Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-Material Decomposition for Single Energy CT Using Material Sparsity Constraint

Multi-material decomposition (MMD) decomposes CT images into basis material images, and is a promising technique in clinical diagnostic CT to identify material compositions within the human body. MMD could be implemented on measurements obtained from spectral CT protocol, although spectral CT data acquisition is not readily available in most clinical environments. MMD methods using single energy CT (SECT), broadly applied in radiological departments of most hospitals, have been proposed in the literature while challenged by the inferior decomposition accuracy and the limited number of material bases due to the constrained material information in the SECT measurement. In this paper, we propose an image-domain SECT MMD method using material sparsity as an assistance under the condition that each voxel of the CT image contains at most two different elemental materials. L0 norm represents the material sparsity constraint (MSC) and is integrated into the decomposition objective function with a least-square data fidelity term, total variation term, and a sum-to-one constraint of material volume fractions. An accelerated primal-dual (APD) algorithm with line-search scheme is applied to solve the problem. The pixelwise direct inversion method with the two-material assumption (TMA) is applied to estimate the initials. We validate the proposed method on phantom and patient data. Compared with the TMA method, the proposed MSC method increases the volume fraction accuracy (VFA) from 92.0% to 98.5% in the phantom study. In the patient study, the calcification area can be clearly visualized in the virtual non-contrast image generated by the proposed method, and has a similar shape to that in the ground-truth contrast-free CT image. The high decomposition image quality from the proposed method substantially facilitates the SECT-based MMD clinical applications.
Automated Identification of Common Disease-Specific Outcomes for Comparative Effectiveness Research Using ClinicalTrials.gov: Algorithm Development and Validation Study

Background Common disease-specific outcomes are vital for ensuring comparability of clinical trial data and enabling meta analyses and interstudy comparisons. Traditionally, the process of deciding which outcomes should be recommended as common for a particular disease relied on assembling and surveying panels of subject-matter experts. This is usually a time-consuming and laborious process. Objective The objectives of this work were to develop and evaluate a generalized pipeline that can automatically identify common outcomes specific to any given disease by finding, downloading, and analyzing data of previous clinical trials relevant to that disease. Methods An automated pipeline to interface with ClinicalTrials.gov’s application programming interface and download the relevant trials for the input condition was designed. The primary and secondary outcomes of those trials were parsed and grouped based on text similarity and ranked based on frequency. The quality and usefulness of the pipeline’s output were assessed by comparing the top outcomes identified by it for chronic obstructive pulmonary disease (COPD) to a list of 80 outcomes manually abstracted from the most frequently cited and comprehensive reviews delineating clinical outcomes for COPD. Results The common disease-specific outcome pipeline successfully downloaded and processed 3876 studies related to COPD. Manual verification indicated that the pipeline was downloading and processing the same number of trials as were obtained from the self-service ClinicalTrials.gov portal. Evaluating the automatically identified outcomes against the manually abstracted ones showed that the pipeline achieved a recall of 92% and precision of 79%. The precision number indicated that the pipeline was identifying many outcomes that were not covered in the literature reviews. Assessment of those outcomes indicated that they are relevant to COPD and could be considered in future research. Conclusions An automated evidence-based pipeline can identify common clinical trial outcomes of comparable breadth and quality as the outcomes identified in comprehensive literature reviews. Moreover, such an approach can highlight relevant outcomes for further consideration.
Greater increase in internal carotid artery shear rate during aerobic interval compared to continuous exercise in healthy adult men

Interval exercise has been determined to be more effective than continuous exercise for achieving improvement in the cardiovascular function of individuals suffering from cardiovascular disease. However, whether interval exercise improves the cerebrovascular function remains unclear. As per our hypothesis, interval exercise induces a higher cerebrovascular shear rate (SR) than continuous exercise. In this study, 11 adult men randomly performed continuous exercise for 12 min or work‐equivalent (57.6 kJ/exercise session) interval exercise of semi‐recumbent cycling. The SR in the internal carotid artery (ICA) represents an index of the cerebrovascular SR, which was measured during both the exercises using Doppler ultrasonography. Both the aerobic exercise modes increased the ICA SR. Moreover, the average ICA SR of the interval exercise for the final 4 min of exercise or 2 min of recovery was significantly higher than that for continuous exercise (exercise, 351 ± 75 vs. 330 ± 61/s, p = .038; recovery, 327 ± 86 vs. 290 ± 56/s, p = .014). To our knowledge, this is the first study to show that aerobic interval exercise increased the ICA SR more than equivalent work volume of aerobic continuous exercise. Thus, aerobic interval exercise may be more effective at stimulating the cerebrovasculature, resulting in greater improvements in cerebrovascular function as compared to continuous aerobic exercise in healthy adult men. These findings provide some important information that would help enhance exercise therapy programs for patients with arteriosclerosis, especially in the cerebral circulation.
Interactions between starch source and gelatinisation degree on performance and small intestinal digestion in broiler chickens

ABSTRACT 1. A 2 × 2 factorial arrangement was used to test the hypothesis that, in pelleted diets, legume starch is digested less rapidly and to a lesser extent than cereal starch, and that increased gelatinisation through extrusion would eliminate the differences between the starch sources. In addition, the trial examined whether a lower ratio of starch to nitrogen disappearance rate (SNDR) could improve feed conversion ratio (FCR). 2. At 17 d of age, male broilers were randomly distributed among four dietary treatments, consisting of either wheat or faba bean starch-rich fraction (FBS) as the sole starch source and pelleting or extrusion as processing methods. Each treatment had 10 replicate pens containing five birds each. 3. Extrusion resulted in a more extensive starch gelatinisation compared to pelleting, as expected. 4. No difference in weight gain at 29 d of age was observed between birds fed starch sources. However, birds fed wheat tended (P = 0.080) to have better FCR than those fed FBS, while the effect of processing methods was insignificant. Thus, there was no interaction between starch source and processing method on FCR. 5. In pelleted diets, FBS had lower and slower starch digestibility compared to wheat in all intestinal segments (P < 0.05). The interaction between starch source and processing method in all intestinal segments (P < 0.001) demonstrated that FBS responded more to gelatinisation through extrusion than did wheat. Thus, differences in starch digestibility between the wheat and FBS were eliminated with extrusion. 6. Feeding extruded diets significantly increased the upper jejunal expression of GLUT1, GLUT2 and SGLT1 compared to pelleted diets, which suggested that glucose absorption was less likely to be a limiting factor for starch utilisation. 7. Pelleting resulted in a lower ratio (P < 0.001) of SNDR compared to extrusion (on average 1.4-fold) but did not improve FCR.
Alleviation of Manganese Phytotoxicity in Barley with Calcium

ABSTRACT In order to clarify the mechanism by which calcium (Ca) alleviates manganese (Mn) phytotoxicity, barley plants were grown under the following conditions: (1) nutrient solution alone (control), (2) nutrient solution + 25 μM Mn (Mn-toxic), and (3) nutrient solution + 25 μ M Mn + 20 mM Ca (Ca-alleviated). Feeding experiments using 54Mn and 59Fe (iron) with 2.0 or 20 mM Ca to the plant roots were also conducted. The absorption and translocation of 54Mn in the control plants were lowered by the high-Ca (20 mM) feeding condition. The translocation of 54Mn to shoots of Mn-toxic or Ca-alleviated plants was also lowered by the high-Ca feeding condition, but 54Mn absorption by roots of the plants was unaffected. The absorption and translocation of 59Fe in the plants was unaffected by the high-Ca feeding condition. Calcium alleviation of Mn phytotoxicity in barley may be induced mainly by the inhibition of Mn translocation to shoots.
Diversification, disparification, and hybridization in the desert shrubs Encelia

There are multiple hypotheses for the spectacular plant diversity found in deserts. We explore how different factors, including the roles of ecological opportunity and selection, promote diversification and disparification in Encelia, a lineage of woody plants in the deserts of the Americas. Using a nearly complete species-level phylogeny along with a broad set of phenotypic traits, we estimate divergence times and diversification rates, identify instances of hybridization, quantify trait disparity, and assess phenotypic divergence across environmental gradients. We show that Encelia originated and diversified recently (mid-Pleistocene) and rapidly, with rates comparable to notable adaptive radiations in plants. Encelia probably originated in the hot deserts of North America, with subsequent diversification across steep environmental gradients. We uncover multiple instances of gene flow between species. The radiation of Encelia is characterized by fast rates of phenotypic evolution, trait lability, and extreme disparity across environments and between species-pairs with overlapping geographic ranges. Encelia exemplifies how interspecific gene flow in combination with high trait lability can enable exceptionally fast diversification and disparification across steep environmental gradients.
Kristallisation für die Aufarbeitung von Proteinen

EINLEITUNG Die Proteinkristallisation ist eine Technik, die ublicherweise fur die Ermittlung der dreidimensionalen Struktur eines Proteins verwendet wird. Fur diese Anwendung hat man viele Jahrzehnte die Techniken optimiert, um moglichst gut analysierbare Kristalle zu erzeugen. Dies sind die Kristalle, mit denen ein eindeutiges Rontgenbeugungsmuster ermittelt werden kann. Proteinkristalle bieten aber daruber hinaus Vorteile gegenuber der gelosten Form, denn oftmals sind die kristallinen Formulierungen lagerbestandiger und reiner. Dadurch ergibt sich eine Anzahl von potentiellen Anwendungen fur die Proteinkristallisation in einem industriellen Aufarbeitungsprozess. Ahnlich wie die niedermolekulare Kristallisation kann die Methode eine preiswerte Alternative fur die Reinigung (z.B. als Ersatz eines chromatographischen Prozessschrittes), die Formulierung (z.B. als Ersatz fur eine Lyophilisation oder als Slow-Release-Formulierung) oder die Proteinlagerung sein. Der beste Einsatzpunkt fur diese Technik muss jedoch in jedem Fall individuell fur jeden Wirkstoff entschieden werden. Gerade im Bereich der Formulierung ist die angestrebte Pharmakokinetik und die Art der Verabreichung entscheidend fur eine Anwendbarkeit.
Characteristics and outcome of pediatric renal cell carcinoma patients registered in the International Society of Pediatric Oncology (SIOP) 93‐01, 2001 and UK‐IMPORT database: A report of the SIOP‐Renal Tumor Study Group

In children, renal cell carcinoma (RCC) is rare. This study is the first report of pediatric patients with RCC registered by the International Society of Pediatric Oncology‐Renal Tumor Study Group (SIOP‐RTSG). Pediatric patients with histologically confirmed RCC, registered in SIOP 93‐01, 2001 and UK‐IMPORT databases, were included. Event‐free survival (EFS) and overall survival (OS) were analyzed using the Kaplan‐Meier method. Between 1993 and 2019, 122 pediatric patients with RCC were registered. Available detailed data (n = 111) revealed 56 localized, 30 regionally advanced, 25 metastatic and no bilateral cases. Histological classification according to World Health Organization 2004, including immunohistochemical and molecular testing for transcription factor E3 (TFE3) and/or EB (TFEB) translocation, was available for 65/122 patients. In this group, the most common histological subtypes were translocation type RCC (MiT‐RCC) (36/64, 56.3%), papillary type (19/64, 29.7%) and clear cell type (4/64, 6.3%). One histological subtype was not reported. In the remaining 57 patients, translocation testing could not be performed, or TFE‐cytogenetics and/or immunohistochemistry results were missing. In this group, the most common RCC histological subtypes were papillary type (21/47, 44.7%) and clear cell type (11/47, 23.4%). Ten histological subtypes were not reported. Estimated 5‐year (5y) EFS and 5y OS of the total group was 70.5% (95% CI = 61.7%‐80.6%) and 84.5% (95% CI = 77.5%‐92.2%), respectively. Estimated 5y OS for localized, regionally advanced, and metastatic disease was 96.8%, 92.3%, and 45.6%, respectively. In conclusion, the registered pediatric patients with RCC showed a reasonable outcome. Survival was substantially lower for patients with metastatic disease. This descriptive study stresses the importance of full, prospective registration including TFE‐testing.
Multiparametric and multilevel characterization of morphological alterations in patients with transient ischemic attack

Transient ischemic attack (TIA), an important risk factor for stroke, is associated with widespread disruptions of functional brain architecture. However, TIA‐related structural alterations are not well established. By analyzing structural MRI data from 50 TIA patients versus 40 healthy controls (HCs), here we systematically investigated TIA‐related morphological alterations in multiple cortical surface‐based indices (cortical thickness [CT], fractal dimension [FD], gyrification index [GI], and sulcal depth [SD]) at multiple levels (local topography, interregional connectivity and whole‐brain network topology). For the observed alterations, their associations with clinical risk factors and abilities as diagnostic and prognostic biomarkers were further examined. We found that compared with the HCs, the TIA patients showed widespread morphological alterations and the alterations depended on choices of morphological index and analytical level. Specifically, the patients exhibited: (a) regional CT decreases in the transverse temporal gyrus and lateral sulcus; (b) impaired FD‐ and GI‐based connectivity mainly involving visual, somatomotor and ventral attention networks and interhemispheric connections; and (c) altered GI‐based whole‐brain network efficiency and decreased FD‐based nodal centrality in the middle frontal gyrus. Moreover, the impaired morphological connectivity showed high sensitivities and specificities for distinguishing the patients from HCs. Altogether, these findings demonstrate the emergence of morphological index‐dependent and analytical level‐specific alterations in TIA, which provide novel insights into neurobiological mechanisms underlying TIA and may serve as potential biomarkers to help diagnosis of the disease. Meanwhile, our findings highlight the necessity of using multiparametric and multilevel approaches for a complete mapping of cerebral morphology in health and disease.
Factors associated with hospitalization, invasive mechanical ventilation treatment and death among all confirmed COVID-19 cases in Norway: Prospective cohort study

Aims: For everyone with a positive test for SARS-CoV-2 in Norway, we studied whether age, sex, comorbidity, continent of birth and nursing home residency were risk factors for hospitalization, invasive mechanical ventilation treatment and death. Methods: Data for everyone who had tested positive for SARS-CoV-2 in Norway by end of June 2020 (N = 8569) were linked at the individual level to hospitalization, receipt of invasive mechanical ventilation treatment and death measured to end of July 2020. Underlying comorbidity was proxied by hospital-based in- or outpatient treatment during the two months before the SARS-CoV-2 test. Multivariable generalized linear models were used to assess risk ratios (RRs). Results: Risk of hospitalization was particularly high for elderly (for those aged 90 and above: RR 9.5; 95% confidence interval (CI) 7.1–12.7; comparison group aged below 50), Norwegian residents born in Asia, Africa or Latin-America (RR 2.1; 95% CI 1.9–2.4; comparison group born in Norway), patients with underlying comorbidity (RR 1.6; 95% CI 1.4–1.8) and men (RR 1.3; 95% CI 1.2–1.5). Men and residents born in Africa, Asia and Latin-America were also at higher risk of receiving ventilation treatment and dying, but the mortality risk was especially high for the elderly (for those aged 90 and above: RR 607.9; 95% CI 145.5–2540.1; comparison group aged below 50) and residents in nursing homes (RR 4.2; 95% CI 3.1–5.7). Conclusions: High age was the most important predictor of severe disease and death if infected with SARS-CoV-2, and nursing home residents were at particularly high risk of death.
Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping

Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs.
Arabidopsis sirtuins and poly(ADP-ribose) polymerases regulate gene expression in the day but do not affect circadian rhythms.

Nicotinamide-adenine dinucleotide (NAD) is involved in redox homeostasis and acts as a substrate for NADases, including poly(ADP-ribose) polymerases (PARPs) that add poly(ADP-ribose) polymers to proteins and DNA, and sirtuins that deacetylate proteins. Nicotinamide, a biproduct of NADases increases circadian period in both plants and animals. In mammals, the effect of nicotinamide on circadian period might be mediated by the PARPs and sirtuins because they directly bind to core circadian oscillator genes. We have investigated whether PARPs and sirtuins contribute to the regulation of the circadian oscillator in Arabidopsis. We found no evidence that PARPs and sirtuins regulate the circadian oscillator of Arabidopsis or are involved in the response to nicotinamide. RNA-seq analysis indicated that PARPs regulate the expression of only a few genes, including FLOWERING LOCUS C. However, we found profound effects of reduced sirtuin 1 expression on gene expression during the day but not at night, and an embryo lethal phenotype in knockouts. Our results demonstrate that PARPs and sirtuins are not associated with NAD regulation of the circadian oscillator and that sirtuin 1 is associated with daytime regulation of gene expression. This article is protected by copyright. All rights reserved.
Heart rate variability and obstructive sleep apnea: Current perspectives and novel technologies

Obstructive sleep apnea (OSA) is a highly prevalent condition, resulting in recurrent hypoxic events, sleep arousal, and daytime sleepiness. Patients with OSA are at an increased risk of cardiovascular morbidity and mortality. The mechanisms underlying the development of cardiovascular disease in OSA are multifactorial and cause a cascade of events. The primary contributing factor is sympathetic overactivity. Heart rate variability (HRV) can be used to evaluate shifts in the autonomic nervous system, during sleep and in response to treatment in patients with OSA. Newer technologies are aimed at improving HRV analysis to accelerate processing time, improve the diagnosis of OSA, and detection of cardiovascular risk. The present review will present contemporary understandings and uses for HRV, specifically in the realms of physiology, technology, and clinical management.
Effect of Decorin and Bevacizumab on oxygen-induced retinopathy in rat models: A comparative study

Purpose: The aims of this study were to evaluate the effects of decorin (DCN) in rat oxygen-induced retinopathy (OIR) model and to compare the results with those of bevacizumab. Methods: Twenty-eight newborn Sprague–Dawley rats were randomly divided into four groups. Group I (control): normoxia plus intraperitoneal (ip) normal saline (NS), Group II (sham): OIR plus ip NS, Group III (DCN): OIR plus ip 0.1 mg/kg DCN, and Group IV (bevacizumab): OIR plus ip 2.5 mg/kg bevacizumab. The OIR model was induced by cycling the oxygen concentration between 50% and 10% every 24 h for 14 days following their birth. In all groups, injections were administered on postnatal day (PD) 15. All animals were sacrificed and their right eyes were enucleated on PD 18. The nuclei of neovascular endothelial cells on the vitreal side of the inner limiting membrane were counted, and vascular endothelial growth factor (VEGF) and tumor necrosis factor-alpha (TNF)-α immunoreactivity were detected in histopathological and immunohistochemical examinations. One-way analysis of variance and post hoc Tukey tests were used for statistical analyses of the data. Results: In Groups II, III, and IV, the mean neovascular cell nuclei counts were 13.14 ± 1.34, 6.57 ± 1.51, and 6.71 ± 1.49, respectively. The mean neovascular cell nuclei count was significantly reduced in treatment groups compared with sham group (P < 0.001). In immunohistochemical staining, the immunoreactivity of VEGF was 0.07 ± 0.02, 0.97 ± 0.21, 0.37 ± 0.12, and 0.23 ± 0.17, respectively. Likewise, immunoreactivity of TNF-α was 0.02 ± 0.02, 1.11 ± 0.36, 0.37 ± 0.13, and 0.62 ± 0.21, respectively. VEGF and TNF-α immunoreactivity increased markedly in the sham group compared with those in the control group (P < 0.001). VEGF and TNF-α immunoreactivity of treatment groups decreased significantly compared to sham group (P < 0.001). Conclusion: The beneficial effects obtained by DCN administration in OIR model were comparable to the effects of bevacizumab.