Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel CCR7-Related Immune Prognostic Signature for Liver Hepatocellular Carcinoma (LIHC) Based on Immunogenomic Profiling

Object: Explore the specific function of CCR7 in immune mechanism of LIHC, and constructed CCR7-related immune prognostic signature (IPS) for LIHC patients.Methods: The RNA-seq data of LIHC was downloaded from TCGA dataset and the samples were divided into CCR7_H and CCR7_L group. Then, ssGSEA analysis, immune microenvironment analysis, expression level analysis of HLA genes and check point genes were conducted. The differential expression immune genes (DEIGs) were conducted and LASSO Cox was applied to construct CCR7-related IPS. A novel nomogram was constructed to predict survival rate of LIHC patients.Results: The Immune score, Stromal score and ESTAMATE score are higher in CCR_H group, while tumor purity higher in CCR_L group. In CCR7_H group, the HLA genes and immune checkpoint genes have higher expression levels. The CCR7_H group have a favorable prognosis than CCR7_L group. There are 903 DEIGs were identified. The DEIGs mainly enriched in complement activation, adaptive immune response, T cell activation, lymphocyte differentiation and cytokine-cytokine receptor interaction. The IPS consists of 10 genes, including GHV4-59, SCML4, AKR1B10, LINC00426, TRGC1, F2RL2, TRBV10-3, SAMD9L, SLC4A10 and ROR2. Univariate and multivariate Cox analysis showed that the IPS was an independent prognostic factor of LIHC. Conclusions: The CCR7-related IPS and nomogram were constructed and provided for LIHC patients to predict survival rate. This study provided a novel way to analyzed the prognostic effect of CCR7 expression from the perspective of immunology.
Effects of the Application of Biochar to Plant Growth and Net Primary Production in an Oak Forest

Few studies have evaluated the application of biochar to forest ecosystems and their responses under field conditions. We manually spread grounded biochar on the forest floor, at rates of 0 (control), 5, and 10 Mg ha−1 (C0, C5 and C10, respectively), of an oak forest in central Japan to test the effects of biochar on tree growth and productivity. The relative growth rate of the diameter at breast height (dbh) of canopy oak trees (dbh > 20 cm) significantly increased in C10 compared with that of the control (C0), but not in C5, in the second to third years after application. Despite the increasing growth rate of canopy trees, foliage production (NPPF) and woody production (NPPW) did not respond to biochar application. Conversely, the production of reproductive organs (NPPR, mainly oak acorns) increased in line with the biochar application rate gradients (1.04 ± 0.09 Mg ha−1 yr−1 in C0, 1.30 ± 0.08 Mg ha−1 yr−1 in C5, and 1.47 ± 0.13 Mg ha−1 yr−1 in C10). Since the contribution of NPPR to total NPP was fairly small, there were no significant differences in total NPP (=NPPW + NPPF + NPPR) for C5 (14.57 ± 0.20 Mg ha−1 yr−1) or C10 (16.11 ± 0.73 Mg ha−1 yr−1) compared with the control (15.07 ± 0.48 Mg ha−1 yr−1).
CO-NNECT: A Framework for Revealing Commonsense Knowledge Paths as Explicitations of Implicit Knowledge in Texts

In this work we leverage commonsense knowledge in form of knowledge paths to establish connections between sentences, as a form of explicitation of implicit knowledge. Such connections can be direct (singlehop paths) or require intermediate concepts (multihop paths). To construct such paths we combine two model types in a joint framework we call Co-nnect: a relation classifier that predicts direct connections between concepts; and a target prediction model that generates target or intermediate concepts given a source concept and a relation, which we use to construct multihop paths. Unlike prior work that relies exclusively on static knowledge sources, we leverage language models finetuned on knowledge stored in ConceptNet, to dynamically generate knowledge paths, as explanations of implicit knowledge that connects sentences in texts. As a central contribution we design manual and automatic evaluation settings for assessing the quality of the generated paths. We conduct evaluations on two argumentative datasets and show that a combination of the two model types generates meaningful, high-quality knowledge paths between sentences that reveal implicit knowledge conveyed in text.
Quantitative analysis of the dynamic properties of chromatin associated proteins by uorescence recovery after photobleaching experiments

Background In recent years in vivo microscopy studies have revealed that the nucleus and its components are more dynamic than previously assumed. A widely used technique in these studies is fluorescence recovery after photobleaching (FRAP) which allows characterizing the dynamic behavior of proteins in vivo. Besides a qualitative interpretation of the data, quantitative FRAP procedures allow measuring the dynamic properties of proteins, namely diffusion and binding to chromatin. Unfortunately, the accuracy of these estimates is uncertain, since no benchmark exists. Results This present study improved FRAP methodology in three areas. First, the establishment of benchmark measurements was begun by comparing three recent studies on transcription factor binding to DNA. The published binding estimates for each protein were significantly different. When comparing the FRAP procedures it was found that that this difference was due to previously unidentified incorrect assumptions. Corrected procedures were developed and when applied to the three proteins consistent estimates were obtained. This showed not only that the errors identified were corrected, but also suggested that these proteins have a similar mode of interaction with chromatin. Second, existing FRAP models were extended to account for inhomogeneous distributions of binding sites by combining different modeling approaches. These models were successfully applied to analyze the binding behavior of two nuclear proteins in more detail. Third, given that quantitative FRAP procedures might still be flawed, the qualitative FRAP approach was improved by developing novel tools to analyze and visualize data. The value of these improved tools was demonstrated in two publications. Conclusions This study illustrated vividly that in vivo binding measurements are not trivial and when done improperly can lead to erroneous biological conclusions. Improved methods for FRAP were presented and it was demonstrated how the combination of different experimental and modeling approaches can be utilized to better understand the dynamic behavior of nuclear proteins. Continuing this combined approach in future studies will improve the accuracy and reliability of these methods and ultimately help to understand protein function in the complex nuclear network.
Untersuchungen zur Charakteristik der freien Grenzflächenkonvektion beim Stoffübergang an fluiden Grenzen

Einführung In den Mitteilungen I, II, III [1] wurden einzelne und im Verband auftretende großräumige Strömungszellen beschrieben, die sich beim Stoffübergang von Natriumalkylsulfaten aus iso-Amylol in die wäßrige Phase ausbilden. Zur Deutung des hydrodynamischen Verhaltens der fluiden Phasengrenze kann die Theorie der hydrodynamischen Instabilität herangezogen werden, die von STERNLING und SCRIVEN [2] für ein zweidimensionales Modell unter vereinfachenden Voraussetzungen entwickelt wurde. Für das Auftreten der Instabilität und den Charakter der sich ausbildenden Konvektion ist bei vorgegebener Konzentrationsabhängigkeit der Grenzflächenspannung — und gegebener Richtung des KonzentrationsAc gradienten an der Grenze der Quotient der Diffusionskoeffizienten der beiden D v Phasen — und der Quotient der kinematischen Zähigkeiten — von entD„ vb scheidendem Einfluß. Eine Abschätzung der Bedingungen für das System Ditalan in iso-Amylol t Da va 3 . — ergibt — < 1 < — , wonach bei Stoffubergang Wasser Db vb
PREPARATION AND EVALUATION OF CHITOSAN SODIUM ALGINATE CARBAMAZEPINE MICROSPHERES

ABSTRACT Objective: The objective behind our study is that a mucoadhesive rectal hydrogel chitosan sodium alginate carbamazepine (CBZ) microspheres for the purpose of controlled release for the treatment of epilepsy to avoid the possible side effects. Methods: The study was conducted to formulate controlled release chitosan sodium alginate CBZ microspheres with the dispersion of CBZ into the natural polymers chitosan and sodium alginate forming microspheres conducting along with their evaluation studies. Results: The formulated microspheres were subjected to various evaluation parameters, and all the physical parameters examined are within the acceptable limits. Further, the optimized microsphere formulation (CM5) was characterized. Hence, the developed optimized microsphere formulation (CM5) seems to be a viable substitute to conventional drug delivery system for the effective management of epilepsy. Conclusion: The prepared formulation also provides a desired CBZ loaded sodium alginate microspheres with the controlled release drug delivery. Keywords: Carbamazepine, Sodium alginate microspheres, Particle size.
Photocleavage of Covalently Immobilized Amphiphilic Block Copolymer: From Bilayer to Monolayer

We developed and verified a method to create a photocleavable smart surface. Using the grafting to approach, we covalently attached an intelligently designed tailor-made diblock copolymer to a silicon wafer. The photocleavable moiety, o-nitrobenzyl (ONB) ester, was integrated into the copolymer at the junction point between the hydrophilic poly(ethylene oxide) (PEO) and the hydrophobic polystyrene (PS) chains. The well-defined azide bearing amphiphilic block copolymer was synthesized via a general stepwise strategy that combines atom transfer radical polymerization (ATRP) and copper(I)-catalyzed azide–alkyne cycloaddition reaction (CuAAC), ending with azidation. The azide end-functionalized copolymer chains were covalently bound to the alkyne-immobilized silicon wafer by CuAAC. The smart surface was exposed to UV irradiation, resulting in photocleavage of the grafted ONB linker. As a result of the photocleavage and subsequent removal of the o-nitrosobenzaldehyde bearing PEO, the PS layer remained on the s.
Modeling Multiphase Flow Within and Around Deformable Porous Materials: A Darcy‐Brinkman‐Biot Approach

We present a new computational fluid dynamics approach for simulating two‐phase flow in hybrid systems containing solid‐free regions and deformable porous matrices. Our approach is based on the derivation of a unique set of volume‐averaged partial differential equations that asymptotically approach the Navier‐Stokes Volume‐of‐Fluid equations in solid‐free regions and multiphase Biot Theory in porous regions. The resulting equations extend our recently developed Darcy‐Brinkman‐Biot framework to multiphase flow. Through careful consideration of interfacial dynamics (relative permeability and capillary effects) and extensive benchmarking, we show that the resulting model accurately captures the strong two‐way coupling that is often exhibited between multiple fluids and deformable porous media. Thus, it can be used to represent flow‐induced material deformation (swelling, compression) and failure (cracking, fracturing). The model's open‐source numerical implementation, hybridBiotInterFoam, effectively marks the extension of computational fluid mechanics into modeling multiscale multiphase flow in deformable porous systems. The versatility of the solver is illustrated through applications related to material failure in poroelastic coastal barriers and surface deformation due to fluid injection in poro‐visco‐plastic systems.
High‐Frequency (6 Hz) PKPab Precursors and Their Sensitivity to Deep Earth Heterogeneity

We present observations on a new precursory phase of seismic waves scattered in the deep Earth. This phase arrives prior to the PKPab wave at epicentral distances larger than 155°, and we call it PKPab precursor. We show that the presence of the PKPab precursor is a necessary consequence of scattering in D″, which is the commonly accepted cause of the PKPdf precursor at distances smaller than 145°. PKPdf waves that propagate through the inner core should arrive before the PKPab precursor but those, are strongly attenuated in the inner core at frequencies between 4 Hz and 8 Hz used here, making the PKPab precursor the earliest teleseismic signal at distances larger than 155°. Calculated PKPab precursor sensitivity kernel shows that this phase is mostly sensitive to scattering along the closest PKPbc path between source and receiver. It can thus help to constrain the lateral distribution of heterogeneity along D″.
(An overview of) Synergistic reconstruction for multimodality/multichannel imaging methods

Imaging is omnipresent in modern society with imaging devices based on a zoo of physical principles, probing a specimen across different wavelengths, energies and time. Recent years have seen a change in the imaging landscape with more and more imaging devices combining that which previously was used separately. Motivated by these hardware developments, an ever increasing set of mathematical ideas is appearing regarding how data from different imaging modalities or channels can be synergistically combined in the image reconstruction process, exploiting structural and/or functional correlations between the multiple images. Here we review these developments, give pointers to important challenges and provide an outlook as to how the field may develop in the forthcoming years. This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 1’.
Synergistic multi-contrast cardiac magnetic resonance image reconstruction

Cardiac magnetic resonance imaging (CMR) is an important tool for the non-invasive diagnosis of a variety of cardiovascular diseases. Parametric mapping with multi-contrast CMR is able to quantify tissue alterations in myocardial disease and promises to improve patient care. However, magnetic resonance imaging is an inherently slow imaging modality, resulting in long acquisition times for parametric mapping which acquires a series of cardiac images with different contrasts for signal fitting or dictionary matching. Furthermore, extra efforts to deal with respiratory and cardiac motion by triggering and gating further increase the scan time. Several techniques have been developed to speed up CMR acquisitions, which usually acquire less data than that required by the Nyquist–Shannon sampling theorem, followed by regularized reconstruction to mitigate undersampling artefacts. Recent advances in CMR parametric mapping speed up CMR by synergistically exploiting spatial–temporal and contrast redundancies. In this article, we will review the recent developments in multi-contrast CMR image reconstruction for parametric mapping with special focus on low-rank and model-based reconstructions. Deep learning-based multi-contrast reconstruction has recently been proposed in other magnetic resonance applications. These developments will be covered to introduce the general methodology. Current technical limitations and potential future directions are discussed. This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 1’.
Improved identification of abdominal aortic aneurysm using the Kernelized Expectation Maximization algorithm

Abdominal aortic aneurysm (AAA) monitoring and risk of rupture is currently assumed to be correlated with the aneurysm diameter. Aneurysm growth, however, has been demonstrated to be unpredictable. Using PET to measure uptake of [18F]-NaF in calcified lesions of the abdominal aorta has been shown to be useful for identifying AAA and to predict its growth. The PET low spatial resolution, however, can affect the accuracy of the diagnosis. Advanced edge-preserving reconstruction algorithms can overcome this issue. The kernel method has been demonstrated to provide noise suppression while retaining emission and edge information. Nevertheless, these findings were obtained using simulations, phantoms and a limited amount of patient data. In this study, the authors aim to investigate the usefulness of the anatomically guided kernelized expectation maximization (KEM) and the hybrid KEM (HKEM) methods and to judge the statistical significance of the related improvements. Sixty-one datasets of patients with AAA and 11 from control patients were reconstructed with ordered subsets expectation maximization (OSEM), HKEM and KEM and the analysis was carried out using the target-to-blood-pool ratio, and a series of statistical tests. The results show that all algorithms have similar diagnostic power, but HKEM and KEM can significantly recover uptake of lesions and improve the accuracy of the diagnosis by up to 22% compared to OSEM. The same improvements are likely to be obtained in clinical applications based on the quantification of small lesions, like for example cancer. This article is part of the theme issue ‘Synergistic tomographic image reconstruction: part 1’.
Joint-level force sensing for indirect hybrid force/position control of continuum robots with friction

Continuum robots offer the dexterity and obstacle circumvention capabilities necessary to enable surgery in deep surgical sites. They also can enable joint-level ex situ force sensing (JEFS), which provides an estimate of end-effector wrenches given joint-level forces. Prior works on JEFS relied on a restrictive embodiment with minimal actuation line friction and captured model and frictional actuation transmission uncertainties using a configuration space formulation. In this work, we overcome these limitations. First, frictional losses are canceled using a feed-forward term based on support vector regression in joint space. Then, regression maps and their interpolation are used to account for actuation hysteresis. The residual joint-force error is then further minimized using a least-squares model parameter update. An indirect hybrid force/position controller using JEFS is presented with evaluation carried out on a realistic pre-clinically deployable insertable robotic effectors platform (IREP) for single-port access surgery. Automated mock force-controlled ablation, exploration, and knot tightening are evaluated. A user study involving the daVinci Research Kit surgeon console and the IREP as a surgical slave was carried out to compare the performance of users with and without force feedback based on JEFS for force-controlled ablation and knot tightening. Results in automated experiments and a user study of telemanipulated experiments suggest that intrinsic force-sensing can achieve levels of force uncertainty and force regulation errors of the order of 0.2 N. Using JEFS and automated task execution, repeatability, and force regulation accuracy is shown to be comparable to using a commercial force sensor for human-in-the-loop feedback.
IWSHM 2019: Perturbation-based Bayesian damage identification using responses at vibration nodes

One important topic for structural health monitoring is to achieve accurate damage detection with a small number of noisy sensors and without the requirement of a high-fidelity finite element model. This article adopts the Bayesian probabilistic approach combined with a perturbation model using responses at a few vibration nodes for damage monitoring. First, the node displacement, or the response at vibration node, is adopted in this study for real-time damage assessment with a relatively small number of sensors. Then, the construction method of the node displacement response curves based on the perturbation model is proposed to replace the expensive finite element model. After that, a Bayesian framework integrated the node displacement measurement and the response curves are adopted to acquire the probability distribution of the damage parameter. In this article, the accuracy of the node displacement–based Bayesian framework with the perturbation method is evaluated. The proposed method is applied to a supporting structure of a sailplane under different noise levels.
Exploring the Mechanism of Zhibai Dihuang Decoction in the Treatment of Ureaplasma Urealyticum-Induced Orchitis Based on Integrated Pharmacology

Background: Ureaplasma urealyticum (UU) infection is the most common cause of male infertility. Zhibai Dihuang Decoction (ZBDHD) can improve the rate of forwarding motility sperm, sperm deformity rate, seminal plasma zinc and refined berry sugar levels. Methods: The potential targets of ZBDHD are obtained from The Encyclopedia of Traditional Chinese Medicine (ETCM). Orchitis-related targets were collected from the Genecards and OMIM databases. The Cytoscape and the Database for Annotation, Visualization and Integrated Discovery (DAVID) were utilized to construct and analyzed the networks. Finally, a rat model of orchitis caused by UU infection was used to detect related indicators of mitochondrial energy metabolism using TUNEL apoptosis detection technology, loss cytometry, Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and Western Blot. Results: A total of 795 ZBDHD targets and 242 orchitis-related targets were obtained. The “ZBDHD- orchitis PPI network” was constructed and analyzed. ZBDHD can regulate signaling pathways and biological processes related to mitochondrial energy metabolism. The results of experimental studies have shown that ZBDHD maintains the integrity of sperm mitochondrial respiratory chain function by enhancing mitochondrial Na+-K+-ATPase and Ca2+-Mg2+-ATPase activities, promotes the synthesis of mitochondrial ATP, and improves sperm energy supply, thereby improving the motility, vitality and survival rate of sperm, and effectively improving the quality of semen in UU-infected rats (p < 0.05). Conclusion:This study discovered the multi-pathway mechanism of ZBDHD intervention in UU-induced orchitis through integrated pharmacological strategies, which provides a reference for further research on the mechanism of ZBDHD intervention in orchitis in the direction of mitochondrial energy metabolism.
Sex-Dependent Effects of the Microbiome on Foraging and Locomotion in Drosophila suzukii

There is growing evidence that symbiotic microbes can influence multiple nutrition-related behaviors of their hosts, including locomotion, feeding, and foraging. However, how the microbiome affects nutrition-related behavior is largely unknown. Here, we demonstrate clear sexual dimorphism in how the microbiome affects foraging behavior of a frugivorous fruit fly, Drosophila suzukii. Female flies deprived of their microbiome (axenic) were consistently less active in foraging on fruits than their conventional counterparts, even though they were more susceptible to starvation and starvation-induced locomotion was notably more elevated in axenic than conventional females. Such behavioral change was not observed in male flies. The lag of axenic female flies but not male flies to forage on fruits is associated with lower oviposition by axenic flies, and mirrored by reduced food seeking observed in virgin females when compared to mated, gravid females. In contrast to foraging intensity being highly dependent on the microbiome, conventional and axenic flies of both sexes showed relatively consistent and similar fruit preferences in foraging and oviposition, with raspberries being preferred among the fruits tested. Collectively, this work highlights a clear sex-specific effect of the microbiome on foraging and locomotion behaviors in flies, an important first step toward identifying specific mechanisms that may drive the modulation of insect behavior by interactions between the host, the microbiome, and food.