Miracle-dz/UniFAR-FTUs huggingface dataset:
Urethral Interfractional Geometric and Dosimetric Variations of Prostate Cancer Patients: A Study Using an Onboard MRI

Purpose For a cohort of prostate cancer patients treated on an MR-guided radiotherapy (MRgRT) system, we retrospectively analyzed urethral interfractional geometric and dosimetric variations based on onboard MRIs acquired at different timepoints and evaluated onboard prostatic urethra visualization for urethra-focused online adaptive RT. Methods Twenty-six prostate cancer patients were prospectively scanned on a 0.35-T MRgRT system using an optimized T2-weighted HASTE sequence at simulation and final fraction. Two radiation oncologists (RO1 and RO2) contoured the urethras on all HASTE images. The simulation and final fraction HASTE images were rigidly registered, and urethral interobserver and interfractional geometric variation was evaluated using the 95th percentile Hausdorff distance (HD95), mean distance to agreement (MDA), center-of-mass shift (COMS), and DICE coefficient. For dosimetric analysis, simulation and final fraction HASTE images were registered to the 3D bSSFP planning MRI and 3D bSSFP final setup MRI, respectively. Both ROs’ urethra contours were transferred from HASTE images for initial treatment plan optimization and final fraction dose estimation separately. Stereotactic body radiotherapy (SBRT) plans, 40 Gy in 5 fractions, were optimized to meet clinical constraints, including urethral V42Gy ≤0.03 cc, on the planning MRI. The initial plan was then forward calculated on the final setup MRI to estimate urethral dose on the final fraction and evaluate urethral dosimetric impact due to anatomy change. Results The average interobserver HD95, MDA, COMS, and DICE were 2.85 ± 1.34 mm, 1.02 ± 0.36 mm, 3.16 ± 1.61 mm, and 0.58 ± 0.15, respectively. The average interfractional HD95, MDA, COMS, and DICE were 3.26 ± 1.54 mm, 1.29 ± 0.54 mm, 3.34 ± 2.01 mm, and 0.49 ± 0.18, respectively. All patient simulation MRgRT plans met all clinical constraints. For RO1 and RO2, 23/26 (88%) and 21/26 (81%) patients’ final fraction estimated urethral dose did not meet the planned constraint. The average urethral V42Gy change was 0.48 ± 0.58 cc. Conclusion Urethral interfractional motion and anatomic change can result in daily treatment violating urethral constraints. Onboard MRI with good visualization of the prostatic urethra can be a valuable tool to help better protect the urethra through patient setup or online adaptive RT.
Risk of New-Diagnosed Atrial Fibrillation After Transient Ischemic Attack

Background Transient ischemic attack (TIA) provides a unique opportunity to optimize secondary preventive treatments to avoid subsequent ischemic stroke (SIS). Although atrial fibrillation (AF) is the leading cause of cardioembolism in IS and anticoagulation prevents stroke recurrence (SR), limited data exists about the risk of new-diagnosed AF (NDAF) after TIA and the consequences of the diagnostic delay. The aim of our study was to determine this risk in a cohort of TIA patients with long-term follow-up. Methods We carried out a prospective cohort study of 723 consecutive TIA patients from January 2006 to June 2010. Median follow-up was 6.5 (5.0–9.6) years. In a subgroup of 204 (28.2%) consecutive patients, a panel of biomarkers was assessed during the first 24 h of the onset of symptoms. Multivariate analyses were performed to find out the associated factors of NDAF. Kaplan-Meier analysis was also performed to analyzed risk of SIS. Results NDAF was indentified in 116 (16.0%) patients: 42 (36.2%) during admission, 18 (15.5%) within first year, 29 (25%) between one and five years and 27 (23.3%) beyond 5 years. NDAF was associated with sex (female) [hazard ratio (HR) 1.61 (95% CI, 1.07- 2.41)], age [[HR 1.05 (95% CI, 1.03–1.07)], previous ischemic heart disease (IHD) [HR 1.84, (95% CI 1.15–2.97)] and cortical DWI pattern [HR 2.81 (95% CI, 1.87–4.21)]. In the Kaplan-Meier analysis, NT-proBNP ≥ 218.2 pg/ml (log-rank test P < 0.001) was associated with significant risk of NDAF during the first 5 years of follow-up. Patients with NDAF after admission and before 5 years of follow-up had the highest risk of SIS (P = 0.002). Conclusion The risk of NDAF after TIA is clinically relevant. We identified clinical and neuroimaging factors of NDAF. In addition, NT-proBNP was related to NDAF. Our results can be used to evaluate the benefit of long-term cardiac monitoring in selected patients.
Screening for an Underlying Tubulopathy in Children With Growth Failure, Simply Maths?

Background Involving pediatric nephrological input in the clinical diagnostic work-up of children with short stature, gave rise to the hypothesis that the presence of an underlying renal tubular disorder in children with short stature is possibly underestimated. This study focussed on the added value of calculated urinary fractional excretion (FE) in the early detection of tubular disorders in children with growth failure. Methods This trial was designed as an observational study analyzing the medical files of children between 5 and 16 years who had been referred for short stature to the pediatric endocrinology outpatient clinic at the University Hospital Antwerp between 25/01/2015 and 01/03/2019. Based on the laboratory results of the simultaneously taken blood and urine sample, the fractional excretions of Sodium, Chloride, Potassium, Calcium, Phosphate, and Magnesium were calculated. Results Of the 299 patients, 54 patients had at least one deviating fractional excretion value, requiring further investigation (control sample of blood and urine, kidney ultrasound or 24 h urine collection). Genetic screening for tubulopathies was performed in 19 patients. In 5 patients (1.7% of the total population) a tubulopathy was confirmed based on genetic analysis. Conclusion This study explored the possibility of using fractional excretions as a screening test to obtain an earlier diagnosis of tubular disorders in children with short stature. Of the 299 patients, 5 patients were diagnosed with a genetically confirmed tubulopathy. Based on these results, we propose a flowchart for an additional work-up in all children with a deviating fractional excretion.
Genomic Regions Associated With Seed Meal Quality Traits in Brassica napus Germplasm

The defatted Brassica napus (rapeseed) meal can be high-protein feed for livestock as the protein value of rapeseed meal is higher than that of the majority of other vegetable proteins. Extensive work has already been carried out on developing canola rapeseed where the focus was on reducing erucic acid and glucosinolate content, with less consideration to other antinutritional factors such as tannin, phytate, sinapine, crude fiber, etc. The presence of these antinutrients limits the use and marketing of rapeseed meals and a significant amount of it goes unused and ends up as waste. We investigated the genetic architecture of crude protein, methionine, tryptophan, total phenols, β-carotene, glucosinolates (GLSs), phytate, tannins, sinapine, and crude fiber content of defatted seed meal samples by conducting a genome-wide association study (GWAS), using a diversity panel comprising 96 B. napus genotypes. Genotyping by sequencing was used to identify 77,889 SNPs, spread over 19 chromosomes. Genetic diversity and phenotypic variations were generally high for the studied traits. A total of eleven genotypes were identified which showed high-quality protein, high antioxidants, and lower amount of antinutrients. A significant negative correlation between protein and limiting amino acids and a significant positive correlation between GLS and phytic acid were observed. General and mixed linear models were used to estimate the association between the SNP markers and the seed quality traits and quantile-quantile (QQ) plots were generated to allow the best-fit algorithm. Annotation of genomic regions around associated SNPs helped to predict various trait-related candidates such as ASP2 and EMB1027 (amino acid biosynthesis); HEMA2, GLU1, and PGM (tryptophan biosynthesis); MS3, CYSD1, and MTO1 (methionine biosynthesis); LYC (β-carotene biosynthesis); HDR and ISPF (MEP pathway); COS1 (riboflavin synthesis); UGT (phenolics biosynthesis); NAC073 (cellulose and hemicellulose biosynthesis); CYT1 (cellulose biosynthesis); BGLU45 and BGLU46 (lignin biosynthesis); SOT12 and UGT88A1 (flavonoid pathway); and CYP79A2, DIN2, and GSTT2 (GLS metabolism), etc. The functional validation of these candidate genes could confirm key seed meal quality genes for germplasm enhancement programs directed at improving protein quality and reducing the antinutritional components in B. napus.
A short-term cooling of root-zone temperature increases bioactive compounds in baby leaf Amaranthus tricolor L.

Leafy vegetables that are offered as seedling leaves with petioles are referred to as baby leaf vegetables. One of the most nutritious baby leaves, amaranth (Amaranthus tricolor L.), contains several bioactive compounds and nutrients. Here, we investigated the growth and quality of baby leaf amaranth using a variety of short-term cooling root-zone temperatures (RZT; 5, 10, 15, and 20°C), periods (1, 3, 5, and 7 days), and combinations thereof. We observed that exposing amaranth seedlings to RZT treatments at 5 and 10°C for 1–3 days increased the antioxidant capacity and the concentrations of bioactive compounds, such as betalain, anthocyanin, phenolic, flavonoid, and ascorbic acid; however, extending the treatment period to 7 days decreased them and adversely affected growth. For RZT treatments at 20°C, leaf photosynthetic pigments, bioactive compounds, nutrients, and antioxidant capacity increased gradually as the treatment period was extended to 7 days. The integration of RZTs at 5 and 10°C for one day preceded or followed by an RZT treatment at 20°C for 2 days had varied effects on the growth and quality of amaranth leaves. After one day of RZT treatment at 5°C followed by 2 days of RZT treatment at 20°C, the highest concentrations of bioactive compounds, nutrients, and antioxidant capacity were 1.4–3.0, 1.7, and 1.7 times higher, respectively, than those of the control, and growth was not impaired. The short-term cooling RZT treatments under controlled environments were demonstrated to be adequate conditions for the improvement of target bioactive compounds in amaranth baby leaf without causing leaf abnormality or growth impairment.
Effects of a Hydropower-Related Temporary Stream Dewatering on Fish Community Composition and Development: From Ecology to Policy

Hydropower use of rivers can exert multiple effects on aquatic species and habitats. Due to limitations of conservation projects in the main channels of hydropower-affected rivers, there has been an increasing focus on tributaries, side channels, and fish passes as target areas for conservation and restoration. However, some of these side channels require frequent dewatering for their maintenance, and the ecological effects of such measures remain largely unknown. In this study, we used two dewatering events in a side channel of the River Inn as an opportunity to assess the effects of these common measures on fish. All stranded fish were collected after the two dewatering events in remaining puddles of formerly restored bank habitats, determined to species level, and measured. The fish community was compared by electrofishing before and seven weeks after the dewatering in a subset of the same habitats. The dewatering created one to three remaining puddles in the bank habitats, covering 3% of the assessed bank habitat area. In these remaining puddles, 184 stranded fish from 12 species were found, including species strictly protected under national and international law. In relation to their relative abundance, smaller and less mobile species such as Cottus gobio were mostly affected by stranding in contrast to larger and open-water-oriented species such as Chondrostoma nasus. The dewatering also caused drying out of important nursery zones, resulting in a distinctly lower recruitment success of endangered riverine fish species in the summer following the dewatering. The evidence about the negative ecological effects documented herein should be transferred into policy measures to reduce the impairment of dewatering to a minimum and to contribute to the fulfilment to national and international legal requirements. This can be achieved by reducing the extent and frequency of periodical dewatering to a minimum, by slowing down the dewatering speed, by selecting the least critical time of the year, as well as by compensation measures.
Effect of Saccharomyces cerevisiae culture mitigates heat stress-related dame in dairy cows by multi-omics

The effect of heat stress on ruminants is an important issue. In recent years, the growth of the Chinese dairy industry has rapidly increased, generating RMB 468,738 million revenue in 2021. A decreased milk yield is the most recognized impact of heat stress on dairy cows and results in significant economic loss to dairy producers. Heat stress also lowers immunity and antioxidant capacity and changes the bacterial composition and metabolites of the rumen. The purpose of this study was to investigate the effect of addition Saccharomyces cerevisiae culture on heat-stressed cows. The impact of S. cerevisiae culture on microbiota composition, functional profiles, and metabolomics was assessed in heat-stressed cows. A total of 45 Holstein cows in mid-lactation were selected and randomly divided into three groups (15 cows per group). Groups D-C, D-A, and D-B were fed with the basal diet, the basal diet + first S. cerevisiae culture 100 g/day, and the basal diet + second S. cerevisiae culture 30 g/day, respectively. The trial lasted 60 days. There was an increased abundance of the Phylum Firmicutes in the rumen of heat-stressed dairy cows fed with S. cerevisiae, of which four genera had significantly higher abundance, Ruminococcus_gauvreauii_group, Butyrivibrio_2, Moryella, and Ruminiclostridium_6. At the functional level, ten pathways differed significantly between the three groups (P < 0.05), with an increase in fatty acid biosynthesis, fatty acid metabolism, PPAR signaling pathway, ferroptosis, and biotin metabolism in the treatment groups. More differential metabolites were found in the D-C and D-A groups than in the D-C and D-B groups. These results indicate that S. cerevisiae cultures can influence the health status of heat-stressed cows by modulating rumen microbial composition, function, and metabolites, thereby improving rumen cellulolytic capacity. This study can provide or offer suggestions or recommendations for the development and utilization of feed additives.
Inhibition of HDAC6 With CAY10603 Ameliorates Diabetic Kidney Disease by Suppressing NLRP3 Inflammasome

Background: Diabetic nephropathy (DN) is one of the leading causes of chronic kidney disease (CKD) worldwide, tubular injury is the driving force during the pathogenesis and progression of DN. Thus, we aim to utilize the connectivity map (CMap) with renal tubulointerstitial transcriptomic profiles of biopsy-proven DN to identify novel drugs for treating DN. Methods: We interrogated the CMap profile with tubulointerstitial transcriptomic data from renal biopsy-proven early- and late-stage DN patients to screen potential drugs for DN. Therapeutic effects of candidate drug were assessed in Murine model of diabetic kidney disease (STZ-induced CD-1 mice), and HK-2 cells and immortalized bone marrow-derived macrophages (iBMDMs). Results: We identified CAY10603, a specific inhibitor of histone deacetylase 6 (HDAC6), as a potential drug that could significantly reverse the altered genes in the tubulointerstitial component. In DN patients and mice, upregulation of HDAC6 was mainly observed in renal tubular cells and infiltrated macrophages surrounding the diluted tubules. In both early- and late-onset diabetic mice, daily CAY10603 administration effectively alleviated renal dysfunction and reduced macrophage infiltration, tubular injury and tubulointerstitial fibrosis. Mechanistically, CAY10603 suppressed NLRP3 activation in both HK-2 cells and iBMDMs. Conclusion: CAY10603 exhibited therapeutic potential for DN by suppressing NLRP3 inflammasome activation in both tubular cells and macrophages.
Nerve Stimulation by Triboelectric Nanogenerator Based on Nanofibrous Membrane for Spinal Cord Injury

Spinal cord injury (SCI) is a devastating and common neurological disorder that is difficult to treat. The pain can sustain for many years, making the sufferer extremely painful. Nerve stimulation was first reported half a century ago as a treatment for neuropathic pain. Since then, the method of electrical stimulation through leads placed in the epidural space on the dorsal side of the spinal cord has become a valuable therapeutic tool for SCI. But nerve stimulation equipment is expensive, and the stimulator design and treatment plan are complicated, which hinders its development. In recent years, wearable and implantable triboelectric nanogenerators (TENGs) developed rapidly, and their low cost and safety have brought a new turning point for the development of nerve stimulation. Nanofibrous membrane has been proved that it is a flexible material with the advantages of ultrathin diameter, good connectivity, easy scale-up, tunable wettability, fine flexibility, tunable porosity, controllable composition and so on. In this paper, we discuss the technology of using nanofiber membrane on clothing to create TENGs to provide continuous electrical energy for nerve stimulation to treat SCI in patients by analyzing previous research.
A New Tobit Ridge-Type Estimator of the Censored Regression Model With Multicollinearity Problem

In the censored regression model, the Tobit maximum likelihood estimator is unstable and inefficient in the occurrence of the multicollinearity problem. To reduce this problem's effects, the Tobit ridge and the Tobit Liu estimators are proposed. Therefore, this study proposes a new kind of the Tobit estimation called the Tobit new ridge-type (TNRT) estimator. Also, the TNRT estimator was theoretically compared with the Tobit maximum likelihood, the Tobit ridge, and the Tobit Liu estimators via the mean squared error criterion. Moreover, we performed a Monte Carlo simulation to study the performance of the TNRT estimator compared with the previously defined estimators. Also, we used the Mroz dataset to confirm the theoretical and the simulation study results.
GDF-15: A Potential Biomarker and Therapeutic Target in Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is a rheumatic disease. Growth differentiation factor 15 (GDF-15) is a member of transforming growth factor-β superfamily. To date, association of GDF-15 with SLE pathogenesis is not clarified. This study discussed GDF-15 serum levels and gene polymorphisms in SLE patients and lupus mouse model further demonstrated the role of GDF-15 in lupus development. We conducted two independent case-control studies for SLE patients. One is to evaluate serum levels of GDF-15 in 54 SLE patients and 90 healthy controls, and the other one is to analyze gene polymorphisms of GDF-15 in 289 SLE patients and 525 healthy controls. Serum levels of GDF-15 were detected by ELISA. GDF-15 gene polymorphisms (rs1055150, rs1058587, rs1059519, rs1059369, rs1227731, rs4808793, and rs16982345) were genotyped by the Kompetitive Allele-Specific PCR (KASP) method. Addition of recombinant GDF-15 into pristane-induced lupus mice evaluated histological and serological changes. Results showed that serum levels of GDF-15 were overexpressed in SLE patients and associated with disease activity. Polymorphisms rs1055150, rs1059369, rs1059519, and rs4808793 of GDF-15 gene were related to SLE risk. Lupus mice showed splenomegaly, severe histological scores, and high levels of autoantibodies [antinuclear antibodies (ANA) and total immunoglobulin G (IgG)], whereas administration of GDF-15 into lupus mice reduced the histological changes. Percentages of CD8+, CD11b+, CD19+, CD11C+ cells, TH2 cells, and pro-inflammatory cytokines (IL-1β, IL-2, IL-4, IL-21, and IL-22) were reduced after GDF-15 treatment in lupus mice. In conclusion, GDF-15 was related to lupus pathogenesis and inhibited lupus development.
The course and determinants of post-traumatic stress over 12 months after hospitalization for COVID-19

Objective To assess the trajectory of symptoms and symptom-defined post-traumatic stress disorder (PTSD) from 1.5 to 12 months after hospitalization for COVID-19 and determine risk factors for persistent symptoms and PTSD. Methods This was a prospective cohort study of consecutive patients discharged after hospitalization for COVID-19 before 1 June 2020 in six hospitals in Southern Norway. Symptom-defined PTSD was assessed by the post-traumatic stress disorder (PTSD) checklist for DSM-5 (PCL-5) at 1.5, 3 and/or 12 months after hospitalization, using DSM-5 criteria. Changes in PCL-5 symptom score and the prevalence of PTSD were analyzed with multivariable mixed models. Results In total, 388 patients were discharged alive, and 251 (65%) participated. Respondents had a mean (SD) age of 58.4 (14.2) years, and 142 (57%) were males. The prevalence of symptom-defined PTSD was 14, 8, and 9% at 1.5, 3, and 12 months, respectively. WHO disease severity for COVID-19 was not associated with PCL-5 scores. Female sex, lower age and non-Norwegian origin were associated with higher PCL-5 scores. The odds ratio (OR) (95%CI) for PTSD was 0.32 (0.12 to 0.83, p = 0.019) at 3 months and 0.38 (0.15 to 0.95, p = 0.039) at 12 months compared to 1.5 months. There was no association between PTSD and WHO severity rating. Conclusions The level of PTSD symptoms decreased from 1.5 to 3 months after hospitalization, but did not decrease further to 12 months, and there was no association between PTSD symptoms and COVID-19 disease severity.
Non-linear association between Mediterranean diet and depressive symptom in U.S. adults: A cross-sectional study

The Mediterranean diet (MED), a dietary pattern rich in fruits and vegetables, whole grains, legumes, nuts, fish, and olive oil, has anti-oxidative and anti-inflammatory effects. Although some data suggest that MED adherence is associated with decreased manifestation of depressive symptoms, it remains necessary to further analyze this apparent non-linear association as well as the influence of different factors on the relationship between MED and depression. Here, we investigated associations between the alternate MED (aMED) score and depressive symptom via multivariate logistic regression, weighted generalized additive (GAM) and two-step linear regression models, analyzing data from the 2005–2018 National Health and Nutrition Examination Survey (NHANES). The most important factor relevant to aMED score that contributed to the prevalence of depressive symptom was assessed using random forest. Furthermore, we examined whether the relationship between aMED score and depressive symptom differs by age, race, sex, socioeconomic variables, lifestyle- and health-related variables, and chronic medical conditions, via subgroup analyses. A total of 19,477 participants (20–80 years of age) were included in this cross-sectional study. In crude and adjusted (1–5) multivariate logistic regression models, increased aMED score was noted to associate with non-depressive status, as defined using the Patient Health Questionnaire-9 (P < 0.05). Data analyses via GAM and two-piecewise linear regression revealed a non-linear association between aMED and depressive symptom, which had an inflection point of 3. Random forest results revealed that vegetable score contributes greatest to the relationship between aMED and depressive symptom. Subgroup analyses revealed that aMED score is significantly negatively related with depressive symptom in most different populations (P < 0.05) with the exception of high annual income, diabetes, borderline blood glucose level and Parkinson's disease (PD) (P > 0.05). In conclusion, we observed a non-linear association between aMED score and depressive symptom. Further studies are needed to validate our results.