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At least 1,027 records · Page 57

Joint Analysis of the Epidemic Evolution and Human Mobility During the First Wave of COVID-19 in Spain: Retrospective Study

Background The initial wave of the COVID-19 pandemic placed a tremendous strain on health care systems worldwide. To mitigate the spread of the virus, many countries implemented stringent nonpharmaceutical interventions (NPIs), which significantly altered human behavior both before and after their enactment. Despite these efforts, a precise assessment of the impact and efficacy of these NPIs, as well as the extent of human behavioral changes, remained elusive. Objective In this study, we conducted a retrospective analysis of the initial wave of COVID-19 in Spain to better comprehend the influence of NPIs and their interaction with human behavior. Such investigations are vital for devising future mitigation strategies to combat COVID-19 and enhance epidemic preparedness more broadly. Methods We used a combination of national and regional retrospective analyses of pandemic incidence alongside large-scale mobility data to assess the impact and timing of government-implemented NPIs in combating COVID-19. Additionally, we compared these findings with a model-based inference of hospitalizations and fatalities. This model-based approach enabled us to construct counterfactual scenarios that gauged the consequences of delayed initiation of epidemic response measures. Results Our analysis demonstrated that the pre–national lockdown epidemic response, encompassing regional measures and heightened individual awareness, significantly contributed to reducing the disease burden in Spain. The mobility data indicated that people adjusted their behavior in response to the regional epidemiological situation before the nationwide lockdown was implemented. Counterfactual scenarios suggested that without this early epidemic response, there would have been an estimated 45,400 (95% CI 37,400-58,000) fatalities and 182,600 (95% CI 150,400-233,800) hospitalizations compared to the reported figures of 27,800 fatalities and 107,600 hospitalizations, respectively. Conclusions Our findings underscore the significance of self-implemented prevention measures by the population and regional NPIs before the national lockdown in Spain. The study also emphasizes the necessity for prompt and precise data quantification prior to enacting enforced measures. This highlights the critical interplay between NPIs, epidemic progression, and human behavior. This interdependence presents a challenge in predicting the impact of NPIs before they are implemented.

Public, Environmental & Occupational Health↗

Sensitivity of D meson azimuthal anisotropies to system size and nuclear structure

Recent experimental data at the Large Hadron Collider (LHC) confirmed that the soft sector azimuthal anisotropies in central XeXe collisions are sensitive to deformations in the wave function of the Xenon nucleus. Additionally, the CMS experiment found that D meson flow is slightly suppressed compared to other particle species when considering quark number scaling in small systems of pPb compared to PbPb. In this talk we used the D and B Mesons Modular (DAB-MOD) code coupled to Trento+v-USPhydro to calculate the R AA and v n ’s of D mesons using different energy loss models and Langevin techniques. Comparing D mesons R AA and v n in PbPb to XeXe collisions it is found that in central collisions D meson azimuthal anisotropies are sensitive to details in the nuclear structure wave function of Xenon. Additionally, we find that in mid-central collisions the smaller system size of XeXe suppresses D meson flow.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Rasterization with Data-Parallel Primitives

Parallel rasterization can suffer from race conditions during fragment generation, which is traditionally addressed by using specialized hardware accessible via vendor graphics APIs. Unfortunately, graphics APIs are increasingly problematic on high-performance computers, either because they are not provided or because of concerns about dependencies with in situ visualization. In response, we present a hardware-agnostic rasterization algorithm that handles race conditions using only data-parallel primitives (DPPs), enabling efficient rendering on HPC systems without graphics API dependencies and aligning with recent efforts to deliver visualization software with DPPs. Our evaluation consists of three phases: (1) evaluating portability across different CPU and GPU architectures, (2) evaluating competitiveness with a community standard, and (3) evaluating performance across varying workloads and available parallelism. The supporting experiments run on both AMD and NVIDIA GPUs, considering data sets as large as 460 million triangles and 160 million pixels. While performance generally falls short of graphics API baselines, it achieves interactive frame rates on most workloads. As a result, we conclude our approach is a viable solution for rasterization on high-performance computers since our approach is portably performant across different architectures without the need for specialized vendor support.

Buckley, Makani [University of Oregon] (ORCID:0009↗

Efficient Distributed Sequence Parallelism for Transformer-Based Image Segmentation

We introduce an efficient distributed sequence parallel approach for training transformer-based deep learning image segmentation models. The neural network models are comprised of a combination of a Vision Transformer encoder with a convolutional decoder to provide image segmentation mappings. The utility of the distributed sequence parallel approach is especially useful in cases where the tokenized embedding representation of image data are too large to fit into standard computing hardware memory. To demonstrate the performance and characteristics of our models trained in sequence parallel fashion compared to standard models, we evaluate our approach using a 3D MRI brain tumor segmentation dataset. We show that training with a sequence parallel approach can match standard sequential model training in terms of convergence. Furthermore, we show that our sequence parallel approach has the capability to support training of models that would not be possible on standard computing resources.

Lyngaas, Isaac↗

FPGA Acceleration of GCN in Light of the Symmetry of Graph Adjacency Matrix

Graph Convolutional Neural Networks (GCNs) are widely used to process large-scale graph data. Different from deep neural networks (DNNs), GCNs are sparse, irregular, and unstructured, posing unique challenges to hardware acceleration with regular processing elements (PEs). In particular, the adjacency matrix of a GCN is extremely sparse, leading to frequent but irregular memory access, low spatial/temporal data locality and poor data reuse. Furthermore, a realistic graph usually consists of unstructured data (e.g., unbalanced distributions), creating significantly different processing times and imbalanced workload for each node in GCN acceleration. To overcome these challenges, we propose an end-to-end hardware-software co-design to accelerate GCNs on resource-constrained FPGAs with the features including: (1) A custom dataflow that leverages symmetry along the diagonal of the adjacency matrix to accelerate feature aggregation for undirected graphs. We utilize either the upper or the lower triangular matrix of the adjacency matrix to perform aggregation in GCN to improve data reuse. (2) Unified compute cores for both aggregation and transform phases, with full support to the symmetry-based dataflow. These cores can be dynamically reconfigured to the systolic mode for transformation or as individual accumulators for aggregation in GCN processing. (3) Preprocessing of the graph in software to rearrange the edges and features to match the custom dataflow. This step improves the regularity in memory access and data reuse in the aggregation phase. Moreover, we quantize the GCN precision from FP32 to INT8 to reduce the memory footprint without losing the inference accuracy. We implement our accelerator design in Intel Stratix10 MX FPGA board with HBM2, and demonstrate 1.3x-110.5x improvement in end-to-end GCN latency as compared to the state-of the-art FPGA implementations, on the graph datasets of Cora, Pubmed, Citeseer and Reddit.

Nair, Gopikrishnan R.↗

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗

PyPop: a mature open-source software pipeline for population genomics

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations.

59 BASIC BIOLOGICAL SCIENCES↗

Individual Nest Site Preferences Do Not Explain Upslope Population Shifts of a Secondary Cavity-Nesting Species

Geographic ranges of plants and animals are shifting due to environmental change. While some species are shifting towards the poles and upslope in elevation, the processes leading to these patterns are not well known. We analyzed 22 years of western bluebird (Sialia mexicana) data from a large nest box network in northern New Mexico at elevations between 1860 m and 2750 m. This population has shifted to higher elevations over time, but whether this is due to changes in nesting behavior and preference for higher elevation within the population or driven by immigration is unclear. We banded adults and nestlings from nest boxes and examined nesting location and elevation for individual birds captured two or more times. Most recaptured birds nested at the same nest boxes in subsequent years, and the number of birds that moved upslope did not significantly differ from the number that moved downslope. Fledglings moved greater distances and elevations than adults, but these movements were not upslope specific. Female fledglings showed greater changes in elevation and distance compared to male fledglings, but again, movements were not consistently upslope. The upslope shift in this population may be due to birds immigrating into the population and not from changes in individual nesting behavior.

59 BASIC BIOLOGICAL SCIENCES↗

Deposition, Diagenesis, and Sequence Stratigraphy of the Pennsylvanian Morrowan and Atokan Intervals at Farnsworth Unit

Farnsworth Field Unit (FWU), a mature oilfield currently undergoing CO2-enhanced oil recovery (EOR) in the northeastern Texas panhandle, is the study area for an extensive project undertaken by the Southwest Regional Partnership on Carbon Sequestration (SWP). SWP is characterizing the field and monitoring and modeling injection and fluid flow processes with the intent of verifying storage of CO2 in a timeframe of 100–1000 years. Collection of a large set of data including logs, core, and 3D geophysical data has allowed us to build a detailed reservoir model that is well-grounded in observations from the field. This paper presents a geological description of the rocks comprising the reservoir that is a target for both oil production and CO2 storage, as well as the overlying units that make up the primary and secondary seals. Core descriptions and petrographic analyses were used to determine depositional setting, general lithofacies, and a diagenetic sequence for reservoir and caprock at FWU. The reservoir is in the Pennsylvanian-aged Morrow B sandstone, an incised valley fluvial deposit that is encased within marine shales. The Morrow B exhibits several lithofacies with distinct appearance as well as petrophysical characteristics. The lithofacies are typical of incised valley fluvial sequences and vary from a relatively coarse conglomerate base to an upper fine sandstone that grades into the overlying marine-dominated shales and mudstone/limestone cyclical sequences of the Thirteen Finger limestone. Observations ranging from field scale (seismic surveys, well logs) to microscopic (mercury porosimetry, petrographic microscopy, microprobe and isotope data) provide a rich set of data on which we have built our geological and reservoir models.

04 OIL SHALES AND TAR SANDS↗

Transformers and Long Short-Term Memory Transfer Learning for GenIV Reactor Temperature Time Series Forecasting

Automated monitoring of the coolant temperature can enable autonomous operation of generation IV reactors (GenIV), thus reducing their operating and maintenance costs. Automation can be accomplished with machine learning (ML) models trained on historical sensor data. However, the performance of ML usually depends on the availability of large amount of training data, which is difficult to obtain for GenIV, as this technology is still under development. We propose the use of transfer learning (TL), which involves utilizing knowledge across different domains, to compensate for this lack of training data. TL can be used to create pre-trained ML models with data from small-scale research facilities, which can then be fine-tuned to monitor GenIV reactors. In this work, we develop pre-trained Transformer and long short-term memory (LSTM) networks by training them on temperature measurements from thermal hydraulic flow loops operating with water and Galinstan fluids at room temperature at Argonne National Laboratory. The pre-trained models are then fine-tuned and re-trained with minimal additional data to perform predictions of the time series of high temperature measurements obtained from the Engineering Test Unit (ETU) at Kairos Power. The performance of the LSTM and Transformer networks is investigated by varying the size of the lookback window and forecast horizon. The results of this study show that LSTM networks have lower prediction errors than Transformers, but LSTM errors increase more rapidly with increasing lookback window size and forecast horizon compared to the Transformer errors.

LSTM↗

In-silico quantification of intersubject variability on aerosol deposition in the oral airway

The extrathoracic oral airway I s not only a major mechanical barrier for pharmaceutical aerosols to reach the lung but also a major source of variability in lung deposition. Using computational fluid dynamics, deposition of 1-30 µm particles was predicted in 11 CT-based models of the oral airways of adults (7 healthy subjects and 4 patients with chronic obstructive pulmonary disease). Simulations were performed for mouth breathing during both inspiration and expiration at two steady-state flow rates representative of resting/light activity (18 L/min) and of that typically used during aerosol inhalation from a dry powder inhaler (45 L/min). For each subject, oral deposition increased with increasing particle size and flow rate. When averaged over all subjects, there was no significant difference in oral deposition efficiency between inspiration and expiration, unlike subregional deposition that show significantly different patterns between the two breathing phases. Consistent with previous in-vitro inspiratory studies, our data showed a large intersubject variability in oral deposition. These results highlight the need for incorporating morphological variation of the upper airway in predictive models of aerosol deposition for accurate predictions of particle dosimetry in the intrathoracic region of the lung.

Computational fluid dynamics (CFD), Inertial impac↗

Admissible Powertrain Alternatives for Heavy-Duty Fleets: A Case Study on Resiliency and Efficiency

Heavy-duty vehicles dominate global freight movement and primarily rely on fossil-derived diesel fuel. However, fluctuations in crude oil prices and evolving emissions regulations have prompted interest in alternative powertrains to enhance fleet energy resiliency. This study paired real-world operational data from a large commercial fleet with high-fidelity vehicle models to evaluate the potential for replacing diesel internal combustion engine (ICE) trucks with alternative powertrain architectures. The baseline vehicle for this analysis is a diesel-powered ICE truck. Alternatives include ICE trucks fueled by bio- and renewable diesel, compressed natural gas (CNG) or hydrogen (H 2 ), as well as plug-in hybrid (PHEV), fuel cell electric (FCEV), and battery electric vehicles (BEV). While most alternative powertrains resulted in some payload capacity loss, the overall fleetwide impact was negligible due to underutilized payload capacity for the specific fleet considered in this study. For sleeper cab trucks, CNG-powered trucks achieved the highest replacement potential, covering 85% of the fleet. In contrast, H 2 and BEV architectures could replace fewer than 10% and 1% of trucks, respectively. Day cab trucks, with shorter daily routes, showed higher replacement potential: 98% for CNG, 78% for H 2 , and 34% for BEVs. However, achieving full fleet replacement would still require significant operational changes such as route reassignment and enroute refueling, along with considerable improvements to onboard energy storage capacity. Additionally, the higher total cost of ownership (TCO) for alternative powertrains remains a key challenge. This study also evaluated lifecycle impacts across various fuel sources, both fossil and bio-derived. Bio-derived synthetic diesel fuels emerged as a practical option for diesel displacement without disrupting operations. Conversely, H 2 and electrified powertrains provide limited lifecycle impacts under the current energy scenario. This analysis highlights the complexity of replacing diesel ICE trucks with admissible alternatives while balancing fleet resiliency, operational demands, and emissions goals. These results reflect a US-based fleet’s duty cycles, payloads, GVWR allowances, and an assumption of depot-only refueling/recharging. Applicability to other fleets and regions may differ based on differing routing practices or technical features such as battery swapping.

BEV↗

Planets Across Space and Time (PAST). II. Catalog and Analyses of the LAMOST–Gaia–Kepler Stellar Kinematic Properties

The Kepler telescope has discovered over 4000 planets (candidates) by searching ~200,000 stars over a wide range of distance (order of kpc) in our Galaxy. Characterizing the kinematic properties (e.g., Galactic component membership and kinematic age) of these Kepler targets (including the planet candidate hosts) is the first step toward studying Kepler planets in the Galactic context, which will reveal fresh insights into planet formation and evolution. In this paper, the second part of the Planets Across the Space and Time (PAST) series, by combining the data from the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) and Gaia and then applying the revised kinematic methods from PAST I, we present a catalog of kinematic properties (i.e., Galactic positions, velocities, and the relative membership probabilities among the thin disk, thick disk, Hercules stream, and the halo) as well as other basic stellar parameters for 35,835 Kepler stars. Further analyses of the LAMOST–Gaia–Kepler catalog demonstrate that our derived kinematic age reveals the expected stellar activity-age trend. Furthermore, we find that the fraction of thin (thick) disk stars increases (decreases) with the transiting planet multiplicity (N {sub p} = 0, 1, 2 and 3+) and the kinematic age decreases with N {sub p}, which could be a consequence of the dynamical evolution of planetary architecture with age. The LAMOST–Gaia–Kepler catalog will be useful for future studies on the correlations between the exoplanet distributions and the stellar Galactic environments as well as ages.

47 OTHER INSTRUMENTATION↗

Magnitude-squared Coherence: A Powerful Tool for Disentangling Doppler Planet Discoveries from Stellar Activity

Abstract If Doppler searches for Earth-mass, habitable planets are to succeed, observers must be able to identify and model out stellar activity signals. Here we demonstrate how to diagnose activity signals by calculating the magnitude-squared coherence C ˆ xy 2 ( f ) between an activity-indicator time series x t and the radial-velocity (RV) time series y t . Since planets only cause modulation in RV, not in activity indicators, a high value of C ˆ xy 2 ( f ) indicates that the signal at frequency f has a stellar origin. We use Welch’s method to measure coherence between activity indicators and RVs in archival observations of GJ 581, α Cen B, and GJ 3998. High RV-H α coherence at the frequency of GJ 3998 b and high RV-S index coherence at the frequency of GJ 3998c, indicate that the planets may actually be stellar signals. We also replicate previous results showing that GJ 581 d and g are rotation harmonics and demonstrate that α Cen B has activity signals that are not associated with rotation. Welch’s power spectrum estimates have cleaner spectral windows than Lomb–Scargle periodograms, improving our ability to estimate rotation periods. We find that the rotation period of GJ 581 is 132 days, with no evidence of differential rotation. Welch’s method may yield unacceptably large bias for data sets with N < 75 observations and works best on data sets with N > 100. Tapering the time-domain data can reduce the bias of the Welch’s power spectrum estimator, but observers should not apply tapers to data sets with extremely uneven observing cadence. A software package for calculating magnitude-squared coherence and Welch’s power spectrum estimates is available on github.

Dodson-Robinson, Sarah E. (ORCID:0000000287964974)↗

What’s the Difference? The Potential for Convolutional Neural Networks for Transient Detection without Template Subtraction

Abstract We present a study of the potential for convolutional neural networks (CNNs) to enable separation of astrophysical transients from image artifacts, a task known as “real–bogus” classification, without requiring a template-subtracted (or difference) image, which requires a computationally expensive process to generate, involving image matching on small spatial scales in large volumes of data. Using data from the Dark Energy Survey, we explore the use of CNNs to (1) automate the real–bogus classification and (2) reduce the computational costs of transient discovery. We compare the efficiency of two CNNs with similar architectures, one that uses “image triplets” (templates, search, and difference image) and one that takes as input the template and search only. We measure the decrease in efficiency associated with the loss of information in input, finding that the testing accuracy is reduced from ∼96% to ∼91.1%. We further investigate how the latter model learns the required information from the template and search by exploring the saliency maps. Our work (1) confirms that CNNs are excellent models for real–bogus classification that rely exclusively on the imaging data and require no feature engineering task and (2) demonstrates that high-accuracy (>90%) models can be built without the need to construct difference images, but some accuracy is lost. Because, once trained, neural networks can generate predictions at minimal computational costs, we argue that future implementations of this methodology could dramatically reduce the computational costs in the detection of transients in synoptic surveys like Rubin Observatory's Legacy Survey of Space and Time by bypassing the difference image analysis entirely.

79 ASTRONOMY AND ASTROPHYSICS↗

Anatomy of a Cooling Flow: The Feedback Response to Pure Cooling in the Core of the Phoenix Cluster

We present new, deep observations of the Phoenix cluster from the Chandra X-ray Observatory, the Hubble Space Telescope, and the Karl Jansky Very Large Array. These data provide an order of magnitude improvement in depth and/or angular resolution at X-ray, optical, and radio wavelengths, yielding an unprecedented view of the core of the Phoenix cluster. We find that the one-dimensional temperature and entropy profiles are consistent with expectations for pure-cooling hydrodynamic simulations and analytic descriptions of homogeneous, steady-state cooling flow models. In the inner ~10 kpc, the cooling time is shorter by an order of magnitude than any other known cluster, while the ratio of the cooling time to freefall time approaches unity, signaling that the ICM is unable to resist multiphase condensation on kpc scales. When we consider the thermodynamic profiles in two dimensions, we find that the cooling is highly asymmetric. The bulk of the cooling in the inner ~20 kpc is confined to a low-entropy filament extending northward from the central galaxy. We detect a substantial reservoir of cool (10^4 K) gas (as traced by the [OII] doublet), which is coincident with the low-entropy filament. The bulk of this cool gas is draped around and behind a pair of X-ray cavities, presumably bubbles that have been inflated by radio jets, which are detected for the first time on kpc scales. These data support a picture in which AGN feedback is promoting the formation of a multiphase medium via a combination of ordered buoyant uplift and locally enhanced turbulence. These processes ought to counteract the tendency for buoyancy to suppress condensation, leading to rapid cooling along the jet axis. The recent mechanical outburst has sufficient energy to offset cooling, and appears to be coupling to the ICM via a cocoon shock, raising the entropy in the direction orthogonal to the radio jets.

79 ASTRONOMY AND ASTROPHYSICS↗

A Hybrid Deep Learning Approach to Cosmological Constraints from Galaxy Redshift Surveys

We present a deep machine learning (ML)–based technique for accurately determining σ g and Ω m from mock 3D galaxy surveys. The mock surveys are built from the AbacusCosmos suite of N -body simulations, which comprises 40 cosmological volume simulations spanning a range of cosmological parameter values, and we account for uncertainties in galaxy formation scenarios through the use of generalized halo occupation distributions (HODs). We explore a trio of ML models: a 3D convolutional neural network (CNN), a power spectrum–based fully connected network, and a hybrid approach that merges the two to combine physically motivated summary statistics with flexible CNNs. We describe best practices for training a deep model on a suite of matched-phase simulations, and we test our model on a completely independent sample that uses previously unseen initial conditions, cosmological parameters, and HOD parameters. Despite the fact that the mock observations are quite small (~0.07 h -3 Gpc 3 ) and the training data span a large parameter space (six cosmological and six HOD parameters), the CNN and hybrid CNN can constrain estimates of σ g and Ω m to ~3% and ~4%, respectively.

79 ASTRONOMY AND ASTROPHYSICS↗

Orbital Modulation of Gamma Rays from PSR J2339-0533

In this work, we report on orbital modulation of the 100–600 MeV gamma-ray emission of the P B = 4.6 hr millisecond pulsar binary PSR J2339-0533 using 11 yr of Fermi Large Area Telescope data. The modulation has high significance (chance probability p ≈ 10 -7 ), is approximately sinusoidal, peaks near pulsar superior conjunction, and is detected only in the low-energy 100–600 MeV band. The modulation is confined to the on-pulse interval, suggesting that the variation is in the 2.9 ms pulsed signal itself. Additionally, this contrasts with the few other known systems exhibiting GeV orbital modulations, as these are unpulsed and generally associated with beamed emission from an intrabinary shock. The origin of the modulated pulsed signal is not yet clear, although we describe several scenarios, including Compton upscattering of photons from the heated companion. This would require high coherence in the striped pulsar wind.

79 ASTRONOMY AND ASTROPHYSICS↗