Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum cortisol assay performance following the 1 mg overnight dexamethasone suppression test

Background The 1 mg overnight dexamethasone suppression test (ONDST) is recommended for the differential diagnosis of Cushing’s syndrome and the investigation of adrenal incidentalomas. Despite documented variation in serum cortisol immunoassay performance, little has been published regarding its effect on the ONDST. Aims Assess the performance of three immunoassay platforms (Roche Elecsys II, Abbott Alinity & Siemens Centaur) when compared to a liquid chromatography tandem mass spectrometry (LC-MS/MS) method. Methods Samples (n = 77) sent to the laboratory as part of an ONDST were retrieved prior to disposal, anonymized, and analysed on all platforms. Samples with factors impacting immunoassay analysis quality were excluded. Results were statistically compared to an LC-MS/MS method that previously demonstrated excellent comparability to a candidate reference method. Results The Roche gen II showed a mean bias of −2.4 nmol/L and a Passing–Bablok fit of y = −0.9 + 0.97x. This was not affected by sex. The Abbott showed a mean bias −18.8 nmol/L, and a fit of y = −11.3 + 0.88x. This bias was −20.7 nmol/L in females versus −17.2 nmol/L in males. The Siemens had a mean bias of 2.3 nmol/L and a fit of y = 1.4 + 1.07x. This bias was 5.7 nmol/L in males versus −1.0 nmol/L in females. Conclusions Clinicians should be aware of the method-dependent variation that exists within serum cortisol analysis during the ONDSTs. Roche and Siemens aligned more closely with LC-MS/MS while the Abbot may cause a reduction in ONDST sensitivity. This data supports assay-specific cut-offs for the ONDST.
How does leaf succulence relate to plant drought resistance in woody shrubs?

Abstract Succulence describes the amount of water stored in cells or organs, regardless of plant life-form, including woody and herbaceous plants. In dry environments, plants with greater survival often have greater leaf succulence. However, it is unclear how leaf succulence relates to plant drought resistance strategies, including isohydry (closing stomata to maintain leaf water status) and anisohydry (adjusting cell turgor to tolerate low leaf water status), which exist on a continuum that can be quantified by hydroscape area (larger hydroscape area indicates more anisohydric). We evaluated 12 woody species with differing leaf succulence in a glasshouse dry-down experiment to determine relationships among leaf succulence (degree of leaf succulence, leaf succulent quotient and leaf thickness) and plant drought response (hydroscape area, plant water use, turgor loss point and predawn leaf water potential when transpiration ceased). Hydroscape areas ranged from 0.72 (Carpobrotus modestus S.T.Blake; crassulacean acid metabolism (CAM) plants) to 7.01 MPa2 (Rhagodia spinescens R.Br.; C3 plants), suggesting that C. modestus was more isohydric and R. spinescens was more anisohydric. More isohydric species C. modestus, Carpobrotus rossii (Haw.) Schwantes and Disphyma crassifolium (L.) L.Bolus (CAM plants) had greater leaf succulence, lower root allocation, used stored water and ceased transpiration at higher predawn leaf water potential, shortly after reaching their turgor loss point. The remaining nine species that are not CAM plants had larger hydroscape areas and ceased transpiration at lower predawn leaf water potential. Greater leaf succulence was not related to cumulative water loss until transpiration ceased in drying soils. All 12 species had high turgor loss points (−1.32 to −0.59 MPa), but turgor loss point was not related to hydroscape area or leaf succulence. Our data suggest that overall greater leaf succulence was related to isohydry, but this may have been influenced by the fact that these species were also CAM plants.
Impact of Energy Slope Averaging Methods on Numerical Solution of 1D Steady Gradually Varied Flow

Abstract In this paper, energy slope averaging in the one-dimensional steady gradually varied flow model is considered. For this purpose, different methods of averaging the energy slope between cross-sections are used. The most popular are arithmetic, geometric, harmonic and hydraulic means. However, from the formal viewpoint, the application of different averaging formulas results in different numerical integration formulas. This study examines the basic properties of numerical methods resulting from different types of averaging.
Association between retinal and cortical visual electrophysiological impairments in schizophrenia

Background: Electrophysiological impairments in the magnocellular visual system have been reported among patients with schizophrenia, but previous theories proposed that these deficits may begin in the retina. We therefore sought to evaluate the potential contribution of the retina by comparing retinal and cortical visual electrophysiological impairments between patients with schizophrenia and healthy controls. Methods: We recruited patients with schizophrenia and age- and sex-matched healthy controls. We recorded the P100 amplitude and latency using electroencephalography (EEG) while projecting low (0.5 cycles/degree) or high (15 cycles/degree) spatial frequency gratings at a temporal frequency of 0 Hz or 8 Hz. We compared the P100 results with previous results for retinal ganglion cell activity (N95) in these participants. We analyzed data using repeated-measures analysis of variance and correlation analyses. Results: We recruited 21 patients with schizophrenia and 29 age- and sex-matched healthy controls. Results showed decreased P100 amplitude and increased P100 latency among patients with schizophrenia compared with healthy controls (p < 0.05). Analyses reported the main effects of spatial and temporal frequency but no interaction effects of spatial or temporal frequency by group. Moreover, correlation analysis indicated a positive association between P100 latency and previous retinal results for N95 latency in the schizophrenia group (p < 0.05). Discussion: Alterations in the P100 wave among patients with schizophrenia are consistent with the deficits in early visual cortical processing shown in the literature. These deficits do not seem to correspond to an isolated magnocellular deficit but appear to be associated with previous retinal measurements. Such an association emphasizes the role of the retina in the occurrence of visual cortical abnormalities in schizophrenia. Studies with coupled electroretinography–EEG measurements are now required to further explore these findings. Clinical trials registration: https://clinicaltrials.gov/ct2/show/NCT02864680
DDT-RELATED PROTEIN4–IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis

Abstract DNA methylation is a conserved epigenetic modification that is typically associated with silencing of transposable elements and promoter methylated genes. However, some DNA-methylated loci are protected from silencing, allowing transcriptional flexibility in response to environmental and developmental cues. Through a genetic screen in Arabidopsis (Arabidopsis thaliana), we uncovered an antagonistic relationship between the MICRORCHIDIA (MORC) protein and the IMITATION SWITCH (ISWI) complex in regulating the DNA-methylated SUPPRESSOR OF DRM1 DRM2 CMT3 (SDC) reporter. We demonstrate that components of the plant-specific ISWI complex, including CHROMATIN REMODELING PROTEIN11 (CHR11), CHR17, DDT-RELATED PROTEIN4 (DDR4), and DDR5, function to partially derepress silenced genes and transposable elements (TEs), through their function in regulating nucleosome distribution. This action also requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. Genome-wide studies revealed that DDR4 causes changes in nucleosome distribution at numerous loci, a subset of which is associated with changes in DNA methylation and/or transcription. Our work reveals a mechanism for balancing transcriptional flexibility and faithful silencing of DNA-methylated loci. As both ISWI and MORC family genes are widely distributed across plant and animal species, our findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic regulation.
Automatic estimation of the cross‐sectional area of the waist of the nerve fibre layer at the optic nerve head

Glaucoma leads to pathological loss of axons in the retinal nerve fibre layer at the optic nerve head (ONH). This study aimed to develop a strategy for the estimation of the cross‐sectional area of the axons in the ONH. Furthermore, improving the estimation of the thickness of the nerve fibre layer, as compared to a method previously published by us.
A finite element algorithm for 3-D transient electromagnetic modeling

Summary We present a 3-D finite-element time-domain (FETD) algorithm for the simulation of electromagnetic (EM) diffusion phenomena. The algorithm simulates transient electric fields and time derivatives of the magnetic fields for a general anisotropic earth. In order to compute transient fields, the electric field wave equation is transformed into a system of ordinary differential equations (ODE) via a Galerkin method with Dirichlet boundary conditions. To ensure both numerical stability and an efficient time step size, the system of ODE is discretized in time using the implicit backward Euler scheme. The resultant FETD matrix-vector equation is solved using a sparse direct solver with a fill-in reducing algorithm. When advancing the solution in time, the algorithm adjusts the tine step by examining if or not a current step size can be doubled without affecting the accuracy of the solution. Instead of directly solving another FETD matrix-vector equation for transient magnetic fields, Faraday’s law is employed to compute time-derivatives of magnetic fields only at receiver positions. The accuracy and efficiency of the FETD algorithm are demonstrated using time-domain controlled source EM (TD-CSEM) simulations.
Intelligibility of Word-Initial Obstruent Consonants in Mandarin-Speaking Prelingually Deafened Children With Cochlear Implants.

PURPOSE This study assessed the intelligibility of obstruent consonants in prelingually deafened Mandarin-speaking children with cochlear implants (CIs). METHOD Twenty-two Mandarin-speaking children with normal hearing (NH) aged 3.25-10.0 years and 35 Mandarin-speaking children with CIs aged 3.77-15.0 years were recruited to produce a list of Mandarin words composed of 17 word-initial obstruent consonants in different vowel contexts. The children with CIs were assigned to chronological age-matched (CA) and hearing age-matched (HA) subgroups with reference to the NH controls. One hundred naïve NH adult listeners were recruited for a consonant identification task that consisted of a total of 2,663 stimulus tokens through an online research platform. For each child speaker, the consonant productions were judged by seven to 12 different adult listeners. An average percentage of consonants correct was calculated across all listeners for each consonant. RESULTS The CI children in both the CA and HA subgroups showed lower intelligibility in their consonant productions than the NH controls. Among the 17 obstruents, both CI subgroups showed higher intelligibility for stops, but they demonstrated major problems with the sibilant fricatives and affricates and showed a different confusion pattern from the NH controls on these sibilants. Of the three places (alveolar, alveolopalatal, and retroflex) in Mandarin sibilants, both CI subgroups showed the lowest intelligibility and the greatest difficulties with alveolar sounds. For the NH children, there was a significant positive relationship between overall consonant intelligibility and chronological age. For the children with CIs, the best fit regression model revealed significant effects of chronological age and age at implantation, with their quadratic terms included. CONCLUSIONS Mandarin-speaking children with CIs experience major challenges in the three-way place contrasts of sibilant sounds in consonant production. Chronological age and the combined effect of CI-related time variables play important roles in the development of obstruent consonants in the CI children.
The effect of subacute co-exposure to carbon tetrachloride and diclofenac on the liver of male wistar rats

Carbon tetrachloride (CCl4) is a potent liver toxin. Diclofenac (Dic), leading adverse effects on the liver, is used among the employees of the industries that use CCl4. The increased use of CCl4 and Dic in industrial workers has prompted us to investigate their synergistic effect on the liver using male Wistar rats as a model. Male Wistar rats were divided into seven groups (n = 6), and the exposure was by intraperitoneal injection for 14 days as follows. Group 1: Control, 2: Olive oil, 3: CCl4 (0.8 mL/kg/day (3 times per week)), 4: Normal saline, 5: Dic (1.5 mg/kg/day per day), 6: Olive oil with normal saline, 7: CCl4 (0.8 mL/kg/day (3 times per week)) and Dic (1.5 mg/kg/day daily). At the end of day 14, the heart blood was collected to measure the liver enzymes, alanine-aminotransferase (ALT), aspartate-aminotransferase (AST), blood alkaline phosphatase (ALP), albumin (ALB), direct bilirubin, and total bilirubin. A pathologist examined the liver tissue. Prism software was used to analyze data using ANOVA and Tukey statistical tests. ALT, AST, ALP, and Total Bilirubin enzymes were increased significantly in the co-administered CCl4 and Dic group, while the ALB levels decreased (p < 0.05). The histological findings reported liver necrosis, focal hemorrhage, adipose tissue change, and lymphocytic portal hepatitis. In conclusion, using Dic while exposed to CCl4 may exacerbate hepatotoxicity in rats. Therefore, it is suggested that more severe restrictions and safety regulations be placed on using CCl4 in the industry, and caution is advised to these industry workers to use Diclofenac.
Size-optimized simvastatin-loaded TPGS modified lipid nanocapsules for targeting epithelial-to-mesenchymal transition in hepatocellular carcinoma: Role of PTEN/AKT signaling

ABSTRACT Objectives Novel D-α-tocopherol polyethylene glycol 1000 succinate (TPGS) modified lipid nanocapsules (LNC) were prepared with the aim of improving the effectiveness of simvastatin (SIM) in hepatocellular carcinoma (HCC). The present study, therefore, sought to investigate the effect of size-optimized SIM-loaded LNC on epithelial-to-mesenchymal transition (EMT) in HCC, providing insights on the implication of phosphatase and tensin homolog (PTEN)/protein kinase B (AKT) axis. Methods Two optimized SIM-loaded LNCs with particle sizes 25 nm (SIM-LNC25) and 50 nm (SIM-LNC50) were prepared and biodistribution studies were performed. The anticancer effect of the prepared LNC was evaluated both in vitro and in vivo. The anti-migratory potential and EMT suppression through PTEN/AKT axis modulation were also explored. Results SIM-LNC50 was superior to SIM-LNC25 in both in vitro and in vivo experiments, as evidenced by cytotoxicity assays, tumor histopathology, and enhanced apoptosis. SIM-LNC50 also alleviated the migratory potential of HCC cells. Moreover, EMT markers implied a transition of tumor cells toward the epithelial rather than the mesenchymal phenotype both in vitro and in vivo. PTEN/AKT axis modulation was also evident with SIM-LNC50. Conclusion The present study, therefore, suggests the efficacy of the 50 nm particles in SIM-loaded LNC in HCC by targeting EMT via modulating the PTEN/AKT signaling axis.
A Generic Approach to Solving the Steiner Tree Problem and Variants

Spawned by practical applications, numerous variations of the classical Steiner tree problem in graphs have been studied during the last decades. Despite the strong relationship between the different variants, solution approaches employed so far have been prevalently problem-specific. In contrast, we pursue a general-purpose strategy resulting in a solver able to solve both the classical Steiner tree problem and ten of its variants without modification. These variants include well-known problems such as the prize-collecting Steiner tree problem, the maximum-weight connected subgraph problem or the rectilinear minimum Steiner tree problem. Bolstered by a variety of new methods, most notably reduction techniques, our solver is not only of unprecedented versatility, but furthermore competitive or even superior to specialized state-of-the-art programs for several Steiner problem variants.
Nonlinear Inflatable Actuators for Distributed Control in Soft Robots

As soft robotic systems grow in complexity and functionality, the size and stiffness of the needed control hardware severely limits their application potential. Alternatively, functionality can be embodied within actuator characteristics, drastically reducing the amount of peripherals. Functions such as memory, computation, and energy storage then result from the intrinsic mechanical behavior of precisely designed structures. Here, actuators are introduced with tunable characteristics to generate complex actuation sequences from a single input. Intricate sequences are made possible by harnessing hysteron characteristics encoded in the buckling of a cone‐shaped shell incorporated in the actuator design. A large variety of such characteristics are generated by varying the actuator geometry. This dependency is mapped and used for creating a tool to determine the actuator geometry that yields a desired characteristic. Using this tool, a system with six actuators is created that plays the final movement of Beethoven's Ninth Symphony with a single pressure supply.
Reinforcement Learning-Based Model Predictive Control for Discrete-Time Systems

This article proposes a novel reinforcement learning-based model predictive control (RLMPC) scheme for discrete-time systems. The scheme integrates model predictive control (MPC) and reinforcement learning (RL) through policy iteration (PI), where MPC is a policy generator and the RL technique is employed to evaluate the policy. Then the obtained value function is taken as the terminal cost of MPC, thus improving the generated policy. The advantage of doing so is that it rules out the need for the offline design paradigm of the terminal cost, the auxiliary controller, and the terminal constraint in traditional MPC. Moreover, RLMPC proposed in this article enables a more flexible choice of prediction horizon due to the elimination of the terminal constraint, which has great potential in reducing the computational burden. We provide a rigorous analysis of the convergence, feasibility, and stability properties of RLMPC. Simulation results show that RLMPC achieves nearly the same performance as traditional MPC in the control of linear systems and exhibits superiority over traditional MPC for nonlinear ones.
A variational approach to self-similar solutions for semilinear heat equations

Such self-similar solutions are global in time and often used to describe the large time behavior of global solutions to (1), see, e.g., [14, 15, 5, 21]. If w(x, t) is a self-similar solution of (1.1) and has an initial value A(x), then we easily see that A has the form A(x) = A(x/|x|)|x|−2/(p−1). Then the problem of existence of self-similar solutions is essentially depend on the solvablity of the Cauchy problem (1)-(2)λ. In this talk we consider the existence of self-similar solutions of the problem (1)-(2)λ. The idea of constructing self-similar solutions by solving the initial value problem for homogeneous initial data goes back to the study by Giga and Miyakawa [12] for the Navier-Stokes equation in vorticity form. It is well known by Fujita [9] that if 1 (N + 2)/N is necessary for the existence of positive self-similar solutions of (1).
The Multifunctional Family of Mammalian Fatty Acid–Binding Proteins

Fatty acid–binding proteins (FABPs) are small lipid-binding proteins abundantly expressed in tissues that are highly active in fatty acid (FA) metabolism. Ten mammalian FABPs have been identified, with tissue-specific expression patterns and highly conserved tertiary structures. FABPs were initially studied as intracellular FA transport proteins. Further investigation has demonstrated their participation in lipid metabolism, both directly and via regulation of gene expression, and in signaling within their cells of expression. There is also evidence that they may be secreted and have functional impact via the circulation. It has also been shown that the FABP ligand binding repertoire extends beyond long-chain FAs and that their functional properties also involve participation in systemic metabolism. This article reviews the present understanding of FABP functions and their apparent roles in disease, particularly metabolic and inflammation-related disorders and cancers.
High‐frequency permeability of sputtered Fe–Co–B‐based soft magnetic thin films

High‐frequency characteristics of a series of soft magnetic Fe–Co–B‐based thin films are investigated in the range of 0.5–5 GHz. It is found that in‐plane anisotropy can be caused by oblique incidence or applying an external field during deposition. The permeability and the resonance frequency are basically consistent with Snoek's law. Ni can improve the magnetic properties greatly except for the decrease of resistivity. In order to reduce the dissipation and increase the resistivity, SiO2 is added to the film. Excellent high‐frequency permeability of (Fe40Co40B20)0.619Ni12. 642–(SiO2)25.416 is obtained: the resonance frequency exceeds 2.2 GHz; the real and the imaginary parts of the permeability at 0.5 GHz are 476 and 92, respectively; the resistivity of the film reaches 682 μΩ cm. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
BRGenomics for analyzing high-resolution genomics data in R

Abstract Summary I present here the R/Bioconductor package BRGenomics, which provides fast and flexible methods for post-alignment processing and analysis of high-resolution genomics data within an interactive R environment. Utilizing GenomicRanges and other core Bioconductor packages, BRGenomics provides various methods for data importation and processing, read counting and aggregation, spike-in and batch normalization, re-sampling methods for robust ‘metagene’ analyses, and various other functions for cleaning and modifying sequencing and annotation data. Simple yet flexible, the included methods are optimized for handling multiple datasets simultaneously, make extensive use of parallel processing, and support multiple strategies for efficiently storing and quantifying different kinds of data, including whole reads, quantitative single-base data, and run-length encoded coverage information. BRGenomics has been used to analyze ATAC-seq, ChIP-seq/ChIP-exo, PRO-seq/PRO-cap, and RNA-seq data; is built to be unobtrusive and maximally compatible with the Bioconductor ecosystem; is extensively tested; and includes complete documentation, examples, and tutorials. Availability and implementation BRGenomics is an R package distributed through Bioconductor (https://bioconductor.org/packages/BRGenomics). Full documentation with examples and tutorials are available online (https://mdeber.github.io).