Data Sheet 1_Inflammatory imbalance and activation deficits in T cells of myasthenia gravis patients revealed by proteomic profiling.pdf by Amol K. Bhandage (6083420)

“…Despite growing interest in the immunological etiology of MG, few functional studies have addressed the role of T cells, and most existing work has focused on quantifying immune cell subsets using flow cytometry. …”

Code by Baoqiang Chen (21099509)

“…We implemented machine learning algorithms using the following R packages: rpart for Decision Trees, gbm for Gradient Boosting Machines (GBM), ranger for Random Forests, the glm function for Generalized Linear Models (GLM), and xgboost for Extreme Gradient Boosting (XGB). …”

Core data by Baoqiang Chen (21099509)

“…We implemented machine learning algorithms using the following R packages: rpart for Decision Trees, gbm for Gradient Boosting Machines (GBM), ranger for Random Forests, the glm function for Generalized Linear Models (GLM), and xgboost for Extreme Gradient Boosting (XGB). …”

Relational network prepared by the authoring team. by Lesedi Mamodise Modise (20826978)

“…The visualization was rendered using React Flow (a node-based graph visualization library), and the layout algorithm was implemented with the support of D3.js (a toolkit for data-driven documents). …”

Landscape17 by Vlad Carare (22092515)

“…</p><p dir="ltr">We utilized TopSearch, an open-source Python package, to perform landscape exploration, at an estimated cost of 10⁵CPUh. …”

<b>Rethinking neighbourhood boundaries for urban planning: A data-driven framework for perception-based delineation</b> by Shubham Pawar (22471285)

“…</p><h2>Project Structure</h2><pre><pre>Perception_based_neighbourhoods/<br>├── raw_data/<br>│ ├── ET_cells_glasgow/ # Glasgow grid cells for analysis<br>│ └── glasgow_open_built/ # Built area boundaries<br>├── svi_module/ # Street View Image processing<br>│ ├── svi_data/<br>│ │ ├── svi_info.csv # Image metadata (output)<br>│ │ └── images/ # Downloaded images (output)<br>│ ├── get_svi_data.py # Download street view images<br>│ └── trueskill_score.py # Generate TrueSkill scores<br>├── perception_module/ # Perception prediction<br>│ ├── output_data/<br>│ │ └── glasgow_perception.nc # Perception scores (demo data)<br>│ ├── trained_models/ # Pre-trained models<br>│ ├── pred.py # Predict perceptions from images<br>│ └── readme.md # Training instructions<br>└── cluster_module/ # Neighbourhood clustering<br> ├── output_data/<br> │ └── clusters.shp # Final neighbourhood boundaries<br> └── cluster_perceptions.py # Clustering algorithm<br></pre></pre><h2>Prerequisites</h2><ul><li>Python 3.8 or higher</li><li>GDAL/OGR libraries (for geospatial processing)</li></ul><h2>Installation</h2><ol><li>Clone this repository:</li></ol><p dir="ltr">Download the zip file</p><pre><pre>cd perception_based_neighbourhoods<br></pre></pre><ol><li>Install required dependencies:</li></ol><pre><pre>pip install -r requirements.txt<br></pre></pre><p dir="ltr">Required libraries include:</p><ul><li>geopandas</li><li>pandas</li><li>numpy</li><li>xarray</li><li>scikit-learn</li><li>matplotlib</li><li>torch (PyTorch)</li><li>efficientnet-pytorch</li></ul><h2>Usage Guide</h2><h3>Step 1: Download Street View Images</h3><p dir="ltr">Download street view images based on the Glasgow grid sampling locations.…”

MCCN Case Study 2 - Spatial projection via modelled data by Donald Hobern (21435904)

“…This study demonstrates: 1) Description of spatial assets using STAC, 2) Loading heterogeneous data sources into a cube, 3) Spatial projection in xarray using different algorithms offered by the <a href="https://pypi.org/project/PyKrige/" rel="nofollow" target="_blank">pykrige</a> and <a href="https://pypi.org/project/rioxarray/" rel="nofollow" target="_blank">rioxarray</a> packages.…”

Data Sheet 1_Machine learning models integrating intracranial artery calcification to predict outcomes of mechanical thrombectomy.pdf by Guangzong Li (16696443)

“…Eleven ML algorithms were trained and validated using Python, and external validation and performance evaluations were conducted. …”

HVTN 705 data repo: Unbiased cell clustering analysis of vaccine-induced T cell responses in the Imbokodo HIV-1 vaccine trial by Valentin Voillet (19201102)

“…Traditional methods for analysing these responses might be biased towards specific functionalities or epitopes. This study presents an unsupervised and unbiased clustering analysis workflow, using the Leiden algorithm followed by selection of antigen-specific clusters using MIMOSA positivity calls, for high-dimensional flow cytometry data to identify distinct T cell populations associated with protection in the HVTN 705/HPX2008/Imbokodo HIV-1 vaccine efficacy trial.…”

Table 1_Demethylase FTO mediates m6A modification of ENST00000619282 to promote apoptosis escape in rheumatoid arthritis and the intervention effect of Xinfeng Capsule.docx by Fanfan Wang (1669474)

“…</p>Methods<p>A retrospective analysis was conducted on 1603 RA patients using association rule mining and random walk algorithms to evaluate the efficacy of XFC. The proliferation and apoptosis of co-cultured RA-FLS were assessed using CCK-8, flow cytometry (FCM), and molecular biology techniques. …”

<b>NanoNeuroBot: Beyond Healing, Toward Human Connection</b> by ahmed hossam (21420446)

“…It uses a flexible electrode array, EMG signal sensors, and a smart AI app (built on TensorFlow and Flutter) to optimize stimulation patterns. …”

An Ecological Benchmark of Photo Editing Software: A Comparative Analysis of Local vs. Cloud Workflows by Pierre-Alexis DELAROCHE (22092572)

“…Performance Profiling Algorithms Energy Measurement Methodology # Pseudo-algorithmic representation of measurement protocol def capture_energy_metrics(workflow_type: WorkflowEnum, asset_vector: List[PhotoAsset]) -> EnergyProfile: baseline_power = sample_idle_power_draw(duration=30) with PowerMonitoringContext() as pmc: start_timestamp = rdtsc() # Read time-stamp counter if workflow_type == WorkflowEnum.LOCAL: result = execute_local_pipeline(asset_vector) elif workflow_type == WorkflowEnum.CLOUD: result = execute_cloud_pipeline(asset_vector) end_timestamp = rdtsc() energy_profile = EnergyProfile( duration=cycles_to_seconds(end_timestamp - start_timestamp), peak_power=pmc.get_peak_consumption(), average_power=pmc.get_mean_consumption(), total_energy=integrate_power_curve(pmc.get_power_trace()) ) return energy_profile Statistical Analysis Framework Our analytical pipeline employs advanced statistical methodologies including: Variance Decomposition: ANOVA with nested factors for hardware configuration effects Regression Analysis: Generalized Linear Models (GLM) with log-link functions for energy modeling Temporal Analysis: Fourier transform-based frequency domain analysis of power consumption patterns Cluster Analysis: K-means clustering with Euclidean distance metrics for workflow classification Data Validation and Quality Assurance Measurement Uncertainty Quantification All energy measurements incorporate systematic and random error propagation analysis: Instrument Precision: ±0.1W for CPU power, ±0.5W for GPU power Temporal Resolution: 1ms sampling with Nyquist frequency considerations Calibration Protocol: NIST-traceable power standards with periodic recalibration Environmental Controls: Temperature-compensated measurements in climate-controlled facility Outlier Detection Algorithms Statistical outliers are identified using the Interquartile Range (IQR) method with Tukey's fence criteria (Q₁ - 1.5×IQR, Q₃ + 1.5×IQR). …”

Table 1_Machine learning integration with multi-omics data constructs a robust prognostic model and identifies PTGES3 as a therapeutic target for precision oncology in lung adenoca... by Lian-jie Ruan (22327876)

“…PTGES3 expression was evaluated via tissue microarray immunohistochemistry. Functional assays (CCK-8, colony formation, flow cytometry, Western blot) after lentiviral knockdown in lung cancer cells assessed its effects on proliferation, apoptosis, and cell cycle. …”

Data Sheet 1_Machine learning integration with multi-omics data constructs a robust prognostic model and identifies PTGES3 as a therapeutic target for precision oncology in lung ad... by Lian-jie Ruan (22327876)

“…PTGES3 expression was evaluated via tissue microarray immunohistochemistry. Functional assays (CCK-8, colony formation, flow cytometry, Western blot) after lentiviral knockdown in lung cancer cells assessed its effects on proliferation, apoptosis, and cell cycle. …”

Navigating complex care pathways–healthcare workers’ perspectives on health system barriers for children with tuberculous meningitis in Cape Town, South Africa by Dzunisani Patience Baloyi (19452687)

“…An integrated data system and alert functions could flag multiple healthcare visits and improve communication between different healthcare facilities during diagnosis and treatment. …”

Table 1_Identification of novel molecular subtypes and construction of a prognostic signature via multi-omics analysis and machine learning in lung adenocarcinoma.xlsx by Ke Ma (260231)

“…</p>Results<p>Our analysis revealed that the novel molecular subtypes exhibited differences in prognoses, biological functions, and immune infiltration profiles in LUAD. …”

Presentation 1_Identification of novel molecular subtypes and construction of a prognostic signature via multi-omics analysis and machine learning in lung adenocarcinoma.zip by Ke Ma (260231)

“…</p>Results<p>Our analysis revealed that the novel molecular subtypes exhibited differences in prognoses, biological functions, and immune infiltration profiles in LUAD. …”

Data Sheet 1_Identification of novel molecular subtypes and construction of a prognostic signature via multi-omics analysis and machine learning in lung adenocarcinoma.docx by Ke Ma (260231)

“…</p>Results<p>Our analysis revealed that the novel molecular subtypes exhibited differences in prognoses, biological functions, and immune infiltration profiles in LUAD. …”

Data Sheet 1_Resveratrol contributes to NK cell-mediated breast cancer cytotoxicity by upregulating ULBP2 through miR-17-5p downmodulation and activation of MINK1/JNK/c-Jun signali... by Bisha Ding (5803799)

“…</p>Methods<p>The effects of RES on ULBP2 expression were detected with qRT-PCR, western blot, flow cytometry analysis and immunohistochemistry. …”