Miracle-dz/UniFAR-FTUs huggingface dataset:
Climate legacies determine grassland responses to future rainfall regimes

Climate variability and periodic droughts have complex effects on carbon (C) fluxes, with uncertain implications for ecosystem C balance under a changing climate. Responses to climate change can be modulated by persistent effects of climate history on plant communities, soil microbial activity, and nutrient cycling (i.e., legacies). To assess how legacies of past precipitation regimes influence tallgrass prairie C cycling under new precipitation regimes, we modified a long‐term irrigation experiment that simulated a wetter climate for >25 years. We reversed irrigated and control (ambient precipitation) treatments in some plots and imposed an experimental drought in plots with a history of irrigation or ambient precipitation to assess how climate legacies affect aboveground net primary productivity (ANPP), soil respiration, and selected soil C pools. Legacy effects of elevated precipitation (irrigation) included higher C fluxes and altered labile soil C pools, and in some cases altered sensitivity to new climate treatments. Indeed, decades of irrigation reduced the sensitivity of both ANPP and soil respiration to drought compared with controls. Positive legacy effects of irrigation on ANPP persisted for at least 3 years following treatment reversal, were apparent in both wet and dry years, and were associated with altered plant functional composition. In contrast, legacy effects on soil respiration were comparatively short‐lived and did not manifest under natural or experimentally‐imposed “wet years,” suggesting that legacy effects on CO2 efflux are contingent on current conditions. Although total soil C remained similar across treatments, long‐term irrigation increased labile soil C and the sensitivity of microbial biomass C to drought. Importantly, the magnitude of legacy effects for all response variables varied with topography, suggesting that landscape can modulate the strength and direction of climate legacies. Our results demonstrate the role of climate history as an important determinant of terrestrial C cycling responses to future climate changes.
Core concepts in pharmacoepidemiology: Confounding by indication and the role of active comparators

Confounding by indication poses a significant threat to the validity of nonexperimental studies assessing effectiveness and safety of medical interventions. While no different from other forms of confounding in theory, confounding by indication often requires specific methods to address the bias it creates in addition to common epidemiological adjustment or restriction methods. Clinical indication influencing treatment prescription is patient‐specific and complex, making it challenging to measure within nonexperimental research. Restriction of the study population to patients with the indication for treatment would effectively mitigate confounding by indication and bring about comparability between exposure and comparator populations with respect to probability of the exposure. Active comparators are often an effective practical solution to restrict the study population in this manner when indication cannot be measured accurately. This article discusses various forms of confounding by indication, the utility of active comparators for nonexperimental studies of treatment effects, and the active comparator, new user (ACNU) study design to implicitly condition on indication. Considerations for selecting active comparators and conducting an ACNU study design are discussed to enable increased adoption of these methods, improve quality of nonexperimental studies, and ultimately strengthen our evidence base for intended and unintended treatment effects in relevant target populations.
Three cases of hepatic epithelioid hemangioendothelioma evaluated using conventional and contrast‐enhanced ultrasound: Case reports

Hepatic epithelioid hemangioendothelioma (HEHE) is a very rare vascular endothelial cell tumor, which lacks typical clinical manifestations and specificity of imaging features. Whether the background of fatty liver and the difference in Contrast enhanced ultrasound (CEUS) characteristics between large and small lesions has not been well defined. In this case reports, we described the ultrasound image features of three patients with HEHE. These three patients with HEHE have certain similar characteristics of conventional ultrasound and CEUS. CEUS imaging features include large nodules show earlier perfusion than liver parenchyma, with rim‐enhancement, nonenhancing regions in the center, while small nodules show earlier perfusion than liver parenchyma, with hyperenhancement. All nodules show faster washout than hepatic parenchyma, showing heterogeneous hypoenhancement, and more washout lesions can be found in the PVP and LP. Conventional ultrasound and CEUS not only help to improve the diagnostic confidence of HEHE of rare liver tumors, but also can guide the biopsy area, making it easier to make accurate pathological diagnosis.
Research Development of GIS Switching Arc Model for VFTO Simulation

Very fast transient overvoltage(VFTO) is produced when the disconnector operations in gas insulated switchgear(GIS),which has a great impact on the power system stability and the safety operation of electric equipment.The simulation technology is an important research method for studying the characteristics of VFTO. Studying the development and parameter variation of switching arc of disconnector in GIS is significant for obtaining the standard VFTO wave form.This paper elaborates almost all switching arc models of disconnector in GIS for the current VFTO simulation.Traditional switching arc models,improved switching arc models and the experimental research of arc characteristic are discussed and summarized.At the same time,the advantages and disadvantages of the different arc models are analyzed.Finally,the trend and further problems of GIS switching arc model for VFTO simulation are overviewed.This paper aims to provide a systematic theory platform for discussion and a beneficial reference to peer scholars.
Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities

Abstract Motivation The advance of mass spectrometry-based technologies enabled the profiling of the phosphoproteomes of a multitude of cell and tissue types. However, current research primarily focused on investigating the phosphorylation dynamics in specific cell types and experimental conditions, whereas the phosphorylation events that are common across cell/tissue types and stable regardless of experimental conditions are, so far, mostly ignored. Results Here, we developed a statistical framework to identify the stable phosphoproteome across 53 human phosphoproteomics datasets, covering 40 cell/tissue types and 194 conditions/treatments. We demonstrate that the stably phosphorylated sites (SPSs) identified from our statistical framework are evolutionarily conserved, functionally important and enriched in a range of core signaling and gene pathways. Particularly, we show that SPSs are highly enriched in the RNA splicing pathway, an essential cellular process in mammalian cells, and frequently disrupted by cancer mutations, suggesting a link between the dysregulation of RNA splicing and cancer development through mutations on SPSs. Availability and implementation The source code for data analysis in this study is available from Github repository https://github.com/PYangLab/SPSs under the open-source license of GPL-3. The data used in this study are publicly available (see Section 2.8). Supplementary information Supplementary data are available at Bioinformatics online.
Selection and identification of an RNA aptamer that specifically binds the HIV-1 capsid lattice and inhibits viral replication

Abstract The HIV-1 capsid core participates in several replication processes. The mature capsid core is a lattice composed of capsid (CA) monomers thought to assemble first into CA dimers, then into ∼250 CA hexamers and 12 CA pentamers. CA assembly requires conformational flexibility of each unit, resulting in the presence of unique, solvent-accessible surfaces. Significant advances have improved our understanding of the roles of the capsid core in replication; however, the contributions of individual CA assembly forms remain unclear and there are limited tools available to evaluate these forms in vivo. Here, we have selected aptamers that bind CA lattice tubes. We describe aptamer CA15-2, which selectively binds CA lattice, but not CA monomer or CA hexamer, suggesting that it targets an interface present and accessible only on CA lattice. CA15-2 does not compete with PF74 for binding, indicating that it likely binds a non-overlapping site. Furthermore, CA15-2 inhibits HIV-1 replication when expressed in virus producer cells, but not target cells, suggesting that it binds a biologically-relevant site during virus production that is either not accessible during post-entry replication steps or is accessible but unaltered by aptamer binding. Importantly, CA15-2 represents the first aptamer that specifically recognizes the HIV-1 CA lattice.
NOVEL PLASMA GLYCOPROTEIN BIOMARKERS PREDICT PROGRESSION-FREE SURVIVAL IN SURGICALLY RESECTED CLEAR CELL RENAL CELL CARCINOMA

Introduction: Limited data exists on utilization of protein post-translational modifications as biomarkers for clear cell renal cell carcinoma (ccRCC). We employed high-throughput glycoproteomics to evaluate differential expression of glycoprotein-isoforms as novel markers for ccRCC progression-free survival (PFS). Methods: Plasma samples were obtained from 77 patients treated surgically for ccRCC. Glycoproteomic analyses were carried out after liquid chromatography tandem mass spectrometry. Age-adjusted Cox proportional hazard models were constructed to evaluate PFS. Optimized Harrells c-index was employed to dichotomize the collective for the construction of Kaplan-Meier curves. Results: The average length of follow-up was 3.4 (range: 0.04-9.83) years. Glycoproteomic analysis identified 39 glycopeptides and 14 non-glycosylated peptides that showed statistically significant (false discovery rate p [≤]0.05) differential expression associated with PFS. Five of the glycosylated peptides conferred continuous hazard ratio of > 6 (range 6.3-11.6). These included prothrombin A2G2S glycan motif (HR=6.47, P=9.53E-05), immunoglobulin J chain FA2G2S2 motif (HR=10.69, P=0.001), clusterin A2G2 motif (HR=7.38, P=0.002), complement component C8A A2G2S2 motif (HR=11.59, P=0.002), and apolipoprotein M glycopeptide with non-fucosylated and non-sialylated hybrid-type glycan (HR=6.30, P=0.003). Kaplan-Meier curves based on dichotomous expression of these five glycopeptides resulted in hazard ratios of 3.9-10.7, all with p-value < 0.03. Kaplan-Meyer plot using the multivariable model comprising 3 of the markers yielded HR of 11.96 (p <0.0001). Conclusion: Differential glyco-isoform abundance of plasma proteins may be a useful source of biomarkers for the clinical course and prognosis of ccRCC.
Gumble Softmax For User Behavior Modeling

Recently, sequential recommendation systems are important in solving the information overload in many online services. Current methods in sequential recommendation focus on learning a fixed number of representations for each user at any time, with a single representation or multi representations for the user. However, when a user is exploring items on an e-commerce recommendation system, the number of this user's hobbies may change overtime (e.g. increase/reduce one more interest), affected by the user's evolving self needs. Moreover, different users may have various number of interests. In this paper, we argue that it is meaningful to explore a personalized dynamic number of user interests, and learn a dynamic group of user interest representations accordingly. We propose a sequential model with dynamic number of representations for recommendation systems (RDRSR). Specifically, RDRSR is composed of a dynamic interest discriminator (DID) module and a dynamic interest allocator (DIA) module. The DID module explores the number of a user's interests by learning the overall sequential characteristics with bi-directional self-attention and Gumbel-Softmax. The DIA module make the historical clicked items into a group of item groups and constructs user's dynamic interest representation. Additionally, experiments on the real-world datasets demonstrates our model's effectiveness.
Operative approach to quantum electrodynamics in dispersive dielectric objects based on a polarization-mode expansion

In this paper we deal with the macroscopic electromagnetic response of a finite size dispersive dielectric object, in unbounded space, in the framework of quantum electrodynamics using the Heisenberg picture. We apply a Hopfield type scheme to account for the dispersion and dissipation of the matter. We provide a general expression of the polarization density field operator as functions of the initial conditions of the matter field operators and of the electromagnetic field operators. It is a linear functional whose kernel is a linear expression of the impulse response of the dielectric object that we obtain within the framework of classical electrodynamics. The electric field operator is expressed as a function of the polarization density field operator by means of the dyadic Green's function for the free space. The statistical functions of these operators are classical functionals of the statistics of the initial conditions of the matter field operators and of the electromagnetic field operators, whose kernels are linear or multilinear expressions of the impulse response of the dielectric object. We keep the polarization and the electromagnetic field distinct to enable the treatment of the polarization and electromagnetic fluctuations on equal footing. We expand the polarization density field operator in terms of the static longitudinal and transverse modes of the object to diagonalize the Coulomb and Ampere interaction energy terms of the Hamiltonian in the Coulomb gauge. We expand the radiation fields in terms of the transverse plane wave modes of free space. Few static longitudinal and transverse modes are needed to calculate each element of the impulse response matrix for dielectric objects with sizes of the order up to $\min\limits_{\omega}\{c_0/[\omega \sqrt{|{\chi}(\omega)|}]\}$ where ${\chi}(\omega)$ is the susceptibility of the dielectric.
Sequential optical response suppression for chemical mixture characterization

The characterization of mixtures of non-interacting, spectroscopically similar quantum components has important applications in chemistry, biology, and materials science. We introduce an approach based on quantum tracking control that allows for determining the relative concentrations of constituents in a quantum mixture, using a single pulse which enhances the distinguishability of components of the mixture and has a length that scales linearly with the number of mixture constituents. To illustrate the method, we consider two very distinct model systems: mixtures of diatomic molecules in the gas phase, as well as solid-state materials composed of a mixture of components. A set of numerical analyses are presented, showing strong performance in both settings.
Transcriptomic Analysis Reveals That Rho GTPases Regulate Trap Development and Lifestyle Transition of the Nematode-Trapping Fungus Arthrobotrys oligospora

Nematode-trapping (NT) fungi are widely distributed in terrestrial and aquatic ecosystems. Their broad adaptability and flexible lifestyles make them ideal agents for controlling pathogenic nematodes. Arthrobotrys oligospora is a model species employed for understanding the interaction between fungi and nematodes. ABSTRACT Nematode-trapping (NT) fungi can form unique infection structures (traps) to capture and kill free-living nematodes and, thus, can play a potential role in the biocontrol of nematodes. Arthrobotrys oligospora is a representative species of NT fungi. Here, we performed a time course transcriptome sequencing (RNA-seq) analysis of transcriptomes to understand the global gene expression levels of A. oligospora during trap formation and predation. We identified 5,752 unique differentially expressed genes, among which the rac gene was significantly upregulated. Alternative splicing events occurred in 2,012 genes, including the rac and rho2 gene. Furthermore, we characterized three Rho GTPases (Rho2, Rac, and Cdc42) in A. oligospora using gene disruption and multiphenotypic analysis. Our analyses showed that AoRac and AoCdc42 play an important role in mycelium growth, lipid accumulation, DNA damage, sporulation, trap formation, pathogenicity, and stress response in A. oligospora. AoCdc42 and AoRac specifically interacted with components of the Nox complex, thus regulating the production of reactive oxygen species. Moreover, the transcript levels of several genes associated with protein kinase A, mitogen-activated protein kinase, and p21-activated kinase were also altered in the mutants, suggesting that Rho GTPases might function upstream from these kinases. This study highlights the important role of Rho GTPases in A. oligospora and provides insights into the regulatory mechanisms of signaling pathways in the trap morphogenesis and lifestyle transition of NT fungi. IMPORTANCE Nematode-trapping (NT) fungi are widely distributed in terrestrial and aquatic ecosystems. Their broad adaptability and flexible lifestyles make them ideal agents for controlling pathogenic nematodes. Arthrobotrys oligospora is a model species employed for understanding the interaction between fungi and nematodes. Here, we revealed that alternative splicing events play a crucial role in the trap development and lifestyle transition in A. oligospora. Furthermore, Rho GTPases exert differential effects on the growth, development, and pathogenicity of A. oligospora. In particular, AoRac is required for sporulation and trap morphogenesis. In addition, our analysis showed that Rho GTPases regulate the production of reactive oxygen species and function upstream from several kinases. Collectively, these results expand our understanding of gene expression and alternative splicing events in A. oligospora and the important roles of Rho GTPases in NT fungi, thereby providing a foundation for exploring their potential application in the biocontrol of pathogenic nematodes.
Analysis of the usage of the Core Public Service Vocabulary Application Profile

Given its generic nature, the Core Public Service Vocabulary Application Profile (CPSV-AP) is a data specification used to capture and describe fundamental characteristics of public services (such as the name of a service, its description, where it can be provided) in order to facilitate the exchange of information between administrations. This specification has been developed in such a way that it can be easily tailored and extended to meet country-specific requirements. As such there are many different ways of using CPSV-AP. Although essential to its adoption and reusability, this implementation leeway can lead to different interpretations of the terms used once CPSV-AP is implemented and therefore impacts the data interoperability across local, regional and national borders. By comparing the several implementation cases of CPSV-AP, a thorough analysis of the use of the terms proposed by CPSV-AP was carried out, allowing the translation of these insights into recommendations for the future versions of the specification.
From enhanced coinduction towards enhanced induction

There exist a rich and well-developed theory of enhancements of the coinduction proof method, widely used on behavioural relations such as bisimilarity. We study how to develop an analogous theory for inductive behaviour relations, i.e., relations defined from inductive observables. Similarly to the coinductive setting, our theory makes use of (semi)-progressions of the form R->F(R), where R is a relation on processes and F is a function on relations, meaning that there is an appropriate match on the transitions that the processes in R can perform in which the process derivatives are in F(R). For a given preorder, an enhancement corresponds to a sound function, i.e., one for which R->F(R) implies that R is contained in the preorder; and similarly for equivalences. We introduce weights on the observables of an inductive relation, and a weight-preserving condition on functions that guarantees soundness. We show that the class of functions contains non-trivial functions and enjoys closure properties with respect to desirable function constructors, so to be able to derive sophisticated sound functions (and hence sophisticated proof techniques) from simpler ones. We consider both strong semantics (in which all actions are treated equally) and weak semantics (in which one abstracts from internal transitions). We test our enhancements on a few non-trivial examples.
Renal, cardiovascular and safety outcomes of canagliflozin in patients with type 2 diabetes and nephropathy in East and South‐East Asian countries: Results from the Canagliflozin and Renal Events in Diabetes with Established Nephropathy Clinical Evaluation Trial

The sodium–glucose cotransporter 2 inhibitor, canagliflozin, reduced kidney failure and cardiovascular events in the Canagliflozin and Renal Events in Diabetes with Established Nephropathy Clinical Evaluation (CREDENCE) trial. We carried out a post‐hoc analysis to evaluate the efficacy and safety of canagliflozin in a subgroup of participants in East and South‐East Asian (EA) countries who are at high risk of renal complications.
Research on Partial Discharge of Oil-paper Insulation Needle-plate Electrode Under Switching Pulse Voltage

The characteristics of partial discharge in oil-paper insulation under switching pulse is of significance to the over voltage protection of oil-immersed transformers, thus we make use of the oil-paper insulation needle-plate defect to simulate the corona discharge in transformer oil, so as to study the discharge characteristics. The characteristics of discharge within the defect under switching pulse voltage(wavefront time 250±20% μs, half peak time 2 500±60% μs) are studied through experiment and simulation. Several conclusions are summarized as follows. Firstly, with the increasing of switching pulse voltage, the variation of partial discharge waveform of the experimental model concentrates on the main impulse during the rise time of the switching pulse, which enhances significantly, while the impulse during the fall time slightly changes. Secondly, with the increasing of switching pulse voltage, the first discharge occurs ahead of time and the corresponding level of switching pulse voltage is higher. Thirdly, the max discharge capacity, mean discharge capacity, impulse numbers, and repetition rate all increase with the increasing of switching pulse voltage. The derived results are helpful to the over-voltage protection and fault diagnosis of transformers, which has practical engineering values.