| 1. |
- Abdellah, Tebani, et al.
(författare)
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Integration of molecular profiles in a longitudinal wellness profiling cohort.
- 2020
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies andimmune cell profiling, complementedwith gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.
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| 2. |
- Almers, Peter, et al.
(författare)
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Exercises
- 2005
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Ingår i: Wireless Communications. - 9780470848883 - 047084888X - 0470848871 ; , s. 561-593
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Alvez, Maria Bueno, et al.
(författare)
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Next generation pan-cancer blood proteome profiling using proximity extension assay
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.
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| 4. |
- Bengtsson, Erik L, et al.
(författare)
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A Case Study on the Influence of Multiple Users on the Effective Channel in a Massive MIMO System
- 2019
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Ingår i: IEEE Wireless Communications Letters. - 2162-2337. ; , s. 1-6
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the importance of weak clusters when modeling a wireless massive MIMO channel. We do this by studying the influence of densely spaced terminals and the number of base-station antennas for a zero-forcing precoded massive MIMO system. In particular, we focus on the influence on the correlation and imbalance between the signals at the terminal antennas, the effective channel-gain, the eigenvalue distributions and the number of clusters.The study is based on measured radio-channels from terminal prototypes with integrated antennas connected to a massive MIMO testbed.We further evaluate the advantage of using block-diagonalized zero-forcing compared to conventional zero-forcing in a massive MIMO system. Unexpectedly, terminals with low antenna envelope correlation coefficient may benefit significantly from block-diagonal zero-forcing in a massive MIMO system.The main conclusion is that weaker clusters are important when modeling multi-user scenarios.
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| 5. |
- Bengtsson, Erik L., et al.
(författare)
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A Simulation Framework for Multiple-Antenna Terminals in 5G Massive MIMO Systems
- 2017
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Ingår i: IEEE Access. - 2169-3536. ; 5, s. 26819-26831
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Tidskriftsartikel (refereegranskat)abstract
- The recent interest in massive MIMO has spurred intensive work on massive MIMO channel modeling in contemporary literature. However, current models fail to take the characteristics of terminal antennas into account. There is no massive MIMO channel model available that can be used for evaluation of the influence of different antenna characteristics at the terminal side. In this paper, we provide a simulation framework that fills this gap. We evaluate the framework with antennas integrated into Sony Xperia handsets operating at 3.7 GHz as this spectrum is identified for the 5G new radio standard by 3GPP. The simulation results are compared with measured terminal performance when communicating with the Lund University’s massive MIMO testbed under the same loading conditions. Expressions are derived for comparison of the gain obtained from different diversity schemes computed from measured far-field antenna patterns. We conclude that the simulation framework yields results close to the measured ones and that the framework can be used for antenna evaluation for terminals in a practical precoded massive MIMO system.
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| 6. |
- Bengtsson, Erik L., et al.
(författare)
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Analysis of Transmission Schemes for Dual-Antenna Terminals in Massive MIMO Systems
- 2018
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Ingår i: 2018 25th International Conference on Telecommunications, ICT 2018. - 9781538623213 ; , s. 76-82
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Konferensbidrag (refereegranskat)abstract
- The overall system performance of massive MIMO is improved by equipping user terminals with multiple antennas. In this paper, we investigate transceiver designs for the case of a single downlink stream and in particular, we study the uplink pilot design. Moreover, we study the consequences of channel estimation errors at the base-station, and to what extent a dual-antenna terminal can get access to relevant channel statistics for optimization of the pilot signal. Gain expressions for comparison of different designs are derived. We verify the analytic results based on antennas integrated into Sony-Xperia handsets measured with the Lund University massive MIMO testbed. The measurements are performed at frequencies <6GHz since this part of the spectrum is a candidate for NR standard according to 3GPP.
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| 7. |
- Bengtsson, Erik L, et al.
(författare)
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Simulation of Multiple-Antenna Terminal Performance in Massive MIMO Systems based on Indoor Measurements
- 2020
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Ingår i: IEEE Transactions on Vehicular Technology. - 0018-9545. ; 69:1, s. 418-427
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Tidskriftsartikel (refereegranskat)abstract
- In massive MIMO systems the uplink pilot signalstransmitted by a terminal define the channel seen by the basestation. This gives the terminal some degree of freedom selectingan uplink pilot transmission strategy. In this paper, we investigatethe benefit of different pilot transmission strategies when increasingthe number of antennas in the terminal. Building on previouswork on a simulation framework for Multiple-antenna terminalsin 5G massive MIMO systems, this paper presents simulatedperformance results for various transmission schemes. The resultsare calibrated to reflect a real communication situation in a largeauditorium. Emulating the measurement set-up, we show that theframework can be tuned to generate channel distributions thatmatch measured data. Under generalized conditions, we performsimulations for different terminal transmission-strategies, bothrelated to single stream and multiple streams. All evaluations arebased on terminals with four antennas integrated into real SonyXperia smartphone-chassis, tuned to 3.7 GHz. The measurementsare conducted by using the Lund University Massive MIMOtestbed with its 100 antennas. The results clearly show theadvantage of increasing the antenna-count also at the terminalside in massive MIMO systems.
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| 8. |
- Bengtsson, Erik L, et al.
(författare)
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Transmission schemes for Multiple Antenna Terminals in Real Massive MIMO systems
- 2016
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Ingår i: 2016 IEEE Global Communications Conference (GLOBECOM). - 9781509013289 - 9781509013296
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Konferensbidrag (refereegranskat)abstract
- In massive MIMO performance evaluations it is often assumed that the terminal has a single antenna. The combination of multiple antennas in a terminal and massive MIMO precoding at the base station side can further improve overall system performance. We present measurement results for multi antenna terminals operating in different transmission schemes and how they perform under varying loading conditions. Gain expressions are derived that enable easy comparison between the transmission schemes. The evaluation is performed on realistic antennas integrated into Sony Xperia handsets tuned to 3.7~GHz and operated together with the Lund University massive MIMO (LuMaMi) test bed. It is concluded that the approach used in today's mobile systems, where up link and down link are addressed independently, will not provide the best performance. The performance can be improved by the selection of transmission schemes optimized for massive MIMO.
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| 9. |
- Bourdoux, Andre, et al.
(författare)
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D1.2 MaMi Channel Characteristics: Measurement Results
- 2015
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This deliverable presents channel measurement results for the scenariosOpen exhibition and Crowded auditiorium. The measurement procedureand equipment are described. Massive MIMO (MaMi) channel characteristicsand key parameters are extracted and used in an extended COST 2100channel model for MaMi. The initial validation performed shows that themodel is capable of reproducing the statistics in terms of temporal behaviorof the user separability, singular value spread, capacity and sum-rate anddirectional characteristics. The model can be used for system and link levelMaMi simulations.
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| 10. |
- Edfors, Fredrik, et al.
(författare)
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Gene-specific correlation of RNA and protein levels in human cells and tissues
- 2016
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Ingår i: Molecular Systems Biology. - : EMBO. - 1744-4292 .- 1744-4292. ; 12:10
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Tidskriftsartikel (refereegranskat)abstract
- An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.
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| 11. |
- Flordelis, Jose, et al.
(författare)
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Exploiting antenna correlation in measured massive MIMO channels
- 2016
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Ingår i: 2016 IEEE 27th Annual International Symposium on Personal, Indoor, and Mobile Radio Communications, PIMRC 2016. - 9781509032549
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Konferensbidrag (refereegranskat)abstract
- We investigate antenna correlation of an M-antenna massive multiple-input multiple-output (MIMO) setup with the purpose of obtaining a low-rank representation of the instantaneous massive MIMO channel. Low-rank representation bases using short-term and long-term antenna correlation statistics are defined, and their performance is evaluated with data sets obtained from channel measurements in both indoor and outdoor environments at 2.6 GHz. Our results indicate that the short-term bases can capture a larger amount of the channel energy compared to the long-term ones, but they have a limited timespan, one coherence time or less. On the other hand, the long-term bases are stable over time-spans of a few seconds. Hence, they can be obtained relatively easily. We also investigate a rank-p vector-scalar LMMSE channel estimator that exploits antenna correlation. Our results show that the investigated estimator can achieve a performance similar to that of full-rank LMMSE at a (2p + 1)/M times lower cost. The investigated estimator may be used in conjunction with estimators that exploit correlation in the frequency and time domains or, alternatively, in situations in which these estimators cannot be used, e.g., when pilot separation is larger than the channel coherence bandwidth or time.
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| 12. |
- Flordelis, Jose, et al.
(författare)
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Massive MIMO Performance - TDD Versus FDD : What Do Measurements Say?
- 2018
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Ingår i: IEEE Transactions on Wireless Communications. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 1536-1276 .- 1558-2248. ; 17:4, s. 2247-2261
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Tidskriftsartikel (refereegranskat)abstract
- Downlink beamforming in Massive MIMO either relies on uplink pilot measurements--exploiting reciprocity and time-division duplexing (TDD) operation, or on the use of a predetermined grid of beams with user equipments reporting their preferred beams, mostly in frequency-division duplexing (FDD) operation. Massive MIMO in its originally conceived form uses the first strategy, with uplink pilots, whereas there is currently significant commercial interest in the second, grid-of- beams. It has been analytically shown that with isotropic scattering (independent Rayleigh fading) the first approach outperforms the second. Nevertheless, there remains controversy regarding their relative performance in practical channels. In this contribution, the performances of these two strategies are compared using measured channel data at 2.6 GHz.
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| 13. |
- Flordelis, Jose, et al.
(författare)
-
Spatial Separation of Closely-Located Users in Measured Massive MIMO Channels
- 2018
-
Ingår i: IEEE Access. - 2169-3536. ; 6, s. 40253-40266
-
Tidskriftsartikel (refereegranskat)abstract
- We investigate the ability of Massive multiple-input multiple-output (MIMO) systems to spatially separate up to eighteen users located close to one another in line-of-sight (LOS) propagation conditions, in both indoor and outdoor environments. For that, we use fully-synchronous measured channels at 2.6 GHz of single-antenna users moving within a small area and concurrently communicating with a base station (BS) equipped with a compact 128-port array. To quantify the degree of spatial user separability, we use three scalar metrics, namely, the achievable sum-rates, the condition number of the channel matrix, and the angle to interference factor. Our results show that Massive MIMO with zero-forcing (ZF) or regularized ZF (RZF) can spatially separate nine, even eighteen, concurrent users at practical SNR values even in the challenging case of dominant LOS propagation. In particular, signal-to-noise ratio losses relative to ideal (non-interfering and equally strong) channels can be reduced dramatically compared with standard multiuser MIMO systems, which typically have the same number of users as BS antennas. Our findings suggest that with RZF or ZF the ratio of BS antennas to number of served users should be at least three to four, to harvest most of the available spatial gains that the environment can offer. Although orthogonality and array gains complement each other, for the suggested ratios of antennas to users, the main contribution to improving system performance, measured in sum-rates, comes from the orthogonality gain.
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| 14. |
- Flordelis, Jose, et al.
(författare)
-
Spatial Separation of Closely-Spaced Users in Measured Massive Multi-User MIMO Channels
- 2015
-
Ingår i: 2015 IEEE International Conference on Communications (ICC). ; , s. 1441-1446
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Konferensbidrag (refereegranskat)abstract
- Fully-synchronous measurements of a massive multi-user multiple-input multiple-output (MU-MIMO) radio propagation channel are presented. We evaluate the ability of a massive MIMO system to spatially separate users located close to each other in line-of-sight (LOS) propagation conditions. The system consists of a base-station (BS) antenna array equipped with 64 dual-polarized antenna elements (128 ports) arranged in a cylindrical configuration, and eight single-antenna users. The users are confined to a five-meter diameter circle and move randomly at pedestrian speeds. The BS antenna array is located on top of a 20 m tall building and has LOS to the users. We examine user separability by studying singular value spread of the MU-MIMO channel matrix for several subsets of BS antenna array ports, along with sum-rate capacity and achievable sum-rates with both zero-forcing and matched-filtering linear precoders. We also analyze the performance of the user with the lowest rate. Finally, a comparison between the performance offered by the massive MIMO system and that of a conventional MU-MIMO system is provided. To the best of our knowledge, this is the first report of fully-synchronous dynamic measurements of a massive MIMO system. Our investigation shows that even users located close to each other in LOS propagation conditions can be spatially separated in a massive MIMO system.
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| 15. |
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| 16. |
- Gao, Xiang, et al.
(författare)
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Channel behavior for very-large MIMO systems - initial characterization
- 2012
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Wireless communication using very-large multiple-input multiple-output (MIMO) antennas is a new research field, where base stations are equipped with a very large number of antennas as compared to previously considered systems. Unlike the conventional small and compact antenna arrays, the very-large arrays may span many wavelengths in space, thus they can experience large-scale fading over the array. This power variation over the antenna array may be critical to algorithm design and performance evaluations for very-large MIMO systems, and it is thus important that it is included in channel models. Based on channel measurements using a 128-antenna linear array in a semi-urban area, we characterize and model the large-scale fading properties. We focus on cluster-based modeling which can be seen as an extension of the current COST 2100 channel model. In the paper, we report our latest channel behavior modeling progress for very-large MIMO systems.
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| 17. |
- Gao, Xiang, et al.
(författare)
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Extension of the COST 2100 channel model for massive MIMO
- 2015
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Massive MIMO has been shown, both in theory and through experiments, to offer very promising properties. These include the possibility to decrease output power by at least an order of magnitude while still achieving large gains in spectral efficiency, as compared to today’s access schemes. To efficiently design communication algorithms and evaluate massive MIMO schemes, channel models that capture important massive MIMO channel characteristics are needed. We pursue this by extending a well-known cluster-based MIMO channel model - the COST 2100 model. In the paper, we suggest a model extension for massive MIMO, and we discuss main concepts, parameters and implementation issues. The modeling work is based on measurement data from a measurement campaign in the 2.6 GHz frequency range using a physically-large array with 128 elements.
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| 18. |
- Gao, Xiang, et al.
(författare)
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Large antenna array and propagation environment interaction
- 2014
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Ingår i: Proc. 48th Asilomar Conference on Signals, Systems and Computers, ACSSC 2015. - 9781479982974 ; , s. 666-670
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Konferensbidrag (refereegranskat)abstract
- In conventional MIMO, propagation conditions are often considered wide-sense stationary over the entire antenna array. In massive MIMO systems, where arrays can span over large physical dimensions, the situation is quite different. For instance, significant variations in signal strength, due to shadowing, can be experienced across a large array. These effects vary with propagation environment in which the array is placed, and influence achievable sum-rates. We characterize these variations for several measured propagation scenarios in the 2.6 GHz frequency range and illustrate how power variations and correlation properties change along the array.
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| 19. |
- Gao, Xiang, et al.
(författare)
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Linear pre-coding performance in measured very-large MIMO channels
- 2011
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Ingår i: Proc. of the 74th IEEE Vehicular Technology Conference.
-
Konferensbidrag (refereegranskat)abstract
- Wireless communication using very-large multiple-input multiple-output (MIMO) antennas is a new research field, where base stations are equipped with a very large number of antennas as compared to previously considered systems. In theory, as the number of antennas increases, propagation properties that were random before start to become deterministic. Theoretical investigations with independent identically distributed (i.i.d.)\ complex Gaussian (Rayleigh fading) channels and unlimited number of antennas have been done, but in practice we need to know what benefits we can get from very large, but limited, number of antenna elements in realistic propagation environments. In this study we evaluate properties of measured residential-area channels, where the base station is equipped with 128 antenna ports. An important property to consider is the orthogonality between channels to different users, since this property tells us how advanced multi-user MIMO (MU-MIMO) pre-coding schemes we need in the downlink. We show that orthogonality improves with increasing number of antennas, but for two single-antenna users there is very little improvement beyond 20 antennas. We also evaluate sum-rate performance for two linear pre-coding schemes, zero-forcing (ZF) and minimum mean squared-error (MMSE), as a function of the number of base station antennas. Already at 20 base station antennas these linear pre-coding schemes reach 98\% of the optimal dirty-paper coding (DPC) capacity for the measured channels.
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| 20. |
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| 21. |
- Gao, Xiang, et al.
(författare)
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Massive MIMO performance evaluation based on measured propagation data
- 2015
-
Ingår i: IEEE Transactions on Wireless Communications. - 1536-1276. ; 14:7, s. 3899-3911
-
Tidskriftsartikel (refereegranskat)abstract
- Massive MIMO, also known as very-large MIMO or large-scale antenna systems, is a new technique that potentially can offer large network capacities in multi-user scenarios. With a massive MIMO system, we consider the case where a base station equipped with a large number of antenna elements simultaneously serves multiple single-antenna users in the same time-frequency resource. So far, investigations are mostly based on theoretical channels with independent and identically distributed (i.i.d.) complex Gaussian coefficients, i.e., i.i.d. Rayleigh channels. Here, we investigate how massive MIMO performs in channels measured in real propagation environments. Channel measurements were performed at 2.6 GHz using a virtual uniform linear array (ULA) which has a physically large aperture, and a practical uniform cylindrical array (UCA) which is more compact in size, both having 128 antenna ports. Based on measurement data, we illustrate channel behavior of massive MIMO in three representative propagation conditions, and evaluate the corresponding performance. The investigation shows that the measured channels, for both array types, allow us to achieve performance close to that in i.i.d. Rayleigh channels. It is concluded that in real propagation environments we have characteristics that can allow for efficient use of massive MIMO, i.e., the theoretical advantages of this new technology can also be harvested in real channels.
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| 22. |
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| 23. |
- Gummesson, Anders, 1973, et al.
(författare)
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Longitudinal plasma protein profiling of newly diagnosed type 2 diabetes
- 2021
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Ingår i: EBioMedicine. - : Elsevier B.V.. - 2352-3964. ; 63
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Tidskriftsartikel (refereegranskat)abstract
- Background: Comprehensive proteomics profiling may offer new insights into the dysregulated metabolic milieu of type 2 diabetes, and in the future, serve as a useful tool for personalized medicine. This calls for a better understanding of circulating protein patterns at the early stage of type 2 diabetes as well as the dynamics of protein patterns during changes in metabolic status. Methods: To elucidate the systemic alterations in early-stage diabetes and to investigate the effects on the proteome during metabolic improvement, we measured 974 circulating proteins in 52 newly diagnosed, treatment-naïve type 2 diabetes subjects at baseline and after 1 and 3 months of guideline-based diabetes treatment, while comparing their protein profiles to that of 94 subjects without diabetes. Findings: Early stage type 2 diabetes was associated with distinct protein patterns, reflecting key metabolic syndrome features including insulin resistance, adiposity, hyperglycemia and liver steatosis. The protein profiles at baseline were attenuated during guideline-based diabetes treatment and several plasma proteins associated with metformin medication independently of metabolic variables, such as circulating EPCAM. Interpretation: The results advance our knowledge about the biochemical manifestations of type 2 diabetes and suggest that comprehensive protein profiling may serve as a useful tool for metabolic phenotyping and for elucidating the biological effects of diabetes treatments. Funding: This work was supported by the Swedish Heart and Lung Foundation, the Swedish Research Council, the Erling Persson Foundation, the Knut and Alice Wallenberg Foundation, and the Swedish state under the agreement between the Swedish government and the county councils (ALF-agreement).
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| 24. |
- Karlsson, Max, et al.
(författare)
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A single-cell type transcriptomics map of human tissues
- 2021
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:31
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Tidskriftsartikel (refereegranskat)abstract
- Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.
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| 25. |
- Karlsson, Max, et al.
(författare)
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Genome-wide single cell annotation of the human protein-coding genes
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- An important quest for the life science community is to deliver a complete annotation of the human building-blocks of life, the genes and the proteins. Here, we report on a genome-wide effort to annotate all protein-coding genes based on single cell transcriptomics data representing all major tissues and organs in the human body, integrated with data from bulk transcriptomics and antibody-based tissue profiling. Altogether, 25 tissues have been analyzed with single cell transcriptomics resulting in genome-wide expression in 444 single cell types using a strategy involving pooling data from individual cells to obtain genome-wide expression profiles of individual cell type. We introduce a new genome-wide classification tool based on clustering of similar expression profiles across single cell types, which can be visualized using dimensional reduction maps (UMAP). The clustering classification is integrated with a new “tau” score classification for all protein-coding genes, resulting in a measure of single cell specificity across all cell types for all individual genes. The analysis has allowed us to annotate all human protein-coding genes with regards to function and spatial distribution across individual cell types across all major tissues and organs in the human body. A new version of the open access Human Protein Atlas (www.proteinatlas.org) has been launched to enable researchers to explore the new genome-wide annotation on an individual gene level.
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