| 1. |
- Bentham, James, et al.
(författare)
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A century of trends in adult human height
- 2016
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Ingår i: eLIFE. - 2050-084X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.522.7) and 16.5 cm (13.319.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 2. |
- Bentham, James, et al.
(författare)
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A century of trends in adult human height
- 2016
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3– 19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8– 144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 3. |
- Danaei, Goodarz, et al.
(författare)
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Effects of diabetes definition on global surveillance of diabetes prevalence and diagnosis: a pooled analysis of 96 population-based studies with 331288 participants
- 2015
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Ingår i: The Lancet Diabetes & Endocrinology. - 2213-8595 .- 2213-8587. ; 3:8, s. 624-637
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Tidskriftsartikel (refereegranskat)abstract
- Background Diabetes has been defined on the basis of different biomarkers, including fasting plasma glucose (FPG), 2-h plasma glucose in an oral glucose tolerance test (2hOGTT), and HbA(1c). We assessed the effect of different diagnostic definitions on both the population prevalence of diabetes and the classification of previously undiagnosed individuals as having diabetes versus not having diabetes in a pooled analysis of data from population-based health examination surveys in different regions. Methods We used data from 96 population-based health examination surveys that had measured at least two of the biomarkers used for defining diabetes. Diabetes was defined using HbA(1c) (HbA(1c) >= 6 . 5% or history of diabetes diagnosis or using insulin or oral hypoglycaemic drugs) compared with either FPG only or FPG-or-2hOGTT definitions (FPG >= 7 . 0 mmol/L or 2hOGTT >= 11 . 1 mmol/L or history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated diabetes prevalence, taking into account complex survey design and survey sample weights. We compared the prevalences of diabetes using different definitions graphically and by regression analyses. We calculated sensitivity and specificity of diabetes diagnosis based on HbA1c compared with diagnosis based on glucose among previously undiagnosed individuals (ie, excluding those with history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated sensitivity and specificity in each survey, and then pooled results using a random-effects model. We assessed the sources of heterogeneity of sensitivity by meta-regressions for study characteristics selected a priori. Findings Population prevalence of diabetes based on FPG- or-2hOGTT was correlated with prevalence based on FPG alone (r= 0 . 98), but was higher by 2-6 percentage points at different prevalence levels. Prevalence based on HbA(1c) was lower than prevalence based on FPG in 42 . 8% of age-sex-survey groups and higher in another 41 . 6%; in the other 15 . 6%, the two definitions provided similar prevalence estimates. The variation across studies in the relation between glucose-based and HbA(1c)-based prevalences was partly related to participants' age, followed by natural logarithm of per person gross domestic product, the year of survey, mean BMI, and whether the survey population was national, subnational, or from specific communities. Diabetes defined as HbA(1c) 6 . 5% or more had a pooled sensitivity of 52 . 8% (95% CI 51 . 3-54 . 3%) and a pooled specificity of 99 . 74% (99 . 71-99 . 78%) compared with FPG 7 . 0 mmol/L or more for diagnosing previously undiagnosed participants; sensitivity compared with diabetes defined based on FPG-or-2hOGTT was 30 . 5% (28 . 7-32 . 3%). None of the preselected study-level characteristics explained the heterogeneity in the sensitivity of HbA(1c) versus FPG. Interpretation Different biomarkers and definitions for diabetes can provide different estimates of population prevalence of diabetes, and differentially identify people without previous diagnosis as having diabetes. Using an HbA(1c)-based definition alone in health surveys will not identify a substantial proportion of previously undiagnosed people who would be considered as having diabetes using a glucose-based test.
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| 4. |
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| 5. |
- Zhou, Bin, et al.
(författare)
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Worldwide trends in diabetes since 1980: A pooled analysis of 751 population-based studies with 4.4 million participants
- 2016
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Ingår i: The Lancet. - : Elsevier B.V.. - 0140-6736 .- 1474-547X. ; 387:10027, s. 1513-1530
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Tidskriftsartikel (refereegranskat)abstract
- Background: One of the global targets for non-communicable diseases is to halt, by 2025, the rise in the age standardised adult prevalence of diabetes at its 2010 levels. We aimed to estimate worldwide trends in diabetes, how likely it is for countries to achieve the global target, and how changes in prevalence, together with population growth and ageing, are aff ecting the number of adults with diabetes.Methods: We pooled data from population-based studies that had collected data on diabetes through measurement of its biomarkers. We used a Bayesian hierarchical model to estimate trends in diabetes prevalence-defined as fasting plasma glucose of 7.0 mmol/L or higher, or history of diagnosis with diabetes, or use of insulin or oral hypoglycaemic drugs-in 200 countries and territories in 21 regions, by sex and from 1980 to 2014. We also calculated the posterior probability of meeting the global diabetes target if post-2000 trends continue.Findings: We used data from 751 studies including 4372000 adults from 146 of the 200 countries we make estimates for. Global age-standardised diabetes prevalence increased from 4.3% (95% credible interval 2.4-17.0) in 1980 to 9.0% (7.2-11.1) in 2014 in men, and from 5.0% (2.9-7.9) to 7.9% (6.4-9.7) in women. The number of adults with diabetes in the world increased from 108 million in 1980 to 422 million in 2014 (28.5% due to the rise in prevalence, 39.7% due to population growth and ageing, and 31.8% due to interaction of these two factors). Age-standardised adult diabetes prevalence in 2014 was lowest in northwestern Europe, and highest in Polynesia and Micronesia, at nearly 25%, followed by Melanesia and the Middle East and north Africa. Between 1980 and 2014 there was little change in age-standardised diabetes prevalence in adult women in continental western Europe, although crude prevalence rose because of ageing of the population. By contrast, age-standardised adult prevalence rose by 15 percentage points in men and women in Polynesia and Micronesia. In 2014, American Samoa had the highest national prevalence of diabetes (>30% in both sexes), with age-standardised adult prevalence also higher than 25% in some other islands in Polynesia and Micronesia. If post-2000 trends continue, the probability of meeting the global target of halting the rise in the prevalence of diabetes by 2025 at the 2010 level worldwide is lower than 1% for men and is 1% for women. Only nine countries for men and 29 countries for women, mostly in western Europe, have a 50% or higher probability of meeting the global target.Interpretation: Since 1980, age-standardised diabetes prevalence in adults has increased, or at best remained unchanged, in every country. Together with population growth and ageing, this rise has led to a near quadrupling of the number of adults with diabetes worldwide. The burden of diabetes, both in terms of prevalence and number of adults aff ected, has increased faster in low-income and middle-income countries than in high-income countries.
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| 6. |
- Hibar, Derrek P., et al.
(författare)
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Novel genetic loci associated with hippocampal volume
- 2017
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (r(g) = -0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness.
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| 7. |
- Satizabal, Claudia L., et al.
(författare)
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Genetic architecture of subcortical brain structures in 38,851 individuals
- 2019
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:11, s. 1624-
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Tidskriftsartikel (refereegranskat)abstract
- Subcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen and thalamus, using genome-wide association analyses in almost 40,000 individuals from CHARGE, ENIGMA and UK Biobank. We show that variability in subcortical volumes is heritable, and identify 48 significantly associated loci (40 novel at the time of analysis). Annotation of these loci by utilizing gene expression, methylation and neuropathological data identified 199 genes putatively implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, inflammation/infection and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease.
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| 8. |
- Gorski, Mathias, et al.
(författare)
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Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies
- 2022
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Ingår i: Kidney International. - : Elsevier. - 0085-2538 .- 1523-1755. ; 102:3, s. 624-639
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Tidskriftsartikel (refereegranskat)abstract
- Estimated glomerular filtration rate (eGFR) reflects kidney function. Progressive eGFR-decline can lead to kidney failure, necessitating dialysis or transplantation. Hundreds of loci from genome-wide association studies (GWAS) for eGFR help explain population cross section variability. Since the contribution of these or other loci to eGFR-decline remains largely unknown, we derived GWAS for annual eGFR-decline and meta-analyzed 62 longitudinal studies with eGFR assessed twice over time in all 343,339 individuals and in high-risk groups. We also explored different covariate adjustment. Twelve genomewide significant independent variants for eGFR-decline unadjusted or adjusted for eGFR- baseline (11 novel, one known for this phenotype), including nine variants robustly associated across models were identified. All loci for eGFR-decline were known for cross-sectional eGFR and thus distinguished a subgroup of eGFR loci. Seven of the nine variants showed variant- by-age interaction on eGFR cross section (further about 350,000 individuals), which linked genetic associations for eGFR-decline with agedependency of genetic cross- section associations. Clinically important were two to four-fold greater genetic effects on eGFR-decline in high-risk subgroups. Five variants associated also with chronic kidney disease progression mapped to genes with functional in- silico evidence (UMOD, SPATA7, GALNTL5, TPPP). An unfavorable versus favorable nine-variant genetic profile showed increased risk odds ratios of 1.35 for kidney failure (95% confidence intervals 1.03- 1.77) and 1.27 for acute kidney injury (95% confidence intervals 1.08-1.50) in over 2000 cases each, with matched controls). Thus, we provide a large data resource, genetic loci, and prioritized genes for kidney function decline, which help inform drug development pipelines revealing important insights into the age-dependency of kidney function genetics.
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| 9. |
- Gorski, Mathias, et al.
(författare)
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Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline
- 2021
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Ingår i: Kidney International. - : Elsevier. - 0085-2538 .- 1523-1755. ; 99:4, s. 926-939
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Tidskriftsartikel (refereegranskat)abstract
- Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m2/year or more ("Rapid3"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m2 at follow-up among those with eGFRcrea 60 mL/min/1.73m2 or more at baseline ("CKDi25"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or LARP4B. Individuals at high compared to those at low genetic risk (8-14 vs 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.
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| 10. |
- Ho, Ching-Tien, et al.
(författare)
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Algorithms for Matrix Transposition on Boolean Cube Configured Ensemble Architectures
- 1987
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Konferensbidrag (refereegranskat)abstract
- In a multiprocessor with distributed storage the data structures have a significant impact on the communication complexity. In this paper we present a few algorithms for performing matrix transposition on a Boolean $n$-cube. One algorithm performs the transpose in a time proportional to the lower bound both with respect to communication start-ups and to element transfer times. We present algorithms for transposing a matrix embedded in the cube by a binary encoding, a binary-reflected Gray code encoding of rows and columns, or combinations of these two encodings. The transposition of a matrix when several matrix elements are identified to a node by consecutive or cyclic partitioning is also considered and lower bound algorithms given. Experimental data are provided for the Intel iPSC and the Connection Machine.
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| 11. |
- Ho, Ching-Tien, et al.
(författare)
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An Efficient Algorithm for Gray–to–Binary Permutation on Hypercubes
- 1994
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Ingår i: Journal of Parallel and Distributed Computing. - 0743-7315 .- 1096-0848. ; 20:1, s. 114-120
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Tidskriftsartikel (refereegranskat)abstract
- Both Gray code and binary code are frequently used in mapping arrays into hypercube architectures. While the former is preferred when communication between adjacent array elements is needed, the latter is preferred for FFT-type communication. When different phases of computations have different types of communication patterns, the need arises to remap the data. We give a nearly optimal algorithm for permuting data from a Gray code mapping to a binary code mapping on a hypercube with communication restricted to one input and one output channel per node at a time. Our algorithm improves over the best previously known algorithm [6] by nearly a factor of two and is optimal to within a factor of n=(n Gamma 1) with respect to data transfer time on an n-cube. The expected speedup is confirmed by measurements on an Intel iPSC/2 hypercube
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| 12. |
- Ho, Ching-Tien, et al.
(författare)
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Distributed Routing Algorithms for Broadcasting and Personalized Communication in Hypercubes
- 1986
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Konferensbidrag (refereegranskat)abstract
- High communication bandwidth in standard technologies is more expensive to realize than a high rate of arithmetic or logic operations. The effective utilization of communication resources is crucial for good overall performance in highly concurrent systems. In this paper we address two different communication problems in Boolean n-cube configured multiprocessors: 1) broadcasting, i.e., distribution of common data from a single source to all other nodes, and 2) sending personalized data from a single source to all other nodes. The well known spanning tree algorithm obtained by bit-wise complementation of leading zeroes (referredto as the SBT algorithm for Spanning Binomial nee) is compared with an algorithm using multiple spanning binomial trees (MSBT). The MSBT dgorithm offers a potential speed-up over the SBT dgorithm by afactor of log2 N. We also present a balanced #panning tree algorithm (BST) that offers a lower complexity than the SBT algorithm for Case 2. The potential improvement is by a factor of 3 log2 N. The analysis takes into account the size of the data sets, the communication bandwidth, and the overhead in communication. We also provide some experimental data for the Intel iPSC'd7.
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| 13. |
- Ho, Ching-Tien, et al.
(författare)
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Embedding Hyper–pyramids in Hypercubes
- 1994
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Ingår i: IBM Journal of Research and Development. - : IBM. - 0018-8646 .- 2151-8556. ; 38:1, s. 31-45
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Tidskriftsartikel (refereegranskat)
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| 14. |
- Ho, Ching-Tien, et al.
(författare)
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Embedding Meshes in Boolean Cubes by Graph Decomposition
- 1990
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Ingår i: Parallel Computing. - : Elsevier BV. - 0167-8191 .- 1872-7336. ; 8:4, s. 325-339
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Tidskriftsartikel (refereegranskat)abstract
- This paper explores the embeddings of multidimensional meshes into minimal Boolean cubes by graph decomposition. The dilation and the congestion of the product graph (G1 × G2) → (H1 × H2) is the maximum of the dilation and congestion for the two embeddings G1 → H1 and G2 → H2. The graph decomposition technique can be used to improve the average dilation and average congestion. The graph decomposition technique combined with some particular two-dimensional embeddings allows for minimal-expansion, dilation-two, congestion-two embeddings of about 87% of all two-dimensional meshes, with a significantly lower average dilation and congestion than by modified line compression. For three-dimensional meshes we show that the graph decomposition technique, together with two three-dimensional mesh embeddings presented in this paper and modified line compression, yields dilation-two embeddings of more than 96% of all three-dimensional meshes contained in a 512 × 512 × 512 mesh. The graph decomposition technique is also used to generalize the embeddings to meshes with wrap-around. The dilation increases by at most one compared to a mesh without wraparound. The expansion is preserved for the majority of meshes, if a wraparound feature is added to the mesh.
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| 15. |
- Ho, Ching-Tien, et al.
(författare)
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Embedding Meshes into Small Boolean Cubes
- 1990
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Konferensbidrag (refereegranskat)abstract
- The embedding of arrays in Boolean cubes, when there are more array elements than nodes in the cube, can always be made with optimal load-factor by reshaping the array to a one-dimensional array. We show that the dilation for such an embedding is of an .to x .t1 x - + x &-I array in an n-cube.Dila tion one embeddings can be obtained by splitting each axis into segments and assigning segments to nodes in the cube by a Gray code. The load-factor is optimal if the axis lengths contain sufficiently many powers of two. The congestion is minimized, if the segment lengths along the different axes are as equal as possible, for the cube configured with at most as many axes as the array. A further decrease in the congestion is possible if the array is partitioned into subarrays, and corresponding axis of different subarrays make use of edge-disjoint Hamiltonian cycles within subcubes. The congestion can also be reduced by using multiple paths between pairs of cube nodes, i.e., by using “fat” edges.
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| 16. |
- Ho, Ching-Tien, et al.
(författare)
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Embedding Three–Dimensional Meshes in Boolean Cubes by Graph Decomposition
- 1990
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Konferensbidrag (refereegranskat)abstract
- This paper explores the embeddings of multidimensional meshes into minimal Boolean cubes by graph decomposition. The graph decomposition technique can be used to improve the average dilation and average congestion. The graph decomposition technique combined with some particular two-dimensional embeddings allows for minimal-expansion, dilation-two, congestion-two embeddings of about 87% of all two-dimensional meshes, with a significantly lower average dilation and congestion than by modified line compression. For three-dimensional meshes the authors show that the graph decomposition technique, together with two three-dimensional mesh embeddings presented in this paper and modified line compression, yields dilation-two embeddings of more than 96% of all three dimensional meshes contained in a 512 {times} 512 {times} 512 mesh.
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| 17. |
- Ho, Ching-Tien, et al.
(författare)
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Matrix Multiplication on Hypercubes Using Full Bandwidth and Constant Storage
- 1991
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Konferensbidrag (refereegranskat)abstract
- For matrix multiplication on hypercube multiproces- sors with the product matrix accumulated in place a processor must receive about P2= p N elements of each input operand, with operands of size P P distributed evenly over N processors. With concurrent communi- cation on all ports, the number of element transfers in sequence can be reduced to P2= p N logN for each input operand. We present a two-level partitioning of the matrices and an algorithm for the matrix multipli- cation with optimal data motion and constant storage. The algorithm has sequential arithmetic complexity 2P3, and parallel arithmetic complexity 2P 3=N. The algorithm has been implemented on the Connection Machine model CM-2. For the performance on the 8K CM-2, we measured about 1.6 G ops, which would scale up to about 13 G ops for a 64K full machine.
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| 18. |
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| 19. |
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| 20. |
- Ho, Ching-Tien, et al.
(författare)
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Optimizing Tridiagonal Solvers for the Alternating Direction Method on Boolean Cube Multiprocessors
- 1990
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Ingår i: SIAM Journal on Scientific Computing. - : Society for Industrial & Applied Mathematics (SIAM). - 1064-8275 .- 1095-7197. ; 11:3, s. 563-592
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Tidskriftsartikel (refereegranskat)abstract
- Sets of tridiagonal systems occur in many applications. Fast Poisson solvers and Alternate Direction Methods make use of tridiagonal system solvers. Network-based multiprocessors provide a cost-effective alternative to traditional supercomputer architectures. The complexity of concurrent algorithms for the solution of multiple tridiagonal systems on Boolean-cube-configured multiprocessors with distributed memory are investigated. Variations of odd-even cyclic reduction, parallel cyclic reduction, and algorithms making use of data transposition with or without substructuring and local elimination, or pipelined elimination, are considered. A simple performance model is used for algorithm comparison, and the validity of the model is verified on an Intel iPSC/ 1. For many combinations of machine and system parameters, pipelined elimination, or equation transposition with or without substructuring is optimum. Hybrid algorithms that at any stage choose the best algorithm among the considered ones for the remainder of the problem are presented. It is shown that the optimum partitioning of a set of independent tridiagonal systems among a set of processors yields the embarrassingly parallel case. If the systems originate from a lattice and solutions are computed in alternating directions, then to first order the aspect ratio of a computational lattice shall be the same as that of the lattice forming the base for the equations. The experiments presented here demonstrate the importance of combining in the communication system for architectures with a relatively high communications start-up time.
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| 21. |
- Ho, Ching-Tien, et al.
(författare)
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Spanning Balanced Trees in Boolean cubes
- 1989
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Ingår i: SIAM JOURNAL ON SCIENTIFIC AND STATISTICAL COMPUTING. - : Society for Industrial & Applied Mathematics (SIAM). - 0196-5204 .- 2168-3417. ; 10:4, s. 607-630
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Tidskriftsartikel (refereegranskat)abstract
- A Spanning Balanced$n$-tree (SBnT) in a Boolean $n$-cube is a spanning tree in which the root has fanout $n$, and all the subtrees of the root have $O({{2^n } / n})$ nodes. The number of tree edges in each dimension of the $n$-cube is of order $O({{2^n } / n})$. The spanning balanced n-tree allows for scheduling disciplines that realize lower bound (within a factor of two) one-to-all personalized communication, all-to-all broadcasting, and all-to-all personalized communication on a Boolean $n$-cube [C.-T. Ho and S. L. Johnsson, Proc. 1986 International Conference on Parallel Processing, pp. 640–648, IEEE Computer Society, 1986; Tech. Report YALEU/DCS/RR–483, May 1986], [S. L. Johnsson and C.-T. Ho, Tech. Report YALEU/DCS/RR–610, Dept. of Computer Science, Yale Univ., New Haven, CT, November 1987]. The improvement in data transfer time over the familiar binomial tree routing is a factor of ${n / 2}$ for concurrent communication on all ports and one-to-all personalized communication and all-to-all broadcasting. For all-to-all personalized communication on all ports concurrently, the improvement is of order $O(\sqrt n )$. Distributed routing algorithms defining the spanning balanced $n$-tree are given. The balanced $n$-tree is not unique, and a few definitions of $n$-trees that are effectively edge-disjoint are provided. Some implementation issues are also discussed. Binary numbers obtained from each other through rotation form necklaces that are full if the period is equal to the length of the number; otherwise, they are degenerate. As an intermediary result, it is shown that the ratio between the number of degenerate necklaces and the total number of necklaces with $l$ bits equal to one is at most ${4 / {(4 + n)}}$ for $1 \leqq l < n$
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| 22. |
- Ho, Ching-Tien, et al.
(författare)
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Systolic FFT Algorithms on Boolean Cubes
- 1988
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Konferensbidrag (refereegranskat)abstract
- A description is given of a systolic Cooley-Tukey fast Fourier transform algorithm for Booleann-cubes with a substantial amount of storage per cube node. In mapping a Cooley-Tukey type FFT to such a network, the main concerns are effective use of the high connectivity/bandwidth of the Booleann-cube, the computational resources, the storage bandwidth, if there is a storage hierarchy, and the pipelines should the arithmetic units have such a feature. Another important consideration in a multiprocessor, distributed storage architecture is the allocation and access to coefficients, if they are precomputed. FFT algorithms are described that use both the storage bandwidth and the communication system optimally and require storage ofP+nNcoefficients for a transform onP⩾Ndata elements. A complex-to-complex FFT on 16 million points is predicted to require about 1.5 s on a Connection Machine model CM-2
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| 23. |
- Johnsson, Lennart, et al.
(författare)
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Algorithms for Matrix Transposition on Boolean N-Cube Configured Ensemble Architectures
- 1988
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Ingår i: SIAM Journal on Matrix Analysis and Applications. - : Society for Industrial & Applied Mathematics (SIAM). - 0895-4798 .- 1095-7162. ; 9:3, s. 419-454
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Tidskriftsartikel (refereegranskat)abstract
- In a multiprocessor with distributed storage the data structures have a significant impact on the communication complexity. In this paper we present a few algorithms for performing matrix transposition on a Boolean $n$-cube. One algorithm performs the transpose in a time proportional to the lower bound both with respect to communication start-ups and to element transfer times. We present algorithms for transposing a matrix embedded in the cube by a binary encoding, a binary-reflected Gray code encoding of rows and columns, or combinations of these two encodings. The transposition of a matrix when several matrix elements are identified to a node by consecutive or cyclic partitioning is also considered and lower bound algorithms given. Experimental data are provided for the Intel iPSC and the Connection Machine
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| 24. |
- Johnsson, Lennart, et al.
(författare)
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Boolean Cube Emulation of Butterfly Networks Encoded by Gray Code
- 1994
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Ingår i: Journal of Parallel and Distributed Computing. - 0743-7315 .- 1096-0848. ; 20:3, s. 261-179
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Tidskriftsartikel (refereegranskat)abstract
- The authors present algorithms for butterfly emulation on binary-reflected Gray coded data that require the same number of element transfers in sequence in a Boolean cube network as for a binary encoding. The required code conversion is either performed in local memories, or through concurrent exchanges not effecting the number of element transfers in sequence. The emulation of a butterfly network with one or two elements per processor requires n communication cycles on an n-cube. For more than two elements per processor, one additional communication cycle is required for every pair of elements. The encoding on completion can be either binary, or binary reflected Gray code, or any combination thereof, without affecting the communication complexity.
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| 25. |
- Johnsson, Lennart, et al.
(författare)
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Generalized Shuffle Permutations on Boolean Cubes
- 1992
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Ingår i: Journal of Parallel and Distributed Computing. - 0743-7315 .- 1096-0848. ; 16:1, s. 1-14
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Tidskriftsartikel (refereegranskat)abstract
- In a generalized permutation an address (a[subscript q-1]a[subscript q-2] ... a0 receives its content from an address obtained through a cyclic shift on a subset of the q dimensions used for the encoding of the addresses. Bit-complementation may be combined with the shift. We give an algorithm that requires K/2 + 2 exchanges for K elements per processor, when storage dimensions are part of the permutation, and concurrent communication on all ports of every processor is possible. The number of element exchanges in sequence is independent of the number of processor dimensions [omega subscript r] in the permutation.
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| 26. |
- Johnsson, Lennart, et al.
(författare)
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On the Conversion between Binary Code and Binary Reflected Gray Code
- 1995
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Ingår i: IEEE Transactions on Computers. - 0018-9340 .- 1557-9956. ; 44:1, s. 47-53
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Tidskriftsartikel (refereegranskat)abstract
- We present a new algorithm for conversion between binary code and binary-reflected Gray code that requires ap proximately 2K/3 element transfers in sequence for K elements per node, compared to K element transfers for previously known algorithms. For a binary cube of n = 2 dimensions the new algorithm degenerates to yield a complexity of K/2 + 1 element transfers, which is optimal. The new algorithm is optimal to within a multiplicative factor of 4/3 with respect to the best known lower bound for any routing strategy. We show that the minimum number of element transfers for minimum path length routing is K with concurrent communication on all channels of every node of a binary cube.
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| 27. |
- Johnsson, Lennart, et al.
(författare)
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Optimal Communication Channel Utilization for Matrix Transposition and Related Permutations on Boolean Cubes
- 1994
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Ingår i: Journal of Discrete Applied Mathematics. - : Elsevier. ; 53:1-3, s. 251-274
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Tidskriftsartikel (refereegranskat)abstract
- We present optimal schedules for permutations in which each node sends one or several unique messages to every other node. With concurrent communication on all channels of every node in binary cube networks, the number of element transfers in sequence for K elements per node is K/2, irrespective of the number of nodes over which the data set is distributed. For a succession of s permutations within disjoint subcubes of d dimensions each, our schedules yield min(K/2 + (s - 1)d, (s + 3)d, K/2 + 2d) exchanges in sequence. The algorithms can be organized to avoid indirect addressing in the intermode data exchanges, a property that increases the performance on some architectures.
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| 28. |
- Johnsson, Lennart, et al.
(författare)
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Spanning Graphs for Optimum Broadcasting and Personalized Communication in Hypercubes
- 1989
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Ingår i: IEEE Transactions on Computers. - : Institute of Electrical and Electronics Engineers (IEEE). - 0018-9340 .- 1557-9956. ; 38:9, s. 1249-1268
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Tidskriftsartikel (refereegranskat)abstract
- Four different communication problems are addressed in Booleann-cube configured multiprocessors: (1) one-to-all broadcasting: distribution of common data from a single source to all other nodes; (2) one-to-all personalized communication: a single node sending unique data to all other nodes; (3) all-to-all broadcasting: distribution of common data from each node to all other nodes; and (4) all-to-all personalized communication: each node sending a unique piece of information to every other node. Three communication graphs (spanning trees) for the Booleann-cube are proposed for the routing, and scheduling disciplines provably optimum within a small constant factor are proposed. With appropriate scheduling and concurrent communication on all ports of every processor, routings based on these two communication graphs offer a speedup of up ton/2, and O(√n) over the routings based on the spanning binomial tree for cases (2)-(4) respectively. All three spanning trees offer optimal communication times for cases (2)-(4) and concurrent communication on all ports of every processor. Timing models and complexity analysis are verified by experiments on a Boolean-cube-configured multiprocessor
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| 29. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 30. |
- Stanaway, Jeffrey D., et al.
(författare)
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Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017
- 2018
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Ingår i: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994
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Tidskriftsartikel (refereegranskat)abstract
- Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
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| 31. |
- Wuttke, Matthias, et al.
(författare)
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A catalog of genetic loci associated with kidney function from analyses of a million individuals
- 2019
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Ingår i: Nature Genetics. - : NATURE PUBLISHING GROUP. - 1061-4036 .- 1546-1718. ; 51:6, s. 957-972
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Tidskriftsartikel (refereegranskat)abstract
- Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through transancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these,147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.
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