| 1. |
- Abolfathi, Bela, et al.
(författare)
-
The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
-
Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
-
Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
|
|
| 2. |
- Huyghe, Jeroen R., et al.
(författare)
-
Discovery of common and rare genetic risk variants for colorectal cancer
- 2019
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:1, s. 76-
-
Tidskriftsartikel (refereegranskat)abstract
- To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 x 10(-8), bringing the number of known independent signals for CRC to similar to 100. New signals implicate lower-frequency variants, Kruppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
|
|
| 3. |
- Schmit, Stephanie L, et al.
(författare)
-
Novel Common Genetic Susceptibility Loci for Colorectal Cancer.
- 2019
-
Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 111:2, s. 146-157
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk.Methods: We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided.Results: The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0.Conclusions: This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.
|
|
| 4. |
- Aguado, D. S., et al.
(författare)
-
The Fifteenth Data Release of the Sloan Digital Sky Surveys : First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library
- 2019
-
Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 240:2
-
Tidskriftsartikel (refereegranskat)abstract
- Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 July-2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGA-we release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020-2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.
|
|
| 5. |
- Kilpeläinen, Tuomas O, et al.
(författare)
-
Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels
- 2016
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered. Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching P<10(-6) in 19,979 additional individuals. We identify five loci robustly associated (P<5 × 10(-8)) with leptin levels in/near LEP, SLC32A1, GCKR, CCNL1 and FTO. Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown experiments in mouse adipose tissue explants show convincing evidence for adipogenin, a regulator of adipocyte differentiation, as the novel causal gene in the SLC32A1 locus influencing leptin levels. Our findings provide novel insights into the regulation of leptin production by adipose tissue and open new avenues for examining the influence of variation in leptin levels on adiposity and metabolic health.
|
|
| 6. |
- Briscoe, Bob, et al.
(författare)
-
Reducing Internet Latency : A Survey of Techniques and Their Merits
- 2016
-
Ingår i: IEEE Communications Surveys and Tutorials. - : IEEE. - 1553-877X. ; 18:3, s. 2149-2196
-
Tidskriftsartikel (refereegranskat)abstract
- Latency is increasingly becoming a performance bottleneck for Internet Protocol (IP) networks, but historically, networks have been designed with aims of maximizing throughput and utilization. This paper offers a broad survey of techniques aimed at tackling latency in the literature up to August 2014, as well as their merits. A goal of this work is to be able to quantify and compare the merits of the different Internet latency reducing techniques, contrasting their gains in delay reduction versus the pain required to implement and deploy them. We found that classifying techniques according to the sources of delay they alleviate provided the best insight into the following issues: 1) The structural arrangement of a network, such as placement of servers and suboptimal routes, can contribute significantly to latency; 2) each interaction between communicating endpoints adds a Round Trip Time (RTT) to latency, particularly significant for short flows; 3) in addition to base propagation delay, several sources of delay accumulate along transmission paths, today intermittently dominated by queuing delays; 4) it takes time to sense and use available capacity, with overuse inflicting latency on other flows sharing the capacity; and 5) within end systems, delay sources include operating system buffering, head-of-line blocking, and hardware interaction. No single source of delay dominates in all cases, and many of these sources are spasmodic and highly variable. Solutions addressing these sources often both reduce the overall latency and make it more predictable.
|
|
| 7. |
- Grinnemo, Karl-Johan, 1968-, et al.
(författare)
-
Deliverable D3.1 - Initial Report on the Extended Transport System
- 2017
-
Rapport (refereegranskat)abstract
- The NEAT System offers an enhanced API for applications that disentangles them from the actual transport protocol being used. The system also enables applications to communicate their service requirements to the transport system in a generic, transport-protocol independent way. Moreover, the architecture of the NEAT System promotes the evolution of new transport services. Work Package 3 (WP3) enhances and extends the core parts of the NEAT Transport. Efforts have been devoted to developing transport-protocol mechanisms that enable a wider spectrum of NEAT Transport Services, and that assist the NEAT System in facilitating several of the commercial use cases. Work has also started on the development of optimal transport-selection mechanisms; mechanisms that enable for the NEAT System to make optimal transport selections on the basis of application requirements and network measurements. Lastly, another research activity has been initiated on how to use SDN to signal application requirements to routers, switches, and similar network elements. This document provides an initial report on all these WP3 activities—both on completed and on near-termplanned work.
|
|
| 8. |
- Grinnemo, Karl-Johan, 1968-, et al.
(författare)
-
Deliverable D3.2 - Final Report on Transport Protocol Enhancements
- 2017
-
Rapport (refereegranskat)abstract
- This deliverable provides a final report on the work on transport protocol enhancements done inWork Package 3. First, we report on the extensions made to the SCTP protocol that turn it into a viable alternative to TCP and allow to deliver a lower-latency transport service. Next, we describe our work to develop a framework for providing a deadline-aware, less-than-best-effort transport service, targeting background traffic and thus addressing requirements on NEAT from the EMC use case. We also present our efforts to design and implement a latency-aware scheduler for MPTCP, which enables NEAT to offer a transport service that meets the needs of latency-sensitive applications, and that efficiently utilises available network resources. Lastly, this document informs on our work on coupled congestion control for TCP, a mechanism that treats a bundle of parallel TCP flows between the same pair of hosts as a single unit. By efficiently multiplexing concurrent TCP flows, our coupled congestion control alleviates the effects of queueing, and tends to result in a more efficient usage of available bandwidth, where the flows’ aggregate capacity share can be apportioned based on application preferences.
|
|
| 9. |
- Grinnemo, Karl-Johan, 1968-, et al.
(författare)
-
Deliverable D3.3 - Extended Transport System and Transparent Support of Non-NEAT Applications
- 2017
-
Rapport (refereegranskat)abstract
- This deliverable summarises and concludes our work in Work Package 3 (WP3) to extend the transport services provided by the NEAT System developed in Work Package 2, and to enable non-NEAT applications to harness the transport services offered by NEAT. We have demonstrated how a policy- and information-based selection of transport protocol by NEAT could provide a more efficient transport service for web applications. The information on which NEAT makes its transport selection decisions resides in the Characteristics Information Base (CIB). The CIB is populated by various CIB sources, and in WP3 we have designed, implemented, and evaluated various CIB sources, including meta data from mobile broadband networks, passive measurements, IPv6 Provisioning Domain protocols and the Happy Eyeballs mechanism, which caches the outcome of its connection attempts. A key property of NEAT is that it not only “vertically” decouples applications from transport protocols, but also “horizontally”. Particularly, it enables applications to harness information about resource availability and policies from Software Defined Networking (SDN) controllers in managed networks, without these applications actually being SDN-aware. To extend the use of NEAT to non-NEAT applications, we have implemented a BSDcompatible sockets API on top of NEAT and a NEAT proxy that intercepts and replaces standard TCP connections with NEAT flows, i.e., with the transport solutions deemed most appropriate by NEAT.We have also proposed a way for non-NEAT applications to make use of NEAT through the deployment of NEAT-enabled virtual appliances in SDN-controlled networks: connections from these applications are routed via an SDN-controlled proxy that terminates the original connection and replaces it with a NEAT-selected connection.
|
|
| 10. |
- Khademi, Naeem, et al.
(författare)
-
NEAT: A Platform- and Protocol-Independent Internet Transport API
- 2017
-
Ingår i: IEEE Communications Magazine. - : IEEE Communications Society. - 0163-6804 .- 1558-1896. ; 55:6, s. 46-54
-
Tidskriftsartikel (refereegranskat)abstract
- The sockets Applications Programming Interface (API) has become the standard way that applications access the transport services offered by the Internet Protocol stack. This paper presents NEAT, a user-space library that can provide an alternate transport API. NEAT allows applications to request the service they need using a new design that is agnostic to the specific choice of transport protocol underneath. This not only allows applications to take advantage of common protocol machinery, but also eases introduction of new network mechanisms and transport protocols. The paper describes the components of the NEAT library and illustrates the important benefits that can be gained from this new approach. NEAT is a software platform for developing advanced network applications that was designed in accordance with the standardization efforts on Transport Services (TAPS) in the Internet Engineering Task Force (IETF), but its features exceed the envisioned functionality of a TAPS system.
|
|
