation was associated with increased odds of diagnostic progression (OR comparing the extreme quartiles = 1.20, 95%CI [1.04, 1.39]) after adjusting for traditional risk factors for dementia and body weight change. The magnitude of the association appeared larger among those older than 80 and those with 3 or more cardiometabolic risk factors at baseline (both p for interaction < 0.05). CONCLUSION Weight loss and substantial weight fluctuation during late-life were associated with increased odds of cognitive decline independent of body weight and traditional risk factors of dementia. Our results suggested the linkage between late-life body weight instability and cognitive decline especially among those with greater age or higher cardiometabolic risk.
Improvement of the Collection, Maintenance, and Analysis of Neoplastic Cells from Urine Specimens with the Use of CytoMatrix

Urine cytology is a non-invasive test used in combination with cystoscopy for screening and follow-up of urothelial carcinoma (UC). Although cytology can be used to efficiently identify high-grade UC, it has a lower accuracy for the diagnosis of low-grade UC or patients with presence of atypical urothelial cells (AUC). For these reasons, ancillary tests have been added to urine cytology in order to improve the accuracy. However, the poor abundance of neoplastic cells in most samples and the absence of a “tissue-like” structure remains a major challenge. We used a novel synthetic support called CytoMatrix which has the property of capturing and storing cells and micro-macro aggregates within its three-dimensional structure. The urine specimens were obtained from 12 patients: 6 with suspected urothelial neoplasia (low- and high-grade) and 6 with AUC or non-neoplastic samples. The first step is the urine samples preparation, through several centrifugation passages; the second step consists in absorbing cells on the CytoMatrix, and in the subsequent formalin fixation, standard processing and paraffin embedding to prepare FFPE-CytoMatrix block. In the final step, sections are consecutively cut, stained with hematoxylin-eosin (H&E), and analyzed via UroVysion FISH and immunohistochemistry (IHC). Using our simple and reliable protocol, we can improve the quality of urine specimens, allowing a better collection, maintenance, and analysis of cells, with the advantage of using ancillary tests to support cytological diagnosis and the advantage of storing cellular material in a FFPE-CytoMatrix block.
The yeastGemMap: A process diagram to assist yeast systems‐metabolic studies

Visualization is a key aspect of the analysis of omics data. Although many tools can generate pathway maps for visualization of yeast metabolism, they fail in reconstructing genome‐scale metabolic diagrams of compartmentalized metabolism. Here we report on the yeastGemMap, a process diagram of whole yeast metabolism created to assist data analysis in systems‐metabolic studies. The map was manually reconstructed with reactions from a compartmentalized genome‐scale metabolic model, based on biochemical process diagrams typically found in educational and specialized literature. The yeastGemMap consists of 3815 reactions representing 1150 genes, 2742 metabolites, and 14 compartments. Computational functions for adapting the graphical representation of the map are also reported. These functions modify the visual representation of the map to assist in three systems‐metabolic tasks: illustrating reaction networks, interpreting metabolic flux data, and visualizing omics data. The versatility of the yeastGemMap and algorithms to assist visualization of systems‐metabolic data was demonstrated in various tasks, including for single lethal reaction evaluation, flux balance analysis, and transcriptomic data analysis. For instance, visual interpretation of metabolic transcriptomes of thermally evolved and parental yeast strains allowed to demonstrate that evolved strains activate a preadaptation response at 30°C, which enabled thermotolerance. A quick interpretation of systems‐metabolic data is promoted with yeastGemMap visualizations.
Multi-trait genomic-enabled prediction enhances accuracy in multi-year wheat breeding trials

Abstract Implementing genomic-based prediction models in genomic selection requires an understanding of the measures for evaluating prediction accuracy from different models and methods using multi-trait data. In this study, we compared prediction accuracy using six large multi-trait wheat data sets (quality and grain yield). The data were used to predict 1 year (testing) from the previous year (training) to assess prediction accuracy using four different prediction models. The results indicated that the conventional Pearson’s correlation between observed and predicted values underestimated the true correlation value, whereas the corrected Pearson’s correlation calculated by fitting a bivariate model was higher than the division of the Pearson’s correlation by the squared root of the heritability across traits, by 2.53–11.46%. Across the datasets, the corrected Pearson’s correlation was higher than the uncorrected by 5.80–14.01%. Overall, we found that for grain yield the prediction performance was highest using a multi-trait compared to a single-trait model. The higher the absolute genetic correlation between traits the greater the benefits of multi-trait models for increasing the genomic-enabled prediction accuracy of traits.
Recent Advances in Carbon Nanostructure-Based Electrochemical Biosensors for Environmental Monitoring

Abstract Environmental pollution has arisen from releasing pollutants into water sources in many parts of the world, endangering human health and marine environments. Chemical discharge may come from various places, including wastewater treatment plants, agriculture, manufacturing, and stormwater overflows. As a result, monitoring pollution including, heavy metals, pesticides, toxic gases, and other contaminants in environmental samples such as water (e.g., groundwater, surface water, and drinking water), air, soil, and vegetables is critical to eliminating or reducing their risk and toxicity. Real-time analysis may also have an effect on reducing consumption of a variety of harsh chemicals and reagents, with the additional benefit of on-site contaminant composition assessment prior to discharge into the setting. Electrochemical biosensors have received a lot of interest in solving this issue as a result of recent technological breakthroughs. This review presents the types and properties of carbon-based nanomaterials and their applications in electrochemical biosensors for environmental toxicants over the past five years. We emphasize the sensing performances of electrochemical biosensors in terms of limit of detection, linear range, and their applicability in real samples. This review would be helpful in raising awareness and understanding of the role of electrochemical biosensors in sustaining the environment. Graphical Abstract
Cerebrospinal fluid dynamics coupled to the global circulation in holistic setting: Mathematical models, numerical methods and applications

This paper presents a mathematical model of the global, arterio‐venous circulation in the entire human body, coupled to a refined description of the cerebrospinal fluid (CSF) dynamics in the craniospinal cavity. The present model represents a substantially revised version of the original Müller‐Toro mathematical model. It includes one‐dimensional (1D), non‐linear systems of partial differential equations for 323 major blood vessels and 85 zero‐dimensional, differential‐algebraic systems for the remaining components. Highlights include the myogenic mechanism of cerebral blood regulation; refined vasculature for the inner ear, the brainstem and the cerebellum; and viscoelastic, rather than purely elastic, models for all blood vessels, arterial and venous. The derived 1D parabolic systems of partial differential equations for all major vessels are approximated by hyperbolic systems with stiff source terms following a relaxation approach. A major novelty of this paper is the coupling of the circulation, as described, to a refined description of the CSF dynamics in the craniospinal cavity, following Linninger et al. The numerical solution methodology employed to approximate the hyperbolic non‐linear systems of partial differential equations with stiff source terms is based on the Arbitrary DERivative Riemann problem finite volume framework, supplemented with a well‐balanced formulation, and a local time stepping procedure. The full model is validated through comparison of computational results against published data and bespoke MRI measurements. Then we present two medical applications: (i) transverse sinus stenoses and their relation to Idiopathic Intracranial Hypertension; and (ii) extra‐cranial venous strictures and their impact in the inner ear circulation, and its implications for Ménière's disease.
Ethical tensions surrounding ‘third-party disclosure’ by participants: Lessons from participatory health research in Eswatini

ABSTRACT Third-party disclosure by participants is inherent to much global health research. It presents ethical tensions with respecting the autonomy and privacy of non-consenting individuals whose data are disclosed but is neglected in ethics guidelines. Our aim was to describe and ethically reflect on, third party disclosure in a community-participatory demographic and health survey (DHS) implemented within participatory health research (PHR) about community-based care of children affected by AIDS in Eswatini. We collected DHS data and analysed it statistically. We studied the PHR process and outcomes ethnographically and analysed the data interpretively, using theories that conceptualise secrecy as relational and power-laden. We found that third parties’ data were disclosed by DHS respondents (typically women), including data about health conditions, abuse perpetration and being a caregiving burden. Ethnographic findings suggested that some third parties may not have consented to us collecting their data. However, respecting third parties’ autonomy and privacy presents ethical tensions related to silencing survey respondents and impairing knowledge creation. To minimise the ethical tensions surrounding third-party disclosure researchers can analyse risks, benefits and power dynamics and extend their ethical responsibilities to protect participants to also protect non-participants, and from data collection to also include reporting.
Ozonated Olive Oil with a High Peroxide Value for Topical Applications: In-Vitro Cytotoxicity Analysis with L929 Cells

ABSTRACT Previous studies have shown that ozonated vegetable oils have been used topically for healing of cutenous wounds. The aim of this study is to evaluate the dose dependent use of ozonated olive oil with high peroxide value (OZ) on the viability of cells for preventing side effects in topical applications. To the best of our knowledge, there are no reports investigaing the effect of peroxide value of ozonated olive oil associated with its cytotoxic activity on mouse non-neoplastc fibroblast cell lines (L929). Therefore, the present study was carried out by using OZ alone and/or in combination with glycerol and olive oil. In our study OZ was prepared by using pure olive oil. Both olive oil and glycerol are non-toxic and can be mixed with OZ uniformly. The cytotoxic activity of samples against L929 fibroblasts was assessed using the tetrazolium salt 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyltetrazolium bromide (MTT) assay. The peroxide value of synthesized OZ was found to be in the range of 2700–2900 mEq O2/kg oil. The OZ/olive oil group did not show any cell death at all concentrations tested (p > 0.05) however OZ/glycerol group showed statistically significant reductions in viability at higher concentrations (p = 0.004–0.006) compared to the control group. Conclusively, using OZ/olive oil with a peroxide value of 2700–2900 mEq O2/kg oil for short-term incubation was non-cytotoxic to the L929 fibroblast cell line.