Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Processing Route on Microstructure and Mechanical Properties in Single-Roll Angular-Rolling

This paper reports the effect of the processing route on the microstructure and mechanical properties in the pure copper sheets processed by single-roll angular-rolling (SRAR). The SRAR process was repeated up to six passes in two processing routes, called routes A and C in equal-channel angular pressing. As the number of passes increased, the heterogeneous evolution of hardness and microstructural heterogeneities between the core and surface regions gradually became intensified in both processing routes. In particular, route A exhibited more prominent partial grain refinement and dislocation localization on the core region than route C. The finite element analysis revealed that the intense microstructural heterogeneities observed in route A were attributed to effective shear strain partitioning between the core and surface regions by the absence of redundant strain. On the other hand, route C induced reverse shearing and cancellation of shear strain over the entire thickness, leading to weak shear strain partitioning and delayed grain refinement. Ultimately, this work suggests that route A is the preferred option to manufacture reverse gradient structures in that the degree of shear strain partitioning and microstructural heterogeneity between the core and surface regions is more efficiently intensified with increasing the number of passes.
Hyperalignment: Modeling shared information encoded in idiosyncratic cortical topographies

Information that is shared across brains is encoded in idiosyncratic fine-scale functional topographies. Hyperalignment captures shared information by projecting pattern vectors for neural responses and connectivities into a common, high-dimensional information space, rather than by aligning topographies in a canonical anatomical space. Individual transformation matrices project information from individual anatomical spaces into the common model information space, preserving the geometry of pairwise dissimilarities between pattern vectors, and model cortical topography as mixtures of overlapping, individual-specific topographic basis functions, rather than as contiguous functional areas. The fundamental property of brain function that is preserved across brains is information content, rather than the functional properties of local features that support that content. In this Perspective, we present the conceptual framework that motivates hyperalignment, its computational underpinnings for joint modeling of a common information space and idiosyncratic cortical topographies, and discuss implications for understanding the structure of cortical functional architecture.
Dioxygenase from Aspergillus fumigatus MC8: molecular modelling and in silico studies on enzyme–substrate interactions

Flavoenzymes have been extensively studied for their structural and mechanistic properties because they find potential application as industrial biocatalysts. They are attractive for biocatalysis because of the selectivity, controllability and efficiency of their reactions. Some of these enzymes catalyse the oxidative modification of protein substrates. Among them oxygenases (monoxoygenases and dioxygenases) are of special interest because they are highly entantio as well as regio-selective and can be used for oxyfunctionalisation. Dioxygenase enzymes catalyse oxygenation reactions in which both di-oxygen atoms are incorporated into the product. A dioxygenase enzyme purified from Aspergillus fumigatus MC8 was subjected to protein digestion followed by peptide sequencing. The sequence analysis of the peptide fragments resulted in identifying its match with that of an extracellular dioxygenase sequence from the same species of fungus existing in the protein database. The sequence was submitted to protein homology/analogy recognition engine online server for homology modelling and the 3D structure was predicted. Subsequently, the in silico studies of the enzyme–substrate (protein–ligand) interaction were carried out by using the method of molecular docking simulations wherein the modelled dioxygenase enzyme (protein) was docked with the substrates (ligands), catechin and epicatechin.
Structure of cytochrome b 5 unique to tardigrades

Cytochrome b5 is an essential electron transfer protein, which is ubiquitously found in living systems and involved in wide variety of biological processes. Tardigrades (also known as water bears), some of which are famous for desiccation resistance, have many proteins unique to them. Here, we report spectroscopic and structural characterization of a cytochrome b5 like protein from one of the desiccation‐tolerant tardigrades, Ramazzottius varieornatus strain YOKOZUNA‐1 (RvCytb5). A 1.4 Å resolution crystal structure revealed that RvCytb5 is a new cytochrome b5 protein specific to tardigrades.
Optimization Techniques Are Best Choice to Segment Blood Vessels from Retinal Fundus Images

The mostly affected disease which has been a curse to human kind is diabetes. This disease, irrespective of the age, causes extreme impact upon the eyes of the patients indicating abnormalities which manifests in tree-like structured blood vessels of the retina. It is so important to diagnose such patients with diabetes at the initial stage so as to save them from reaching blindness. Blood vessel segmentation in retinal fundus images is an adequate way and takes a critical role in medication and diagnosis of distinct retinal-related diseases and disorders. In this paper, a comprehensive review of various categories of segmentation techniques is presented with main focus on proving the magnificence of optimization techniques as the right choice in the process segmentation. The effectiveness of this work is straightened in relative study of discrete methods.
The My Cancer Genome clinical trial data model and trial curation workflow

Abstract Objective As clinical trials evolve in complexity, clinical trial data models that can capture relevant trial data in meaningful, structured annotations and computable forms are needed to support accrual. Material and Methods We have developed a clinical trial information model, curation information system, and a standard operating procedure for consistent and accurate annotation of cancer clinical trials. Clinical trial documents are pulled into the curation system from publicly available sources. Using a web-based interface, a curator creates structured assertions related to disease-biomarker eligibility criteria, therapeutic context, and treatment cohorts by leveraging our data model features. These structured assertions are published on the My Cancer Genome (MCG) website. Results To date, over 5000 oncology trials have been manually curated. All trial assertion data are available for public view on the MCG website. Querying our structured knowledge base, we performed a landscape analysis to assess the top diseases, biomarker alterations, and drugs featured across all cancer trials. Discussion Beyond curating commonly captured elements, such as disease and biomarker eligibility criteria, we have expanded our model to support the curation of trial interventions and therapeutic context (ie, neoadjuvant, metastatic, etc.), and the respective biomarker-disease treatment cohorts. To the best of our knowledge, this is the first effort to capture these fields in a structured format. Conclusion This paper makes a significant contribution to the field of biomedical informatics and knowledge dissemination for precision oncology via the MCG website. Key words knowledge representation, My Cancer Genome, precision oncology, knowledge curation, cancer informatics, clinical trial data model
Cancer Chemopreventive Properties of Sulfated Enterolobium cyclocarpum Extract

Abstract Enterolobium cyclocarpum (EC) is an edible plant and a gum source for food industries. Its sulfated polysaccharide extract (SEC) was examined for cancer chemopreventive properties to estimate its anti-tumor activity. The modulation of carcinogen metabolism and the antioxidant activity revealed that SEC is a potent tumor anti-initiator since it inhibited cytochrome P450-1A (CYP1A) and induced carcinogen detoxification enzyme glutathione-S-transferase. SEC is also a weak scavenger for hydroxyl and peroxyl radicals. SEC was found to modulate macrophage functions into an anti-inflammatory pattern, where it enhanced macrophage proliferation and phagocytosis of fluorescein isothiocyanate-lipopolysaccharide (FITC-LPS). In addition, SEC strongly inhibited the nitric oxide (NO) generation in LPS-stimulated macrophages and induced the binding affinity of FITC–LPS to macrophages. SEC exhibited specific cytotoxicity against human hepatocellular Hep G2 carcinoma cells. SEC disturbed the cell cycle phase, as indicated by the concomitant arrest in S- and G2/M-phases that was associated with necrosis induction. A short-term initiation model for liver cancer was prepared using diethylnitrosamine (DEN) in rats. SEC inhibited the DEN-histopathological findings and reduced both CYP1A and the tumor initiation marker placental glutathione S-transferase (GSTP). Taken together, SEC could be used as an alternative gum in health food industries to provide cancer prevention in high-risk populations.
A multicomponent intervention to decrease sedentary time during hospitalization: a quasi-experimental pilot study

Objective: The aim of this study was to evaluate the feasibility and preliminary effects of a multicomponent intervention to decrease sedentary time during and shortly after hospitalization. Design: This is a quasi-experimental pilot study comparing outcomes in patients admitted before and after the implementation of the intervention. Setting: The study was conducted in a university hospital. Subjects: Participants were adult patients undergoing elective organ transplantation or vascular surgery. Interventions: In the control phase, patients received usual care, whereas in the intervention phase, patients also received a multicomponent intervention to decrease sedentary time. The intervention comprised eight elements: paper and digital information, an exercise movie, an activity planner, a pedometer and Fitbit Flex™, a personal activity coach and an individualized digital training program. Measures: Measures of feasiblity were the self-reported use of the intervention components (yes/no) and satisfaction (low–high = 0–10). Main outcome measure was the median % of sedentary time measured by an accelerometer worn during hospitalization and 7–14 days thereafter. Results: A total of 42 controls (mean age = 59 years, 62% male) and 52 intervention patients (58 years, 52%) were included. The exercise movie, paper information and Fitbit Flex were the three most frequently used components, with highest satisfaction scores for the fitbit, paper information, exercise movie and digital training. Median sedentary time decreased from 99.6% to 95.7% and 99.3% to 91.0% between Days 1 and 6 in patients admitted in the control and intervention phases, respectively. The difference at Day 6 reached statistical significance (difference = 41 min/day, P = 0.01). No differences were seen after discharge. Conclusion: Implementing a multicomponent intervention to reduce sedentary time appeared feasible and may be effective during but not directly after hospitalization.
Master–Slave Synchronization of Delayed Neural Networks With Time-Varying Control

This brief investigates the master–slave synchronization problem of delayed neural networks with general time-varying control. Assuming a linear feedback controller with time-varying control gain, the synchronization problem is recast into the stability problem of a delayed system with a time-varying coefficient. The main theorem is established in terms of the time average of the control gain by using the Lyapunov–Razumikhin theorem. Moreover, the proposed framework encompasses some general intermittent control schemes, such as the switched control gain with external disturbance and intermittent control with pulse-modulated gain function, while some useful corollaries are consequently deduced. Interestingly, our theorem also provides a solution for regaining stability under control failure. The validity of the theorem and corollaries is further demonstrated with numerical examples.
Modelling the adaptive dynamics of traits involved in inter‐ and intraspecific interactions: An assessment of three methods

In recent years, three related methods have been used to model the phenotypic dynamics of traits under the influence of natural selection. The first is based on an approximation to quantitative genetic recursion equations for sexual populations. The second is based on evolution in asexual lineages with mutation-generated variation. The third method finds an evolutionarily stable set of phenotypes for species characterized by a given set of fitness functions, assuming that the mode of reproduction places no constraints on the number of distinct types that can be maintained in the population. The three methods share the property that the rate of change of a trait within a homogeneous population is approximately proportional to the individual fitness gradient. The methods differ in assumptions about the potential magnitude of phenotypic differences in mutant forms, and in their assumptions about the probability that invasion or speciation occurs when a species has a stable, yet invadable phenotype. Determining the range of applicability of the different methods is important for assessing the validity of optimization methods in predicting the evolutionary outcome of ecological interactions. Methods based on quantitative genetic models predict that fitness minimizing traits will often be evolutionarily stable over significant time periods, while other approaches suggest this is likely to be rare. A more detailed study of cases of disruptive selection might reveal whether fitness-minimizing traits occur frequently in natural communities.
Development of transgenic cucumber expressing TPSP gene and morphological alterations

Abstract To develop transgenic cucumber tolerant to abi-otic stress, a cotyledonary-node explants were co-cultivated with Agrobacterium tumefaciens (EHA101) carrying TPSP gene (pHC30-TPSP). After transfer to fresh medium every two week for eight weeks, putative transgenic plants were selected when shoots grown a length greater than 3 cm from the cotyledonary-node explants on selection medium supple-mented with 5 mgl -1 phospinotricin as selectable agent. The confirmation of transgenic cucumber was based on the North-ern blot analysis. Thirty four shoots (5.2%) with resistance to phospinotricin were obtained from 660 explants inoculated. Of them, transformants were only confirmed from 11 plants (1.7%). Transgenic cucumber expressing TPSP gene was more synthesized at 3.8 times amounts of trehalose (0.014 mg g fresh wt -1 ) than non-transformants (0.0037 mg g fresh wt -1 ). However, all of transgenic plants showed abnormal morphology, including stunted growth ( height 150 cm) under the same growth envi-ronment. These results lead us to speculate that the over-production of trehalose was toxic for cucumber, even though that had known for rice as non-toxic.
Antioxidant properties of polysaccharides from Ganoderma sinense by diffident cultivations

Ganoderma sinense were available in the form of log-cultivated and sawdust-cultivated fruit bodies, solid-fermentation products and liquid-fermentation mycelia. From these four forms, water extracted polysaccharides were prepared and their antioxidant properties were investigated. Among the four forms of G. sinense, mycelia showed the largest extraction polysaccharide content (14.68%). Compared with ascorbic acid, the extracted polysaccharides from four forms exhibited stronger capability of inhibiting lipid oxidation in a linoleic acid system and more efficient radical-scavenging activity on 2, 2-diphenyl-1-picrylhydrazyl (DPPH). The extracted polysaccharides from four forms could scavenge hydroxyl radicals and showed good reducing powers evidenced by their low EC50 values (< 13 mg/mL). However, the scavenging ability on superoxide-anion radicals was not found in our investigation. All extracted polysaccharides possessed good antioxidant properties except for scavenging ability on superoxide-anion radicals and could be utilized as a new dietary supplement and functional food or tea.
Diabetes enhances translation of Cd40 mRNA in murine retinal Müller glia via a 4E-BP1/2–dependent mechanism

Activation of the immune costimulatory molecule cluster of differentiation 40 (CD40) in Müller glia has been implicated in the initiation of diabetes-induced retinal inflammation. Results from previous studies support that CD40 protein expression is elevated in Müller glia of diabetic mice; however, the mechanisms responsible for this increase have not been explored. Here, we evaluated the hypothesis that diabetes augments translation of the Cd40 mRNA. Mice receiving thiamet G (TMG), an inhibitor of the O-GlcNAc hydrolase O-GlcNAcase, exhibited enhanced retinal protein O-GlcNAcylation and increased Cd40 mRNA translation. TMG administration also promoted Cd40 mRNA association with Müller cell–specific ribosomes isolated from the retina of RiboTag mice. Similar effects on O-GlcNAcylation and Cd40 mRNA translation were also observed in the retina of a mouse model of type 1 diabetes. In cultured cells, TMG promoted sequestration of the cap-binding protein eIF4E (eukaryotic translation in initiation factor 4E) by 4E-BP1 (eIF4E-binding protein 1) and enhanced cap-independent Cd40 mRNA translation as assessed by a bicistronic reporter that contained the 5′-UTR of the Cd40 mRNA. Ablation of 4E-BP1/2 prevented the increase in Cd40 mRNA translation in TMG-exposed cells, and expression of a 4E-BP1 variant that constitutively sequesters eIF4E promoted reporter activity. Extending on the cell culture results, we found that in contrast to WT mice, diabetic 4E-BP1/2–deficient mice did not exhibit enhanced retinal Cd40 mRNA translation and failed to up-regulate expression of the inflammatory marker nitric-oxide synthase 2. These findings support a model wherein diabetes-induced O-GlcNAcylation of 4E-BP1 promotes Cd40 mRNA translation in Müller glia.
Remdesivir (GS-5734) is Efficacious in Cynomolgus Macaques Infected with Marburg Virus.

Marburg virus (MARV) is a filovirus with documented human case-fatality rates of up to 90%. Here, we evaluated the therapeutic efficacy of remdesivir (GS-5734) in nonhuman primates experimentally infected with MARV. Beginning 4 or 5 days post-inoculation, cynomolgus macaques were treated once daily for 12 days with vehicle, 5 mg/kg remdesivir, or a 10 mg/kg loading dose followed by 5 mg/kg remdesivir. All vehicle-control animals died, whereas 83% of animals receiving a 10 mg/kg loading dose of remdesivir survived, as did 50% of animals receiving a 5 mg/kg remdesivir regimen. Remdesivir-treated animals exhibited improved clinical scores, lower plasma viral RNA, and improved markers of kidney function, liver function, and coagulopathy versus vehicle-control animals. The small molecule remdesivir showed therapeutic efficacy in this Marburg virus disease model with treatment initiation 5 days post-inoculation, supporting further assessment of remdesivir for the treatment of Marburg virus disease in humans.
Localizing the seizure onset zone by comparing patient postictal hypoperfusion to healthy controls

Arterial spin labeling (ASL) MRI can provide seizure onset zone (SOZ) localizing information in up to 80% of patients. Clinical implementation of this technique is limited by the need to obtain two scans per patient: a postictal scan that is subtracted from an interictal scan. We aimed to determine whether it is possible to limit the number of ASL scans to one per patient by comparing patient postictal ASL scans to baseline scans of 100 healthy controls. Eighteen patients aged 20–55 years underwent ASL MRI <90 min after a seizure and during the interictal period. Each postictal cerebral blood flow (CBF) map was statistically compared to average baseline CBF maps from 100 healthy controls (pvcASL; patient postictal CBF vs. control baseline CBF). The pvcASL maps were compared to subtraction ASL maps (sASL; patient baseline CBF minus patient postictal CBF). Postictal CBF reductions from pvcASL and sASL maps were seen in 17 of 18 (94.4%) and 14 of 18 (77.8%) patients, respectively. Maximal postictal hypoperfusion seen in pvcASL and sASL maps was concordant with the SOZ in 10 of 17 (59%) and 12 of 14 (86%) patients, respectively. In seven patients, both pvcASL and sASL maps showed similar results. In two patients, sASL showed no significant hypoperfusion, while pvcASL showed significant hypoperfusion concordant with the SOZ. We conclude that pvcASL is clinically useful and although it may have a lower overall concordance rate than sASL, pvcASL does provide localizing or lateralizing information for specific cases that would be otherwise missed through sASL.
Investigating Low-Dose Image Quality in Whole-Body Pediatric 18F-FDG Scans Using Time-of-Flight PET/MRI

In this study, we investigated the diagnostic performance of whole-body 18F-FDG imaging using a PET/MRI scanner with time-of-flight capability for low-dose clinical imaging of pediatric patients. In addition to clinically acquired image data using a dosing regimen of 3.7 MBq/kg, images from simulated low-dose regimens (1.9–0.41 MBq/kg) were evaluated using several metrics: SUV quantitation, qualitative image quality, and lesion detectability. Methods: Low-dose images were generated by truncating the list-mode PET data to reduce the count statistics. Changes in PET quantitation for low-dose images were assessed using volume-of-interest analysis of healthy tissue and suspected lesions. Three pediatric radiologists reviewed the image volumes without knowing the dose level. Qualitative image quality was assessed on the basis of Likert scoring. Radiologists were also asked to identify suspected lesions within the liver for PET-only and PET/MR images. Lesion detectability was measured using a receiver-operating-characteristic study and quantified using a free-response receiving-operating-characteristic (FROC) methodology to assess changes in performance for low-dose images. Results: Our analysis of volume-of-interest quantitation showed that SUVs remain stable down to ⅓ dose (1.2 MBq/kg). Likert scoring of PET/MR images showed no noticeable trend with dose level; however, scores of PET-only images were lower for low-dose scans, with a 12% reduction for ⅓-dose images compared with full-dose images. There was minimal change in total lesion count for different dose levels; however, all 3 readers had an increase in false-negatives for ⅓-dose images compared with full-dose images. Using the FROC methodology to quantify lesion-detection performance for human observers, no significant differences were observed for the 3 dosing levels when using the averaged reader data (all P values > 0.103). For all readers, the FROC performance was higher for PET/MRI than for PET alone. Conclusion: Reductions to the lowest recommended pediatric dosing regimens are possible when using PET/MRI. The data suggest that the administered dose can be decreased to 2.46 MBq/kg, a 33% reduction in PET activity, with no degradation in image quality, leading to a corresponding reduction in absorbed dose.