Miracle-dz/UniFAR-FTUs huggingface dataset:
This information is current as Activation Differences in Immune Signaling Pathway Donors Reveals Age-and Race-Associated Blood Mononuclear Cells from Healthy Single-Cell Network Profiling of Peripheral Cesano

A greater understanding of the function of the human immune system at the single-cell level in healthy individuals is critical for discerning aberrant cellular behavior that occurs in settings such as autoimmunity, immunosenescence, and cancer. To achieve this goal, a systems-level approach capable of capturing the response of the interdependent immune cell types to external stimuli is required. In this study, an extensive characterization of signaling responses in multiple immune cell subpopulations within PBMCs from a cohort of 60 healthy donors was performed using single-cell network profiling (SCNP). SCNP is a multiparametric flow cytometry-based approach that enables the simultaneous measurement of basal and evoked signaling in multiple cell subsets within heterogeneous populations. In addition to establishing the interindividual degree of variation within a broad panel of immune sig-naling responses, the possible association of any observed variation with demographic variables including age and race was investigated. Using half of the donors as a training set, multiple age-and race-associated variations in signaling responses in discrete cell subsets were identified, and several were subsequently confirmed in the remaining samples (test set). Such associations may provide insight into age-related immune alterations associated with high infection rates and diminished protection following vaccination and into the basis for ethnic differences in autoimmune disease incidence and treatment response. SCNP allowed for the generation of a functional map of healthy immune cell signaling responses that can provide clinically relevant information regarding both the mechanisms underlying immune pathological conditions and the selection and effect of therapeutics. A systems-level approach is required to provide a comprehensive understanding of how the function of the human immune system arises from the interactions among numerous interconnected components, pathways, and cell types. Reduc-tionist approaches that analyze individual components within the immune system have dominated in the past several decades primarily due to technological limitations. The recent development of high-throughput technologies is beginning to change the landscape of immunological studies, and researchers are ushering in the new field of systems immunology (1). In this study, we describe a novel technology that has the potential to have an enormous impact on this burgeoning field because it allows for simultaneous functional measurements from multiple cell subpopulations without the need for prior cell separation. This enables a more integrated description of immune cell signaling responses than traditional studies, which often focus on the behavior of specific cell types that have been physically isolated from heterogeneous tissues such as …
A comparison of the semiﬂexed (MTP) view with the standing extended view (SEV) in the radiographic assessment of knee osteoarthritis in a busy routine X-ray department

Objective . To compare the reproducibility of the standing extended view (SEV) (also known as the standing anteroposterior view) with the semiﬂexed, postero-anterior view [the ‘metatarsophalangeal’ (MTP)] view for assessing joint space width (JSW) and osteophytes in osteoarthritis of the knee when used in a busy routine X-ray department. Methods . Forty-seven patients (24 men) had both SEV and MTP views taken on the same day in a busy National Health Service radiography department. Repeat views were taken as entirely separate procedures some time over the following 2 weeks, in the same department and with no special arrangements for the selection of radiographers, time of day, or X-ray machine. The ﬁrst 24 patients had second views in the SEV position whilst the remaining 23 had second MTP views. Radiographs were read independently by two experienced observers who measured JSW with a transparent ruler to the nearest 0.5 mm at the narrowest point in both medial and lateral compartments of the tibiofemoral joint in both knees. Osteophytes were graded 0–2 according to a standard atlas. Ten SEV and 10 MTP radiographs selected randomly were re-read by one observer. Results . Mean (95% conﬁdence interval) JSW in the medial compartment measured on SEV radiographs was 3.54 mm (3.08, 3.99) and on MTP radiographs it was 2.80 mm (2.37, 3.23); in the lateral compartment it was 6.04 mm (5.71, 6.37) when measured on SEV radiographs and 5.47 mm (5.09,
Density‐dependence produces spurious relationships among demographic parameters in a harvested species

Abstract Harvest of wild organisms is an important component of human culture, economy, and recreation, but can also put species at risk of extinction. Decisions that guide successful management actions therefore rely on the ability of researchers to link changes in demographic processes to the anthropogenic actions or environmental changes that underlie variation in demographic parameters. Ecologists often use population models or maximum sustained yield curves to estimate the impacts of harvest on wildlife and fish populations. Applications of these models usually focus exclusively on the impact of harvest and often fail to consider adequately other potential, often collinear, mechanistic drivers of the observed relationships between harvest and demographic rates. In this study, we used an integrated population model and long‐term data (1973–2016) to examine the relationships among hunting and natural mortality, the number of hunters, habitat conditions, and population size of blue‐winged teal Spatula discors, an abundant North American dabbling duck with a relatively fast‐paced life history strategy. Over the last two and a half decades of the study, teal abundance tripled, hunting mortality probability increased slightly (<0.02), and natural mortality probability increased substantially (>0.1) at greater population densities. We demonstrate strong density‐dependent effects on natural mortality and fecundity as population density increased, indicative of compensatory harvest mortality and compensatory natality. Critically, an analysis that only assessed the relationship between survival and hunting mortality would spuriously indicate depensatory mortality due to multicollinearity between abundance, natural mortality and hunting mortality. Our findings demonstrate that models that only consider the direct effect of hunting on survival or natural mortality can fail to accurately assess the mechanistic impact of hunting on population dynamics due to multicollinearity among demographic drivers. This multicollinearity limits inference and may have strong impacts on applied management actions globally.
Nonlinear combustion instabilities and stochastic sources

An investigation of combustion instabilities was conducted using an approximate analysis which allows any relevant physical processes to be included. The resulting system of coupled nonlinear oscillator equations was studied using the methods of dynamical systems theory. Previous investigations have further simplified the system using the method of time-averaging and truncation to a small number of modes. We have investigated the consequences of using these additional approximations, a case which had not been addressed completely in the literature. It was determined that application of the method of time-averaging introduces a stability boundary which limits the range in which the averaged equations are valid. Transverse oscillations in a cylindrical chamber were also treated. It was established that in addition to its role in energy transfer between modes, nonlinear gasdynamics also provides a means of shifting the frequencies of oscillations to integral multiples of the fundamental. This additional role can reduce the efficiency of energy transfer, thus increasing the acoustic amplitudes. An example of a low amplitude transverse oscillation was produced suggesting a means by which the amplitudes of transverse modes, as well as nonintegral longitudinal modes, may be reduced. The coupling between combustion processes and acoustic oscillations was studied as a possible explanation of the phenomenon known as triggering. Using several ad hoc models, the effects of nonlinear pressure coupling and velocity coupling on the behavior of the system were investigated. Substantial regions of possible triggering were produced when using a model of velocity coupling with a threshold, but only if nonlinear gas dynamics was also included. The interaction between combustion noise and acoustic instabilities has received relatively little attention. The sources of noise in a combustion chamber are associated with vorticity and entropy waves. By including these contributions in the approximate analysis, the general forms of the stochastic excitations were obtained. Subsequently, the efects of these excitations on the amplitudes of acoustic modes were studied. When only nonlinear gasdynamics was included, no cases of bimodal probability density functions, characteristic of triggering, were found. However, when the model of velocity coupling with a threshold is added, bimodal probability densities can occur.
5036 - NONLOCAL ELASTICITY COUPLED WITH NONLOCAL DAMAGE

In the framework of irreversible thermodynamics of nonlocal continua, the Clausius-Duhem inequality enriched by the addition of two (nonlocality) energy residuals (one for elasticity, the other for damage) is employed to devise a coupled nonlocal elastic/nonlocal damage phenomenological constitutive model. With a particular choice of the nonlocal variables (average of the strain difference and of the kinematic internal variable (k.i.v) difference), the constitutive model turns out to satisfy the criterion in virtue of which, in the case of macroscopically uniform strain and k.i. v. , both energy residuals vanish identically hence all the state equations collapse into their local forms and as consequence all the state variables (stress, energy release force, damage hardening force) take on their respective local values. Furthermore, the inhomogeneity of the elastic moduli tensor, caused by damage, reflects on the greater attenuation effects upon the long distance particle interactions, which are accounted for through the equivalent distance. This replaces the Euclidean (or geodetical) distance as argument of the attenuation function and increases with the damage variation along the optimal path (while the internal length is taken constant). Linear isotropic damage is considered, with the nonlocality introduced through the k.i. v. controlling the related hardening effects. The above thermodynamic procedure leads to the (nonnegative) intrinsic damage dissipation density having the shape of a bilinear form. The damage evolutive law is then formulated through the normality rule, such that a maximum dissipation principle can be shown to hold.
Suppression of high mobility group box 1 in B16F10 tumor does not inhibit the induction of neoantigen‐specific T cells

Accumulated clinical data of immune checkpoint blockades have suggested the importance of neoantigens in cancer immunity. Tumor antigens are released from dead cancer cells together with cellular components, such as damage‐associated molecular patterns (DAMPs), into the tumor microenvironment. We recently reported that high mobility group box 1 (HMGB1), a representative DAMP molecule, showed a negative impact on anti‐tumor immunity. However, a positive role of HMGB1 in the initiation of innate and subsequent adaptive immunity has also been demonstrated; thus, the effects of HMGB1 on anti‐tumor immunity have not been well understood. In this study, we identified nine immunogenic neoantigen epitopes of B16F10 murine melanoma cells and subsequently investigated the effects of suppression of HMGB1 on the induction of neoantigen‐specific immunity using HMGB1‐knockout tumors. Neoantigen‐reactive T cells were expanded in B16F10 tumor‐bearing mice, and T cell receptor repertoire analysis suggested that neoantigen‐reactive T cells were oligo‐clonally increased in B16F10 tumor bearers. An increase of neoantigen‐reactive T cells and oligoclonal expansion of the T cells were similarly detected in HMGB1‐knockout tumor‐bearing mice. The induction of neoantigen‐specific immunity under the suppression of HMGB1 in the tumor microenvironment shown in this study supports further development of combination therapy of HMGB1 suppression with neoantigen‐targeted cancer immunotherapies, including immune checkpoint blockade therapy.
Phosphorus additions imbalance terrestrial ecosystem C:N:P stoichiometry

Carbon (C):nitrogen (N):phosphorus (P) stoichiometry in plants, soils, and microbial biomass influences productivity and nutrient cycling in terrestrial ecosystems. Anthropogenic inputs of P to ecosystems are increasing; however, our understanding of the impacts of P addition on terrestrial ecosystem C:N:P ratios remains elusive. By conducting a meta‐analysis with 1413 paired observations from 121 publications, we showed that P addition significantly decreased plant, soil, and microbial biomass N:P and C:P ratios, but had negligible effects on C:N ratios. The reductions in N:P and C:P ratios became more evident as the P application rates and experimental duration increased. The P addition effects on terrestrial ecosystem C:N:P stoichiometry did not vary with ecosystem types or climates. Moreover, the responses of N:P and C:P ratios in soil and microbial biomass were associated with the responses of soil pH and fungi:bacteria ratios. Additionally, P additions increased net primary productivity, microbial biomass, soil respiration, N mineralization, and N nitrification, but decreased ammonium and nitrate contents. Decreases in plant N:P and C:P ratios were both negatively correlated to net primary productivity and soil respiration, but positively correlated to ammonium and nitrate contents; microbial biomass, soil respiration, ammonium contents, and nitrate contents all increased with declining soil N:P and C:P ratios. Our findings highlight that P additions could imbalance C:N:P stoichiometry and potentially impact the terrestrial ecosystem functions.
Recent Advances in Conventional and Deep Learning-Based Depth Completion: A Survey

Depth completion aims to recover pixelwise depth from incomplete and noisy depth measurements with or without the guidance of a reference RGB image. This task attracted considerable research interest due to its importance in various computer vision-based applications, such as scene understanding, autonomous driving, 3-D reconstruction, object detection, pose estimation, trajectory prediction, and so on. As the system input, an incomplete depth map is usually generated by projecting the 3-D points collected by ranging sensors, such as LiDAR in outdoor environments, or obtained directly from RGB-D cameras in indoor areas. However, even if a high-end LiDAR is employed, the obtained depth maps are still very sparse and noisy, especially in the regions near the object boundaries, which makes the depth completion task a challenging problem. To address this issue, a few years ago, conventional image processing-based techniques were employed to fill the holes and remove the noise from the relatively dense depth maps obtained by RGB-D cameras, while deep learning-based methods have recently become increasingly popular and inspiring results have been achieved, especially for the challenging situation of LiDAR-image-based depth completion. This article systematically reviews and summarizes the works related to the topic of depth completion in terms of input modalities, data fusion strategies, loss functions, and experimental settings, especially for the key techniques proposed in deep learning-based multiple input methods. On this basis, we conclude by presenting the current status of depth completion and discussing several prospects for its future research directions.
Development of intranasal Sendai virus vector-based vaccine against COVID-19

Sendai virus (SeV) vectors are able to infect a diverse range of cells. They have a high affinity for epithelial cells in the respiratory tract, which provides advantageous properties for intranasal inoculation. Vaccination of the respiratory tract, the main route of infection for Coronavirus (COVID-19), can strongly induce mucosal immunity, which is difficult to induce through injected vaccines, in addition to systemic immunity in a manner similar to innate immunity. A SeV vector vaccine carrying part of the SARS-CoV-2 spike-protein gene showed high immunogenicity in pharmacological studies using intranasally inoculated rodents and is a promising next-generation vaccine.
Embryonic and neonatal waves generate distinct populations of hepatic ILC1s

Group 1 innate lymphoid cells (ILCs) comprising circulating natural killer (cNK) cells and tissue-resident ILC1s are critical for host defense against pathogens and tumors. Despite a growing understanding of their role in homeostasis and disease, the ontogeny of group 1 ILCs remains largely unknown. Here, we used fate mapping and single-cell transcriptomics to comprehensively investigate the origin and turnover of murine group 1 ILCs. Whereas cNK cells are continuously replaced throughout life, we uncovered tissue-dependent development and turnover of ILC1s. A first wave of ILC1s emerges during embryogenesis in the liver and transiently colonizes fetal tissues. After birth, a second wave quickly replaces ILC1s in most tissues apart from the liver, where they layer with embryonic ILC1s, persist until adulthood, and undergo a specific developmental program. Whereas embryonically derived ILC1s give rise to a cytotoxic subset, the neonatal wave establishes the full spectrum of ILC1s. Our findings uncover key ontogenic features of murine group 1 ILCs and their association with cellular identities and functions. Description Characterization of murine group 1 ILC development reveals a layered ontogeny influenced by tissue and age. Innate cell waves Group 1 innate lymphoid cells (ILCs), classified as either circulating natural killer (cNK) cells or tissue-resident ILC1s, are critical to innate immune responses against pathogens and tumors. Sparano et al. examined the origin and turnover of murine ILC1s to better understand how their development influences their biology. Through genetic fate mapping and single-cell RNA sequencing studies, they observed that cNK cells emerge shortly after birth and continuously turn over throughout life. In contrast, a first wave of ILC1s develops during the fetal stage, persists in the liver, and gives rise to cytotoxic ILC1s, whereas ILC1s that arise during the neonatal wave seed tissues as helper-like ILC1s. These observations were complemented by analysis of human adult and fetal liver NK cells and together illustrate ontogenic characteristics of ILC1s that influence their phenotype and function.
Neural Network-Based Fixed-Time Tracking Control for Input-Quantized Nonlinear Systems With Actuator Faults

This study reports a fixed-time tracking control problem for strict-feedback nonlinear systems with quantized inputs and actuator faults where the total number of faults is allowed to be infinite. By taking advantage of radial basis function neural networks (RBFNNs), unknown nonlinear function terms in the system dynamic model can be effectively approached. In addition, based on the sector property of quantization nonlinearities and the structure of the actuator fault model, novel adaptive estimations and innovative auxiliary design signals are constructed to compensate for the influence caused by actuator faults and quantized inputs properly in the fixed-time convergence settings. Then, rigorous theoretical analysis manifests that the proposed control scheme can make the output tracking error converge to a small neighborhood of the origin within a fixed time, and the upper bound of the setting time not only does not depend on initial states of the system but also can be preassigned by selecting parameters appropriately. Meanwhile, all the signals in the closed-loop system remain bounded. Finally, a numerical example and a practical example of a single-link manipulator are presented to demonstrate the effectiveness of the proposed control algorithm.
Low cell number ChIP‐seq reveals chromatin state‐based regulation of gene transcription in the rice male meiocytes

Authors: Aicen Zhang1,#, Hanli You 2,4,#, Lei Cao2,4,#, Yining Shi1,#, Jiawei Chen2,4, Yi Shen2, Shentong Tao1, Zhukuan Cheng3*, Wenli Zhang1* 1State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P. R. China. 2State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. 3Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 225009 Yangzhou, China. 4 University of Chinese Academy of Sciences, Beijing 100049, China.
Natural course of Rathke's cleft cysts and risk factors for progression.

OBJECTIVE Rathke's cleft cysts (RCCs) are relatively common and often detected incidentally. They are usually asymptomatic and managed conservatively. However, little is known about their natural history. Thus, the authors aimed to examine the natural course of RCCs and identify the risk factors for their progression. METHODS This retrospective study examined 229 patients (median age 43.0 years) diagnosed with RCCs by MRI and followed up without surgery (median period 36.6 months). The median cyst height on the initial MRI was 10 mm. Progression or regression of RCC was defined as cyst height changes of ≥ 1 mm. RESULTS In total, 23 (10.0%) RCCs progressed, whereas 73 (31.9%) RCCs spontaneously regressed. The remaining 133 were noted to be stable throughout the follow-up period. Patients with progressed RCCs were significantly older than those with stable RCCs. In patients with acute headache as an initial symptom, RCCs were significantly more likely to spontaneously regress. New symptoms occurred in 6 patients, 5 of whom underwent surgery for RCC progression. Of these 6 patients, 1 patient had persistent adrenocorticotropic hormone deficiency and 1 patient developed diabetes insipidus. Kaplan-Meier analysis results showed RCC progression and new symptom development rates to be 12.0% and 4.1% at 5 years and 13.7% and 5.7% at 10 years, respectively. CONCLUSIONS RCCs rarely progress or cause new symptoms in the long term. Patients with asymptomatic RCC should be followed up for at least 5 years to ensure RCC inactivity. RCCs in older adults may require greater surveillance.