Supporting Information for the paper entitled Cytoscape stringApp: Network analysis and visualization of proteomics data (preprint available at bioRxiv). The Cytoscape session contains networks generated with the stringApp for the analysis of a phosphoproteomics dataset of ovarian cancer by Francavilla et al. (Cell Rep. 2017).

Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import, and visualization of additional data. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics data set, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.

Market Overview: The global Electric Adjustable Steering market is estimated to be valued at XXX million in 2023 and is projected to grow at a compound annual growth rate (CAGR) of XX% during the forecast period from 2023 to 2033. The increasing demand for advanced driver assistance systems (ADAS) and autonomous driving technologies, coupled with stringent government regulations on vehicle safety, is driving the growth of the market. Electric adjustable steering systems provide enhanced stability and control, reducing the risk of accidents and improving the driving experience. Market Drivers and Trends: Key market drivers include the rising adoption of electric vehicles, the proliferation of connected and autonomous vehicles, and the growing awareness of driver safety. The trend towards personalized driving experiences is also fueling the demand for electric adjustable steering systems, which allow drivers to tailor their steering response to their individual preferences. Additionally, the integration of advanced sensors and actuators is enabling the development of more sophisticated steering systems that can adapt to changing road conditions and driver inputs, further enhancing safety and driving comfort. This comprehensive report provides an in-depth analysis of the global electric adjustable string market, valued at approximately 100 million units in 2022.

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Landing String Equipment Market Size 2024-2028

The landing string equipment market size is forecast to increase by USD 424.91 million at a CAGR of 7.06% between 2023 and 2028.

The market is experiencing significant growth due to the increasing deep-water and ultra-deepwater exploration and production (E and P) activities, particularly In the offshore oil industry. Advanced landing string control systems are gaining popularity as they enhance the efficiency and safety of subsea processing in both shallow and deep waters. The offshore drilling sector, which relies heavily on landing string equipment, is undergoing a transformation. Furthermore, the rise of renewable energy is expanding the market scope, as landing strings are essential for installing and maintaining underwater wind turbines. Crude oil prices and technological advancements continue to influence market trends, making this a dynamic and evolving industry.

What will be the Size of the Landing String Equipment Market During the Forecast Period?

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The market plays a crucial role in the oil and gas industry, particularly In the context of deepwater drilling and subsea wells. This equipment, which includes completion strings and drilling activities, is essential for the successful execution of drilling projects in various water depths, from shallow to ultradeep. The demand for landing string equipment is influenced by several market dynamics. The primary driver is the ongoing need for crude oil and natural gas, with fuel demand remaining a significant factor. Renewable resources are gaining traction, but the transition is gradual, and the oil industry continues to be a significant contributor to the global energy mix. Floating vessels have emerged as a popular choice for deepwater drilling, enabling exploration in previously inaccessible areas. Subsea processing is another trend that has gained momentum, reducing the need for large offshore rigs and associated infrastructure. Construction and maintenance of subsea wellheads and completion strings are critical aspects of the market. Finishing and manufacturing processes must adhere to stringent quality standards to ensure the longevity and reliability of the equipment. In the context of deepwater drilling, well control and adverse weather conditions pose significant challenges, necessitating strong landing control systems.
The market for landing string equipment is segmented into various categories, including equipment segment, construction and maintenance, and finishing and manufacturing. Each segment presents unique opportunities and challenges, requiring specialized expertise and resources. Drilling activities in shallow water and ultradeep water present distinct challenges. In shallow water, the focus is on maximizing efficiency and minimizing costs, while in ultradeep water, the emphasis is on safety and reliability. Summer air temperatures and oil consumption patterns can also impact the demand for landing string equipment. The dynamics of the market are influenced by various factors, including oil demand, crude oil prices, and technological advancements. As the industry evolves, there is a growing emphasis on sustainability and reducing the carbon footprint of drilling operations. This trend is expected to shape the future of the market In the oil and gas industry.

How is this Landing String Equipment Industry segmented and which is the largest segment?

The landing string equipment industry research report provides comprehensive data (region-wise segment analysis), with forecasts and estimates in 'USD million' for the period 2024-2028, as well as historical data from 2018-2022 for the following segments.

Type

  Equipment
  Services


End-user

  Deepwater
  Ultra-deepwater
  Shallow water


Geography

  APAC

    China


  Middle East and Africa



  Europe

    Germany
    UK


  North America

    US


  South America

By Type Insights

The equipment segment is estimated to witness significant growth during the forecast period.

In the oil and gas sector, the market encompasses the diverse range of tools utilized In the construction and maintenance of landing strings. Landing strings, also known as completion strings, play a pivotal role In the completion and production processes. Two essential components of landing strings are tubing hangers and tubing head adapters. Tubing hangers serve to seal off the wellhead from the tubing string, facilitating the production or injection of fluids. They regulate the flow through the wellbore and provide support to the tubing string. Tubing head adapters enable the installation and removal of landing strings by connecting tubing hangers to the wellhead.

These components are integral to the efficient operation of oil and gas wells. The global market for landing string equipment caters to the demands of the industry for

The global string cheese market is on a constant growth trajectory on account of the increasing demand for easy and healthy snack items. By 2025, the total market value is expected to hit the USD 4.3 billion mark, which is associated with a forecasted CAGR of 5.8% from 2025 to 2035.

Company Performance

Cumulative malaria parasite exposure in endemic regions often results in the acquisition of partial immunity and asymptomatic infections. There is limited information on how host-parasite interactions mediate maintenance of chronic symptomless infections that sustain malaria transmission. Here, we have determined the gene expression profiles of the parasite population and the corresponding host peripheral blood mononuclear cells (PBMCs) from 21 children (<15 years). We compared children who were defined as uninfected, asymptomatic and those with febrile malaria. Children with asymptomatic infections had a parasite transcriptional profile characterized by a bias toward trophozoite stage (~12 hours-post invasion) parasites and low parasite levels, while earlier ring stage parasites were characteristic of febrile malaria. The host response of asymptomatic children was characterized by downregulated transcription of genes associated with inflammatory responses, compared to children with ..., Proteins were extracted from PBMCs by resuspending the pellet with 5µl of 6M UREA (Thermo scientific). The protein samples were then adjusted with 50mM Triethylamonium bicarbonate (TEAB, Sigma-Aldrich) to 100µl and the protein concentration determined using the Bicinchoninic acid (BCA) protein assay (Thermo scientific). The protein samples were then reduced with 40mM dithiothretol, alkylated with 80mM iodoacetamide in the dark, and quenched with 80mM iodoacetamide at room temperature, followed by digestion with1µg/µl of trypsin (57). Nine pools, each containing 9 samples and 1 control for batch correction, were prepared by combining 1µl aliquots from each sample. The samples were pooled using a custom randomization R script. The pooled samples were then individually labelled using the Tandem Mass Tag (TMT) 10-plex kit (Thermo Scientific) according to the manufacturer’s instructions. One isobaric tag was used solely for the pooled samples and combined with peptides samples labelled with ..., The files can be opened using MaxQuant software, specifically version 2.0.3.0 was used for analysis. Differential protein abundance analysis of MaxQuant output was done using PERSEUS version 2.05.0 software. Protein-protein interaction and Gene ontology analyses was perforened using STRING database version 11.5 (https://string-db.org/)., # Proteome of peripheral mononuclear cells (PBMCs) from asymptomatic malaria and uninfected individuals and the ensuing febrile malaria episodes

Proteins were extracted from peripheral mononuclear cells (PBMCs), pooled using Tandem Mass Tags (TMT) (10-plex) and injected into the LC-MS/MS for proteomics analysis. The output raw files were loaded into MaxQuant software v2.0.3.0 for protein quantification. The output from MaxQuant was then read using PERSEUS software v2.05.0 and differential protein abundance analysis performed. The Proteomics_metadata file contains the metadata that links each sample to the raw data files and the treatment group (condition).

Description of the data and file structure

The RAW data files provided contains the output data from the LC-MS/MS per each pool. The pools serve as the input data for MaxQuant software.

The Proteomics_metadata contains the metadata information that links each sample to the condition/treatment group (i.e. asymptomatic, uninfecte...

This study aimed to analyze metabolite abundances and proteome differences between Binglangjiang buffalo milk (BBM) and Dehong buffalo milk (DBM). Untargeted ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), label-free quantitative proteomics approaches, and bioinformatics analyses including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) were performed.

Market Analysis for Purstring Autosuture Purse String Device The global market for Purstring Autosuture Purse String Devices is projected to reach USD XX million by 2033, exhibiting a CAGR of XX% during the forecast period 2023-2033. Key drivers include the increasing prevalence of surgical procedures, technological advancements, and rising awareness about minimally invasive techniques. Growth is further attributed to favorable reimbursement policies and the expansion of healthcare infrastructure in emerging markets. The application in surgical specialties such as laparoscopic surgery, endoscopic surgery, and open surgery contributes to the segment's growth. Furthermore, the availability of various types of devices, including single-use, reusable, and needleless options, caters to the diverse needs of surgeons. Regional analysis indicates that North America and Europe hold significant market shares due to the presence of established healthcare systems and leading market players. However, Asia Pacific is expected to witness a high growth rate owing to the increasing demand for gastrointestinal surgeries and the expansion of laparoscopic procedures in this region.

This dataset provides the raw recordings and analysis code used in the research article titled “Assessing Playability Limits of Bowed-String Transients using Experimental Measurements” (currently under review in Acta Acustica). The data explores the characteristics of bow-string interaction during transients, focusing on achieving successful attacks (Helmholtz motion). The recordings capture bridge force signals at different bow forces and bow accelerations.

This dataset offers resources for researchers interested in:

• Investigating bow-string interaction phenomena
• Analysing characteristics of bowed-string transients
• Developing or validating models of bowed-string instruments

Data Organization:

The main folder of this repository contains the following:

• raw_data: This subfolder stores the raw multi-channel audio recordings (.wav format) captured during the measurement sessions (a more detailed description later).
• main.m: This script serves as the central processing unit for the analysis. It guides the processing of raw data from the "raw_data" folder, including:
  • Feature extraction: Calculates relevant features related to bow-string interaction in transients, such as transient time and friction coefficients.
  • Guettler diagram generation: Creates Guettler diagrams, which are visualizations commonly used in bowed-string research.
• Additional Analysis Scripts: Alongside the "main.m" script, several other MATLAB scripts are provided for further in-depth analysis and visualisation of results. These scripts can be used to:
  • averaged_transient_time_gd.m: Computes and analyzes the average pre-Helmholtz transient time across multiple repetitions (e.g., six repetitions).
  • waveform_examples.m: Plot examples of waveforms of bridge force captured during the experiments.
  • experimental_theoretical_limits.m: Analyzes and visualizes the theoretical limits of playability in comparison to the experimentally determined boundaries.
  • theoretical_limits.m: Visualizes the theoretical limits of playability computed with different coefficient of frictions.
  • string_parameters_from_pluck_response.m: Extracts string properties, such as tension or stiffness, from the analysis of pluck responses.
  • performance_setup.m: Assesses the overall performance and stability of the experimental setup.
• Publication-related scripts: Some additional scripts are present, named descriptively (e.g., "guettler_example.m", "gd_different_betas.m", or "comparison_repetitions.m"). These scripts were used specifically for generating figures presented in the research publication.

Note:

The specific functionalities of each additional script are likely explained within the code itself. For detailed information about how each script works, it's recommended to consult the code comments within the MATLAB scripts.

Data Organization of raw_data: The raw data is stored within a folder named “raw_data”. This folder contains subfolders for each measurement session, organized as follows:

• first_repetitions: contains the repetitions of measurements done in consecutive days; after_dismounting: measurements done one month apart from the first repetitions; different_betas: measurements done at different position along the string;
• Subfolder Naming: Subfolders are named using the date of the measurement session (YYYY-MM-DD format). If the recordings within a session were captured in reverse order, the subfolder name will include an "r" suffix (e.g., YYYY-MM-DD_r).
• Data Content: Each subfolder contains the following:
  • Raw Recordings (.wav): The primary data consists of multi-channel audio recordings (.wav format) captured during the measurement session. These recordings contain 11 channels of sensor data as described in the README.
  • Feature Files: In the subfolders, you will find additional files containing extracted features from the raw recordings. These features might include transient time, friction coefficients, or other characteristics calculated using the provided MATLAB scripts.

Data Accessibility:

The raw recordings and code are provided in their original format to ensure transparency and facilitate reusability for further research on playability of bowed-string.

Additional Notes:

• The code requires MATLAB software to run. Additional Toolboxes: Statistics and Machine Learning Toolbox, Optimization Toolbox, Signal Processing Toolbox.

The global landing string equipment market is projected to grow at a CAGR of almost 7% over the forecast period of 2025-2034.

RNA expression analysis was performed on the corpus luteum tissue at five time points after prostaglandin F2 alpha treatment of midcycle cows using an Affymetrix Bovine Gene v1 Array. The normalized linear microarray data was uploaded to the NCBI GEO repository (GSE94069). Subsequent statistical analysis determined differentially expressed transcripts ± 1.5-fold change from saline control with P ≤ 0.05. Gene ontology of differentially expressed transcripts was annotated by DAVID and Panther. Physiological characteristics of the study animals are presented in a figure. Bioinformatic analysis by Ingenuity Pathway Analysis was curated, compiled, and presented in tables. A dataset comparison with similar microarray analyses was performed and bioinformatics analysis by Ingenuity Pathway Analysis, DAVID, Panther, and String of differentially expressed genes from each dataset as well as the differentially expressed genes common to all three datasets were curated, compiled, and presented in tables. Finally, a table comparing four bioinformatics tools' predictions of functions associated with genes common to all three datasets is presented. These data have been further analyzed and interpreted in the companion article "Early transcriptome responses of the bovine mid-cycle corpus luteum to prostaglandin F2 alpha includes cytokine signaling". Resources in this dataset:Resource Title: Supporting information as Excel spreadsheets and tables. File Name: Web Page, url: http://www.sciencedirect.com/science/article/pii/S2352340917304031?via=ihub#s0070

Global String Wound Filter Materials Market size will exceed a valuation of USD 1.94 billion by 2032, to grow at a CAGR of 4.3% during the forecast period.

The size and share of the market is categorized based on Type (4-Channel, 8-Channel, 16-Channel) and Application (Aerospace, Communication, Energy, Agriculture) and geographical regions (North America, Europe, Asia-Pacific, South America, and Middle-East and Africa).

aThe significance of the GO biological process derived from the cytosolic protein network was determined by FDR correction (p

Supplemental data for the manuscript

"Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments".

Content

• functional_annotations.tar.gz
  • functional annotations for 10 different functional annotation systems, for 5090 species
• genome_info_and_statistics.tar.gz
  • basic genome info, annotation system statistics, user query statistics
• example_user_queries.tar.gz
  • three example files for user query inputs used in the analysis
• README.txt
  • details about the files and file formats

Raw data outputs 1-18

Raw data output 1. Differentially expressed genes in AML CSCs compared with GTCs as well as in TCGA AML cancer samples compared with normal ones. This data was generated based on the results of AML microarray and TCGA data analysis.

Raw data output 2. Commonly and uniquely differentially expressed genes in AML CSC/GTC microarray and TCGA bulk RNA-seq datasets. This data was generated based on the results of AML microarray and TCGA data analysis.

Raw data output 3. Common differentially expressed genes between training and test set samples the microarray dataset. This data was generated based on the results of AML microarray data analysis.

Raw data output 4. Detailed information on the samples of the breast cancer microarray dataset (GSE52327) used in this study.

Raw data output 5. Differentially expressed genes in breast CSCs compared with GTCs as well as in TCGA BRCA cancer samples compared with normal ones.

Raw data output 6. Commonly and uniquely differentially expressed genes in breast cancer CSC/GTC microarray and TCGA BRCA bulk RNA-seq datasets. This data was generated based on the results of breast cancer microarray and TCGA BRCA data analysis. CSC, and GTC are abbreviations of cancer stem cell, and general tumor cell, respectively.

Raw data output 7. Differential and common co-expression and protein-protein interaction of genes between CSC and GTC samples. This data was generated based on the results of AML microarray and STRING database-based protein-protein interaction data analysis. CSC, and GTC are abbreviations of cancer stem cell, and general tumor cell, respectively.

Raw data output 8. Differentially expressed genes between AML dormant and active CSCs. This data was generated based on the results of AML scRNA-seq data analysis.

Raw data output 9. Uniquely expressed genes in dormant or active AML CSCs. This data was generated based on the results of AML scRNA-seq data analysis.

Raw data output 10. Intersections between the targeting transcription factors of AML key CSC genes and differentially expressed genes between AML CSCs vs GTCs and between dormant and active AML CSCs or the uniquely expressed genes in either class of CSCs.

Raw data output 11. Targeting desirableness score of AML key CSC genes and their targeting transcription factors. These scores were generated based on an in-house scoring function described in the Methods section.

Raw data output 12. CSC-specific targeting desirableness score of AML key CSC genes and their targeting transcription factors. These scores were generated based on an in-house scoring function described in the Methods section.

Raw data output 13. The protein-protein interactions between AML key CSC genes with themselves and their targeting transcription factors. This data was generated based on the results of AML microarray and STRING database-based protein-protein interaction data analysis.

Raw data output 14. The previously confirmed associations of genes having the highest targeting desirableness and CSC-specific targeting desirableness scores with AML or other cancers’ (stem) cells as well as hematopoietic stem cells. These data were generated based on a PubMed database-based literature mining.

Raw data output 15. Drug score of available drugs and bioactive small molecules targeting AML key CSC genes and/or their targeting transcription factors. These scores were generated based on an in-house scoring function described in the Methods section.

Raw data output 16. CSC-specific drug score of available drugs and bioactive small molecules targeting AML key CSC genes and/or their targeting transcription factors. These scores were generated based on an in-house scoring function described in the Methods section.

Raw data output 17. Candidate drugs for experimental validation. These drugs were selected based on their respective (CSC-specific) drug scores. CSC is the abbreviation of cancer stem cell.

Raw data output 18. Detailed information on the samples of the AML microarray dataset GSE30375 used in this study.

Middle East and Africa Plucked String Instruments Market size will be USD XX million in 2024 and will expand at a compound annual growth rate (CAGR) of 7.7% from 2024 to 2031.

Proteins differentially expressed during the cortical development and their potential functions in the nervous system.

The global cheese strings market is projected to exhibit a healthy CAGR of XX% from 2025 to 2033, driven by factors such as the rising popularity of on-the-go snacks and the increasing demand for healthy and convenient food options. The market was valued at $XXX million in 2025 and is expected to reach $XXX million by 2033. North America holds a significant share of the market, followed by Europe and Asia Pacific. Key market players include Kraft Foods, Arla Foods, Puck, and Froneri Ltd. The demand for cheese strings is increasing due to their versatility and convenience. They can be eaten as a snack on their own or used as an ingredient in other dishes. They are also a good source of protein and calcium. The market is expected to witness further growth in the coming years due to the rising popularity of online grocery shopping and the increasing penetration of modern retail formats. The increasing demand for healthy and natural ingredients is also expected to boost the growth of the market.

The global string wound filter material market size was valued at USD XXX million in 2023 and is projected to reach USD XXX million by 2033, exhibiting a CAGR of XX% during the forecast period. The increasing demand for clean water and the rising awareness about water pollution drive the market. Additionally, the growing adoption of string wound filter materials in various industries, such as water & wastewater treatment, chemical & petrochemical, and food & beverage, fuels the market expansion. The oil & gas industry also utilizes string wound filter material for filtration purposes, contributing to the market growth. The market is segmented based on application, type, company, and region. In terms of application, the water & wastewater treatment segment held the largest market share in 2023 due to the increasing demand for clean water and the stringent regulations imposed by governments worldwide. The chemical & petrochemical segment is anticipated to witness significant growth during the forecast period owing to the rising demand for string wound filter material in the chemical and petrochemical industries. Based on type, the polypropylene segment dominated the market in 2023 and is expected to maintain its dominance throughout the forecast period. Key manufacturers in the string wound filter material market include Johns Manville, COATS, MMP Filtration, Reliance Industries, Dongguan Donggang Chemical Fiber, Jiangsu Sisiyuan Fiber, and Shanghai Jin Chi Industrial.