| 1. |
- Abate, E., et al.
(författare)
-
Combined performance tests before installation of the ATLAS Semiconductor and Transition Radiation Tracking Detectors
- 2008
-
Ingår i: Journal of Instrumentation. - 1748-0221. ; 3
-
Tidskriftsartikel (refereegranskat)abstract
- The ATLAS (A Toroidal LHC ApparatuS) Inner Detector provides charged particle tracking in the centre of the ATLAS experiment at the Large Hadron Collider (LHC). The Inner Detector consists of three subdetectors: the Pixel Detector, the Semiconductor Tracker (SCT), and the Transition Radiation Tracker (TRT). This paper summarizes the tests that were carried out at the final stage of SCT+TRT integration prior to their installation in ATLAS. The combined operation and performance of the SCT and TRT barrel and endcap detectors was investigated through a series of noise tests, and by recording the tracks of cosmic rays. This was a crucial test of hardware and software of the combined tracker detector systems. The results of noise and cross-talk tests on the SCT and TRT in their final assembled configuration, using final readout and supply hardware and software, are reported. The reconstruction and analysis of the recorded cosmic tracks allowed testing of the offline analysis chain and verification of basic tracker performance parameters, such as efficiency and spatial resolution, in combined operation before installation.
|
|
| 2. |
- Diez, Paula, et al.
(författare)
-
Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project
- 2015
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 14:9, s. 3530-3540
-
Tidskriftsartikel (refereegranskat)abstract
- A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of different proteins active in a cell. Thus, the Chromosome-centric Human Proteome Project (C-HPP) is promoting a full characterization of the human proteome combining high-throughput proteomics with the data derived from genome-wide expression profiling of protein-coding genes. Here we present a full proteomic profiling of a human lymphoma B-cell line (Ramos) performed using a nanoUPLC-LTQ-Orbitrap Velos proteomic platform, combined to an in-depth transcriptomic profiling of the same cell type. Data are available via ProteomeXchange with identifier PXD001933. Integration of the proteomic and transcriptomic data sets revealed a 94% overlap in the proteins identified by both -omics approaches. Moreover, functional enrichment analysis of the proteomic profiles showed an enrichment of several functions directly related to the biological and morphological characteristics of B-cells. In turn, about 30% of all protein-coding genes present in the whole human genome were identified as being expressed by the Ramos cells (stable average of 30% genes along all the chromosomes), revealing the size of the protein expression-set present in one specific human cell type. Additionally, the identification of missing proteins in our data sets has been reported, highlighting the power of the approach. Also, a comparison between neXtProt and UniProt database searches has been performed. In summary, our transcriptomic and proteomic experimental profiling provided a high coverage report of the expressed proteome from a human lymphoma B-cell type with a clear insight into the biological processes that characterized these cells. In this way, we demonstrated the usefulness of combining -omics for a comprehensive characterization of specific biological systems.
|
|
| 3. |
- Horvatovich, Péter, et al.
(författare)
-
In vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins
- 2015
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 14:9, s. 3441-3451
-
Tidskriftsartikel (refereegranskat)abstract
- Approximately 18% of all human genes purported to encode proteins have not been directly evidenced at the protein level, according to the validation criteria established by neXtProt, and are considered as “missing” proteins. One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to identify as many of these “missing” proteins as possible in human samples using mass spectrometry-based methods. To further this goal, a consortium of C–HPP teams (chromosomes 5, 10, 16 and 19) has joined forces to devise new strategies to identify “missing” proteins by use of a cell-free in vitro transcription/translation system (IVTT). The proposed strategy employs LC-MS/MS data-dependent acquisition (DDA) and targeted selective reaction monitoring (SRM) methods to scrutinize low complexity samples derived from IVTT translation. The optimized assays are then applied to identify “missing” proteins in human cells and tissues. We describe the approach and show proof-of-concept results for development of LC-SRM assays for identification of eighteen “missing” proteins. We believe that the IVTT system, when coupled with downstream mass spectrometric identification, can be applied to identify proteins that have eluded more traditional methods of detection.
|
|
| 4. |
- Horvatovich, Peter, et al.
(författare)
-
Quest for Missing Proteins : Update 2015 on Chromosome-Centric Human Proteome Project
- 2015
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 14:9, s. 3415-3431
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed "missing proteins") in biological samples that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP's activities; therefore, we have summarized some of the key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled to bioinformatics tools and some publicly available resources that can be used to improve data analysis or support the development of analytical assays. Most of this paper's content has been compiled from posters, slides, and discussions presented in the series of C-HPP workshops held during 2014. All data (posters, presentations) used are available at the C-HPP Wild (http://c-hpp.webhosting.rug.nl/) and in the Supporting Information.
|
|
| 5. |
- Marto, João Pedro, et al.
(författare)
-
Safety and Outcome of Revascularization Treatment in Patients With Acute Ischemic Stroke and COVID-19: The Global COVID-19 Stroke Registry.
- 2023
-
Ingår i: Neurology. - 1526-632X. ; 100:7
-
Tidskriftsartikel (refereegranskat)abstract
- COVID-19-related inflammation, endothelial dysfunction, and coagulopathy may increase the bleeding risk and lower the efficacy of revascularization treatments in patients with acute ischemic stroke (AIS). We aimed to evaluate the safety and outcomes of revascularization treatments in patients with AIS and COVID-19.This was a retrospective multicenter cohort study of consecutive patients with AIS receiving intravenous thrombolysis (IVT) and/or endovascular treatment (EVT) between March 2020 and June 2021 tested for severe acute respiratory syndrome coronavirus 2 infection. With a doubly robust model combining propensity score weighting and multivariate regression, we studied the association of COVID-19 with intracranial bleeding complications and clinical outcomes. Subgroup analyses were performed according to treatment groups (IVT-only and EVT).Of a total of 15,128 included patients from 105 centers, 853 (5.6%) were diagnosed with COVID-19; of those, 5,848 (38.7%) patients received IVT-only and 9,280 (61.3%) EVT (with or without IVT). Patients with COVID-19 had a higher rate of symptomatic intracerebral hemorrhage (SICH) (adjusted OR 1.53; 95% CI 1.16-2.01), symptomatic subarachnoid hemorrhage (SSAH) (OR 1.80; 95% CI 1.20-2.69), SICH and/or SSAH combined (OR 1.56; 95% CI 1.23-1.99), 24-hour mortality (OR 2.47; 95% CI 1.58-3.86), and 3-month mortality (OR 1.88; 95% CI 1.52-2.33). Patients with COVID-19 also had an unfavorable shift in the distribution of the modified Rankin score at 3 months (OR 1.42; 95% CI 1.26-1.60).Patients with AIS and COVID-19 showed higher rates of intracranial bleeding complications and worse clinical outcomes after revascularization treatments than contemporaneous non-COVID-19 patients receiving treatment. Current available data do not allow direct conclusions to be drawn on the effectiveness of revascularization treatments in patients with COVID-19 or to establish different treatment recommendations in this subgroup of patients with ischemic stroke. Our findings can be taken into consideration for treatment decisions, patient monitoring, and establishing prognosis.The study was registered under ClinicalTrials.gov identifier NCT04895462.
|
|
| 6. |
- Megido, Loerto, et al.
(författare)
-
Understanding and utilizing the biomolecule/nanosystems interface: Soft materials and coatings for controlled drug release
- 2017
-
Ingår i: Nanotechnologies in Preventive and Regenerative Medicine: An Emerging Big Picture. - 9780323480642 ; , s. 244-260
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Combining biomolecules with materials used in medicine allows for local control of the biological response and can be used for modulating the host immune response, a major challenge in the efficacy of many medical devices. In Subchapter 3.1, we will review different methods used to attach biomolecules to materials, focusing on protein conjugation methods. We will begin by describing noncovalent immobilization strategies, including encapsulation within biomaterials and adsorption to material surfaces. We will then discuss strategies to covalently attach biomolecules to materials via the use of specific functional groups, thus enhancing the stability of the interaction. Finally, we will describe emerging methods to site specifically immobilize biomolecules to materials such that proteins are presented in an oriented manner, improving their overall functionality. Throughout the subchapter, we will emphasize the advantages and disadvantages of each technique, successes achieved, as well as the challenges remaining in this growing field.During last years, increasing development of nanoparticles as targeted drug delivery agents, has led to a wide amount of studies involving their characterization to the application as novel therapeutic agents. Hence, the nanoparticles interact with biological environments when they enter in the human body, and then proteins bind to the nanomaterial surface forming the protein corona. Protein corona has a great relevance in the interaction and function of the nanoparticle-drug conjugates. In fact, its characterization is one of the main challenges for nanoscience development. Herein, it is reviewed the main proteomic methods described for quantify and qualify the protein corona formed around nanoparticles to better understand the process of interaction with the biological media, and to decipher key parameters to control the effects of the protein corona.In Subchapter 3.3, the structure and working principles of coatings for controlled drug release in oral drug administration are presented. The release mechanisms, including diffusion, dissolution, osmotic pumping, and swelling are described. The soft materials used in the majority of controlled drug release formulations are natural and synthetic polymers. They are presented here and examples of specific polymers applied in controlled release formulations are provided. There is also a section containing characterization of soft materials using in situ electron microscopy for studying water transport through coatings at high-spatial resolution. The reason for this is that the detailed properties and release mechanisms of the controlled release depend on the material nanostructure. The in situ characterization gives access not only the information about the nanostructure but also the direct correlation between structure and properties on different length scales. Finally, an overview of the present major challenges and future possibilities concerning controlled drug release formulations is presented.Targeting cancer cells with functional nanoprobes possessing a targeting drug unit and an imaging moiety carries great potential for early detection, accurate diagnosis, and targeted therapy of various diseases. Given their nanoscopic dimensions, ultrasmall particles ( < 100nm) are in general well suited for interactions with the cells; however, the current challenge of the nanomedicine is to transform inorganic nanoparticles of metals (e.g., gold) or metal oxide (e.g., magnetite) into signal-generating vectors. Engineered nanostructures can act as vehicles for a large number of signaling centers and/or targeting units thereby offering unique opportunity to enhance the sensitivity by locally enhancing the density of signal groups. For this purpose, creation of surface groups enabling chemical attachment of antibodies or other targeting biomolecules are essential that will allow the delivery of therapeutic payloads to the diseased sites. Multimodal nanoprobes functionalized with different diagnostic and therapeutic options within a single nanoparticle followed by their functionalization with organic ligands and biomolecules can provide specific uptake and high sensitivity toward anatomical information. However, the vision of making clinical theranostics a routine clinical procedure is encumbered by limited stability of complex nanoparticles in biological milieu and lack of standardization of therapy response. Despite the widely acclaimed advantages of integrating diagnostic imaging, drug delivery, and therapeutic monitoring in a single nanotheranostic probe, the clinical utilization of engineered nanoprobes demands concerted efforts in the domains of nanoparticle and surface chemistry/charge, new chelator ligands, pharmaceutical technology, radioactive labeling of nanovectors, biokinetics, and pharmacodynamics of nanoprobes, and biological tests (cell tests and animal models).
|
|
| 7. |
- Sierra-Sanchez, Alvaro, et al.
(författare)
-
Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies
- 2017
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 16:5, s. 1890-1899
-
Tidskriftsartikel (refereegranskat)abstract
- Osteoarthritis (OA) is one of the most prevalent articular diseases. The identification of proteins closely associated with the diagnosis, progression, prognosis, and treatment response is dramatically required for this pathology. In this work, differential serum protein profiles have been identified in OA and rheumatoid arthritis (RA) by antibody arrays containing 151 antibodies against 121 antigens in a cohort of 36 samples. Then the identified differential serum protein profiles have been validated in a larger cohort of 282 samples. The overall immunoreactivity is higher in the pathological situations in comparison with the controls. Several proteins have been identified as biomarker candidates for OA and RA. Most of these biomarker candidates are proteins related to inflammatory response, lipid metabolism, or bone and extracellular matrix formation, degradation, or remodeling.
|
|
