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| 3. |
- Toppi, M., et al.
(författare)
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Measurement of fragmentation cross sections of C-12 ions on a thin gold target with the FIRST apparatus
- 2016
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Ingår i: Physical Review C. - 2469-9985 .- 2469-9993. ; 93:6
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Tidskriftsartikel (refereegranskat)abstract
- A detailed knowledge of the light ions interaction processes with matter is of great interest in basic and applied physics. As an example, particle therapy and space radioprotection require highly accurate fragmentation cross-section measurements to develop shielding materials and estimate acute and late health risks for manned missions in space and for treatment planning in particle therapy. The Fragmentation of Ions Relevant for Space and Therapy experiment at the Helmholtz Center for Heavy Ion research (GSI) was designed and built by an international collaboration from France, Germany, Italy, and Spain for studying the collisions of a C-12 ion beam with thin targets. The collaboration's main purpose is to provide the double-differential cross-section measurement of carbon-ion fragmentation at energies that are relevant for both tumor therapy and space radiation protection applications. Fragmentation cross sections of light ions impinging on a wide range of thin targets are also essential to validate the nuclear models implemented in MC simulations that, in such an energy range, fail to reproduce the data with the required accuracy. This paper presents the single differential carbon-ion fragmentation cross sections on a thin gold target, measured as a function of the fragment angle and kinetic energy in the forward angular region (theta less than or similar to 6 degrees), aiming to provide useful data for the benchmarking of the simulation softwares used in light ions fragmentation applications. The C-12 ions used in the measurement were accelerated at the energy of 400 MeV/nucleon by the SIS (heavy ion synchrotron) GSI facility.
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| 5. |
- Mondello, Stefania, et al.
(författare)
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Exploring serum glycome patterns after moderate to severe traumatic brain injury : A prospective pilot study
- 2022
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Ingår i: eClinicalMedicine. - : Elsevier. - 2589-5370. ; 50
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Tidskriftsartikel (refereegranskat)abstract
- Background: Glycans play essential functional roles in the nervous system and their pathobiological relevance has become increasingly recognized in numerous brain disorders, but not fully explored in traumatic brain injury (TBI). We investigated longitudinal glycome patterns in patients with moderate to severe TBI (Glasgow Coma Scale [GCS] score ≤12) to characterize glyco-biomarker signatures and their relation to clinical features and long-term outcome.Methods: This prospective single-center observational study included 51 adult patients with TBI (GCS ≤12) admitted to the neurosurgical unit of the University Hospital of Pecs, Pecs, Hungary, between June 2018 and April 2019. We used a high-throughput liquid chromatography-tandem mass spectrometry platform to assess serum levels of N-glycans up to 3 days after injury. Outcome was assessed using the Glasgow Outcome Scale-Extended (GOS-E) at 12 months post-injury. Multivariate statistical techniques, including principal component analysis and orthogonal partial least squares discriminant analysis, were used to analyze glycomics data and define highly influential structures driving class distinction. Receiver operating characteristic analyses were used to determine prognostic accuracy.Findings: We identified 94 N-glycans encompassing all typical structural types, including oligomannose, hybrid, and complex-type entities. Levels of high mannose, hybrid and sialylated structures were temporally altered (p<0·05). Four influential glycans were identified. Two brain-specific structures, HexNAc5Hex3DeoxyHex0NeuAc0 and HexNAc5Hex4DeoxyHex0NeuAc1, were substantially increased early after injury in patients with unfavorable outcome (GOS-E≤4) (area under the curve [AUC]=0·75 [95%CI 0·59-0·90] and AUC=0·71 [0·52-0·89], respectively). Serum levels of HexNAc7Hex7DeoxyHex1NeuAc2 and HexNAc8Hex6DeoxyHex0NeuAc0 were persistently increased in patients with favorable outcome, but undetectable in those with unfavorable outcome. Levels of HexNAc5Hex4DeoxyHex0NeuAc1 were acutely elevated in patients with mass lesions and in those requiring decompressive craniectomy.Interpretation: In spite of the exploratory nature of the study and the relatively small number of patients, our results provide to the best of our knowledge initial evidence supporting the utility of glycomics approaches for biomarker discovery and patient phenotyping in TBI. Further larger multicenter studies will be required to validate our findings and to determine their pathobiological value and potential applications in practice.
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| 6. |
- Pleskac, R., et al.
(författare)
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The FIRST experiment at GSI
- 2012
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 678, s. 130-138
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Tidskriftsartikel (refereegranskat)abstract
- The FIRST (Fragmentation of Ions Relevant for Space and Therapy) experiment at the SIS accelerator of GSl laboratory in Darmstadt has been designed for the measurement of ion fragmentation crosssections at different angles and energies between 100 and 1000 MeV/nucleon. Nuclear fragmentation processes are relevant in several fields of basic research and applied physics and are of particular interest for tumor therapy and for space radiation protection applications. The start of the scientific program of the FIRST experiment was on summer 2011 and was focused on the measurement of 400 MeV/nucleon C-12 beam fragmentation on thin (8 mm) graphite target. The detector is partly based on an already existing setup made of a dipole magnet (ALADiN). a time projection chamber (TP-MUSIC IV), a neutron detector (LAND) and a time of flight scintillator system (TOFWALL). This pre-existing setup has been integrated with newly designed detectors in the Interaction Region, around the carbon target placed in a sample changer. The new detectors are a scintillator Start Counter, a Beam Monitor drift chamber, a silicon Vertex Detector and a Proton Tagger scintillator system optimized for the detection of light fragments emitted at large angles. In this paper we review the experimental setup, then we present the simulation software, the data acquisition system and finally the trigger strategy of the experiment.
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| 7. |
- Rescigno, R., et al.
(författare)
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Performance of the reconstruction algorithms of the FIRST experiment pixel sensors vertex detector
- 2014
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 767, s. 34-40
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Tidskriftsartikel (refereegranskat)abstract
- Hadrontherapy treatments use charged particles (e.g. protons and carbon ions) to treat tumors. During a therapeutic treatment with carbon ions, the beam undergoes nuclear fragmentation processes giving rise to significant yields of secondary charged particles. An accurate prediction of these production rates is necessary to estimate precisely the dose deposited into the tumours and the surrounding healthy tissues. Nowadays, a limited set of double differential carbon fragmentation cross-section is available. Experimental data are necessary to benchmark Monte Carlo simulations for their use in hadrontherapy. The purpose of the FIRST experiment is to study nuclear fragmentation processes of ions with kinetic energy in the range from 100 to 1000 MeV/u. Tracks are reconstructed using information from a pixel silicon detector based on the CMOS technology. The performances achieved using this device for hadrontherapy purpose are discussed. For each reconstruction step (clustering, tracking and vertexing), different methods are implemented. The algorithm performances and the accuracy on reconstructed observables are evaluated on the basis of simulated and experimental data.
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| 8. |
- Wang, Qisi, et al.
(författare)
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High-Temperature Charge-Stripe Correlations in La1.675Eu0.2Sr0.125CuO4
- 2020
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Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 1079-7114 .- 0031-9007. ; 124:18
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Tidskriftsartikel (refereegranskat)abstract
- We use resonant inelastic x-ray scattering to investigate charge-stripe correlations in La1.675Eu0.2Sr0.125CuO4. By differentiating elastic from inelastic scattering, it is demonstrated that charge-stripe correlations precede both the structural low-temperature tetragonal phase and the transport-defined pseudogap onset. The scattering peak amplitude from charge stripes decays approximately as T-2 towards our detection limit. The in-plane integrated intensity, however, remains roughly temperature independent. Therefore, although the incommensurability shows a remarkably large increase at high temperature, our results are interpreted via a single scattering constituent. In fact, direct comparison to other stripe-ordered compounds (La1.875Ba0.125CuO4, La1.475Nd0.4Sr0.125CuO4, and La1.875Sr0.125CuO4) suggests a roughly constant integrated scattering intensity across all these compounds. Our results therefore provide a unifying picture for the charge-stripe ordering in La-based cuprates. As charge correlations in La1.675Eu0.2Sr0.125CuO4 extend beyond the low-temperature tetragonal and pseudogap phase, their emergence heralds a spontaneous symmetry breaking in this compound.
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| 10. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 11. |
- El-Fouly, Fatma H., et al.
(författare)
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ERCP : Energy-Efficient and Reliable-Aware Clustering Protocol for Wireless Sensor Networks
- 2022
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Ingår i: Sensors. - : MDPI. - 1424-8220. ; 22:22
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Tidskriftsartikel (refereegranskat)abstract
- Wireless Sensor Networks (WSNs) have been around for over a decade and have been used in many important applications. Energy and reliability are two of the major problems with these kinds of applications. Reliable data delivery is an important issue in WSNs because it is a key part of how well data are sent. At the same time, energy consumption in battery-based sensors is another challenge. Therefore, efficient clustering and routing are techniques that can be used to save sensors energy and guarantee reliable message delivery. With this in mind, this paper develops an energy-efficient and reliable clustering protocol (ERCP) for WSNs. First, an efficient clustering technique is proposed for sensor nodes’ energy savings considering different clustering parameters, including the link quality metric, the energy, the distance to neighbors, the distance to the sink node, and the cluster load metric. The proposed routing protocol works based on the concept of a reliable inter-cluster routing technique that saves energy. The routing decisions are made based on different parameters, such as the energy balance metric, the distance to the sink node, and the wireless link quality. Many experiments and analyses are examined to determine how well the ERCP performs. The experiment results showed that the ECRP protocol performs much better than some of the recent algorithms in both homogeneous and heterogeneous networks. © 2022 by the authors.
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| 12. |
- Golosio, B., et al.
(författare)
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The FIRST experiment for nuclear fragmentation measurements at GSI
- 2011
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Ingår i: Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), 2011 IEEE. ; , s. 2277-2280
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Konferensbidrag (refereegranskat)abstract
- Nuclear fragmentation processes are relevant in different fields of physics concerning both basic research and applications. FIRST (Fragmentation of Ions Relevant for Space and Therapy) is an experiment aimed at the measurement of double differential cross sections (DDCS), with respect to kinetic energy and scattering polar angle, of nuclear fragmentation processes relevant for hadron therapy and for space radiation protection applications, in the energy range between 100 and 1000 MeV/u. The experiment was mounted at the GSI laboratories of Darmstadt, in Germany. A first data taking was performed in August 2011, using 400 MeV/u 12C on carbon and gold targets. In this work we present a description of the experimental apparatus and some figures from the data acquisition and from the preliminary work on data analysis
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| 13. |
- Kobeissy, Firas, et al.
(författare)
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Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma : Towards Personalized Markers
- 2022
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Ingår i: Cells. - : MDPI. - 2073-4409. ; 11:3
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Forskningsöversikt (refereegranskat)abstract
- The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how-at a biomolecular level-mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine.
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| 15. |
- Saghir, Hani, et al.
(författare)
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How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? A Study of Paired Core-Needle Biopsies and Surgical Specimens in Early Breast Cancer
- 2022
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 14:16, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- In early breast cancer, a preoperative core-needle biopsy (CNB) is vital to confirm the malignancy of suspected lesions and for assessing the expression of treatment predictive and prognostic biomarkers in the tumor to choose the optimal treatments, emphasizing the importance of obtaining reliable results when biomarker status is assessed on a CNB specimen. This study aims to determine the concordance between biomarker status assessed as part of clinical workup on a CNB compared to a medically untreated surgical specimen. Paired CNB and surgical specimens from 259 patients that were part of the SCAN-B cohort were studied. The concordance between immunohistochemical (IHC) and gene expression (GEX) based biomarker status was investigated. Biomarkers of interest included estrogen receptor (ER; specifically, the alpha variant), progesterone receptor (PgR), Ki67, HER2, and tumor molecular subtype. In general, moderate to very good correlation in biomarker status between the paired CNB and surgical specimens was observed for both IHC assessment (83–99% agreement, kappa range 0.474–0.917) and GEX assessment (70–97% agreement, kappa range 0.552–0.800), respectively. However, using IHC, 52% of cases with low Ki67 status in the CNB shifted to high Ki67 status in the surgical specimen (McNemar’s p = 0.011). Similarly, when using GEX, a significant shift from negative to positive ER (47%) and from low to high Ki67 (16%) was observed between the CNB and surgical specimen (McNemar’s p = 0.027 and p = 0.002 respectively). When comparing biomarker status between different techniques (IHC vs. GEX) performed on either CNBs or surgical specimens, the agreement in ER, PgR, and HER2 status was generally over 80% in both CNBs and surgical specimens (kappa range 0.395–0.708), but Ki67 and tumor molecular subtype showed lower concordance levels between IHC and GEX (48–62% agreement, kappa range 0.152–0.398). These results suggest that both the techniques used for collecting tissue samples and analyzing biomarker status have the potential to affect the results of biomarker assessment, potentially also impacting treatment decisions and patient survival outcomes
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