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| 2. |
- Bravo, L, et al.
(author)
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- 2021
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swepub:Mat__t
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| 3. |
- Tabiri, S, et al.
(author)
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- 2021
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swepub:Mat__t
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| 4. |
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| 5. |
- Glasbey, JC, et al.
(author)
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- 2021
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swepub:Mat__t
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| 6. |
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| 7. |
- Menden, MP, et al.
(author)
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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
- 2019
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 2674-
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Journal article (peer-reviewed)abstract
- The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
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| 8. |
- Moore, MR, et al.
(author)
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Automated digital TIL analysis (ADTA) adds prognostic value to standard assessment of depth and ulceration in primary melanoma
- 2021
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In: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1, s. 2809-
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Journal article (peer-reviewed)abstract
- Accurate prognostic biomarkers in early-stage melanoma are urgently needed to stratify patients for clinical trials of adjuvant therapy. We applied a previously developed open source deep learning algorithm to detect tumor-infiltrating lymphocytes (TILs) in hematoxylin and eosin (H&E) images of early-stage melanomas. We tested whether automated digital (TIL) analysis (ADTA) improved accuracy of prediction of disease specific survival (DSS) based on current pathology standards. ADTA was applied to a training cohort (n = 80) and a cutoff value was defined based on a Receiver Operating Curve. ADTA was then applied to a validation cohort (n = 145) and the previously determined cutoff value was used to stratify high and low risk patients, as demonstrated by Kaplan–Meier analysis (p ≤ 0.001). Multivariable Cox proportional hazards analysis was performed using ADTA, depth, and ulceration as co-variables and showed that ADTA contributed to DSS prediction (HR: 4.18, CI 1.51–11.58, p = 0.006). ADTA provides an effective and attainable assessment of TILs and should be further evaluated in larger studies for inclusion in staging algorithms.
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| 9. |
- Mindur, B, et al.
(author)
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Gas gain stabilisation in the ATLAS TRT detector
- 2016
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In: Journal of Instrumentation. - 1748-0221. ; 11:4
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Journal article (peer-reviewed)abstract
- The ATLAS (one of two general purpose detectors at the LHC) Transition Radiation Tracker (TRT) is the outermost of the three tracking subsystems of the ATLAS Inner Detector. It is a large straw-based detector and contains about 350,000 electronics channels. The performance of the TRT as tracking and particularly particle identification detector strongly depends on stability of the operation parameters with most important parameter being the gas gain which must be kept constant across the detector volume. The gas gain in the straws can vary significantly with atmospheric pressure, temperature, and gas mixture composition changes. This paper presents a concept of the gas gain stabilisation in the TRT and describes in detail the Gas Gain Stabilisation System (GGSS) integrated into the Detector Control System (DCS). Operation stability of the GGSS during Run-1 is demonstrated.
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| 10. |
- Hokelek, I., et al.
(author)
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TUBITAK BILGEM wireless telecommunication technologies research laboratory
- 2013
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Conference paper (peer-reviewed)abstract
- In this paper, we provide information about Wireless Telecommunication Technologies Research Laboratory (KITAL) which has been established at TUBITAK BILGEM under the sponsorship of Ministry of Development. KITAL, which will significantly increase the R&D capabilities of Turkey in the area of wireless telecommunication technologies, provides a laboratory infrastructure for experimenting different aspects of heterogenous networks. It will include equipments for R&D activities of both second and third generation technologies (GSM, UMTS, etc.) and fourth generation technologies (LTE, WiMax, etc.) whose standardization has been going on. KITAL will also provide infrastructure for R&D of next generation tactical wireless telecommunication technologies towards enabling Network Centric Warfare. KITAL infrastructure will be available to other organizations to support wireless telecommunication R&D activities in Turkey.
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| 11. |
- Kuyuk, R. T., et al.
(author)
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An interoperability testbed for VoIP terminals
- 2013
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Conference paper (peer-reviewed)abstract
- We present an interoperability test automation system developed by TUBITAK BILGEM for Wireless Telecommunication Technologies Research Lab (KITAL) project under the sponsorship of Ministry of Development. This test system, called Shadow Coordinator, aims to verify the behavior of various wired and wireless terminals developed either at BILGEM or by industrial vendors as defined by SIP, SCIP and other related protocol specifications. Minimum-length and maximum coverage test sequences are generated using EFSM models and techniques defined in test theory. At the first stage of the project, interoperability of MILSEC-4 terminals is targeted.
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| 12. |
- Kuyuk, R. T., et al.
(author)
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Interoperability of secure VoIP terminals
- 2013
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Conference paper (peer-reviewed)abstract
- An interoperability test automation system has been implemented at the Wireless Communication Technologies Research Laboratory (KITAL) at TUBITAK BILGEM for secure IP communication terminals. Designed and manufactured at BILGEM, MILSEC-4 terminals provide VoIP signalling using SIP and end-to-end secure communication using SCIP protocols. This test system, called Shadow Coordinator, aims to verify the interoperability of terminals implementing SCIP, SIP and other related protocols. A simplified EFSM model for the expected behavior of a terminal implementing SCIP is introduced. A more advanced version of this model is used to genearate minimum-length and maximum coverage test sequences.
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| 13. |
- Sowerby, Leigh J., et al.
(author)
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International registry of otolaryngologist–head and neck surgeons with COVID-19
- 2020
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In: International Forum of Allergy and Rhinology. - : Wiley. - 2042-6976 .- 2042-6984. ; 10:11, s. 1201-1208
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Journal article (peer-reviewed)abstract
- Background: It has become clear that healthcare workers are at high risk, and otolaryngology has been theorized to be among the highest risk specialties for coronavirus disease 2019 (COVID-19). The purpose of this study was to detail the international impact of COVID-19 among otolaryngologists, and to identify instructional cases. Methods: Country representatives of the Young Otolaryngologists–International Federation of Otolaryngologic Societies (YO-IFOS) surveyed otolaryngologists through various channels. Nationwide surveys were distributed in 19 countries. The gray literature and social media channels were searched to identify reported deaths of otolaryngologists from COVID-19. Results: A total of 361 otolaryngologists were identified to have had COVID-19, and data for 325 surgeons was available for analysis. The age range was 25 to 84 years, with one-half under the age of 44 years. There were 24 deaths in the study period, with 83% over age 55 years. Source of infection was likely clinical activity in 175 (54%) cases. Prolonged exposure to a colleague was the source for 37 (11%) surgeons. Six instructional cases were identified where infections occurred during the performance of aerosol-generating operations (tracheostomy, mastoidectomy, epistaxis control, dacryocystorhinostomy, and translabyrinthine resection). In 3 of these cases, multiple operating room attendees were infected, and in 2, the surgeon succumbed to complications of COVID-19. Conclusion: The etiology of reported cases within the otolaryngology community appear to stem equally from clinical activity and community spread. Multiple procedures performed by otolaryngologists are aerosol-generating procedures (AGPs) and great care should be taken to protect the surgical team before, during, and after these operations.
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