| 1. |
- Djurfeldt, Mikael, 1967-, et al.
(författare)
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Brain-scale simulation of the neocortex on the IBM Blue Gene/L supercomputer
- 2008
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Ingår i: IBM Journal of Research and Development. - : IBM. - 0018-8646 .- 2151-8556. ; 52:1-2, s. 31-41
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Tidskriftsartikel (refereegranskat)abstract
- Biologically detailed large-scale models of the brain can now be simulated thanks to increasingly powerful massively parallel supercomputers. We present an overview, for the general technical reader, of a neuronal network model of layers II/III of the neocortex built with biophysical model neurons. These simulations, carried out on an IBM Blue Gene/Le supercomputer, comprise up to 22 million neurons and 11 billion synapses, which makes them the largest simulations of this type ever performed. Such model sizes correspond to the cortex of a small mammal. The SPLIT library, used for these simulations, runs on single-processor as well as massively parallel machines. Performance measurements show good scaling behavior on the Blue Gene/L supercomputer up to 8,192 processors. Several key phenomena seen in the living brain appear as emergent phenomena in the simulations. We discuss the role of this kind of model in neuroscience and note that full-scale models may be necessary to preserve natural dynamics. We also discuss the need for software tools for the specification of models as well as for analysis and visualization of output data. Combining models that range from abstract connectionist type to biophysically detailed will help us unravel the basic principles underlying neocortical function.
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| 2. |
- Gad, Helge, et al.
(författare)
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MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool
- 2014
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 508:7495, s. 215-221
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Tidskriftsartikel (refereegranskat)abstract
- Cancers have dysfunctional redox regulation resulting in reactive oxygen species production, damaging both DNA and free dNTPs. The MTH1 protein sanitizes oxidized dNTP pools to prevent incorporation of damaged bases during DNA replication. Although MTH1 is non-essential in normal cells, we show that cancer cells require MTH1 activity to avoid incorporation of oxidized dNTPs, resulting in DNA damage and cell death. We validate MTH1 as an anticancer target in vivo and describe small molecules TH287 and TH588 as first-in-class nudix hydrolase family inhibitors that potently and selectively engage and inhibit the MTH1 protein in cells. Protein co-crystal structures demonstrate that the inhibitors bindin the active site of MTH1. The inhibitors cause incorporation of oxidized dNTPs in cancer cells, leading to DNA damage, cytotoxicity and therapeutic responses in patient-derived mouse xenografts. This study exemplifies the non-oncogene addiction concept for anticancer treatment and validates MTH1 as being cancer phenotypic lethal.
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| 3. |
- Johansson, Ann-Sofi, et al.
(författare)
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Cytotoxicity of superoxide dismutase 1 in cultured cells is linked to Zn2+ chelation
- 2012
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:4, s. e36104-
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Tidskriftsartikel (refereegranskat)abstract
- Neurodegeneration in protein-misfolding disease is generally assigned to toxic function of small, soluble protein aggregates. Largely, these assignments are based on observations of cultured neural cells where the suspect protein material is titrated directly into the growth medium. In the present study, we use this approach to shed light on the cytotoxic action of the metalloenzyme Cu/Zn superoxide dismutase 1 (SOD1), associated with misfolding and aggregation in amyotrophic lateral sclerosis (ALS). The results show, somewhat unexpectedly, that the toxic species of SOD1 in this type of experimental setting is not an aggregate, as typically observed for proteins implicated in other neuro-degenerative diseases, but the folded and fully soluble apo protein. Moreover, we demonstrate that the toxic action of apoSOD1 relies on the protein's ability to chelate Zn(2+) ions from the growth medium. The decreased cell viability that accompanies this extraction is presumably based on disturbed Zn(2+) homeostasis. Consistently, mutations that cause global unfolding of the apoSOD1 molecule or otherwise reduce its Zn(2+) affinity abolish completely the cytotoxic response. So does the addition of surplus Zn(2+). Taken together, these observations point at a case where the toxic response of cultured cells might not be related to human pathology but stems from the intrinsic limitations of a simplified cell model. There are several ways proteins can kill cultured neural cells but all of these need not to be relevant for neurodegenerative disease.
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| 4. |
- Schmidt, Henning, et al.
(författare)
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DESIREE as a new tool for interstellar ion chemistry
- 2008
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Ingår i: International Journal of Astrobiology. - 1473-5504 .- 1475-3006. ; 7:3-4, s. 205-208
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Tidskriftsartikel (refereegranskat)abstract
- A novel cryogenic electrostatic storage device consisting of two ion-beam storage rings with a common straight section for studies of interactions between oppositely charged ions at low and well-defined relative velocities is under construction at Stockholm University. Here we consider the prospect of using this new tool to measure cross-sections and rate coefficients for mutual neutralization reactions of importance in interstellar ion chemistry in general and specifically in cosmic pre-biotic ion chemistry.
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| 5. |
- Thomas, Richard D., et al.
(författare)
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The double electrostatic ion ring experiment : A unique cryogenic electrostatic storage ring for merged ion-beams studies
- 2011
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 82:6, s. 065112-
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Tidskriftsartikel (refereegranskat)abstract
- We describe the design of a novel type of storage device currently under construction at Stockholm University, Sweden, using purely electrostatic focussing and deflection elements, in which ion beams of opposite charges are confined under extreme high vacuum cryogenic conditions in separate rings and merged over a common straight section. The construction of this double electrostatic ion ring experiment uniquely allows for studies of interactions between cations and anions at low and well-defined internal temperatures and centre-of-mass collision energies down to about 10 K and 10 meV, respectively. Position sensitive multi-hit detector systems have been extensively tested and proven to work in cryogenic environments and these will be used to measure correlations between reaction products in, for example, electron-transfer processes. The technical advantages of using purely electrostatic ion storage devices over magnetic ones are many, but the most relevant are: electrostatic elements which are more compact and easier to construct; remanent fields, hysteresis, and eddy-currents, which are of concern in magnetic devices, are no longer relevant; and electrical fields required to control the orbit of the ions are not only much easier to create and control than the corresponding magnetic fields, they also set no upper mass limit on the ions that can be stored. These technical differences are a boon to new areas of fundamental experimental research, not only in atomic and molecular physics but also in the boundaries of these fields with chemistry and biology. For examples, studies of interactions with internally cold molecular ions will be particular useful for applications in astrophysics, while studies of solvated ionic clusters will be of relevance to aeronomy and biology.
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| 6. |
- Abrahamsson, Maria, et al.
(författare)
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A new strategy for the improvement of photophysical properties in ruthenium(II) polypyridyl complexes. Synthesis and photophysical and electrochemical characterization of six mononuclear ruthenium(II) bisterpyridine-type complexes
- 2005
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 44:9, s. 3215-3225
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Tidskriftsartikel (refereegranskat)abstract
- The synthesis and characterization of six ruthenium(II) bistridentate polypyridyl complexes is described. These were designed on the basis of a new approach to increase the excited-state lifetime of ruthenium(II) bisterpyridine-type complexes. By the use of a bipyridylpyridyl methane ligand in place of terpyridine, the coordination environment of the metal ion becomes nearly octahedral and the rate of deactivation via ligand-field (i.e., metal-centered) states was reduced as shown by temperature-dependent emission lifetime studies. Still, the possibility to make quasi-linear donor-ruthenium-acceptor triads is maintained in the complexes. The most promising complex shows an excited-state lifet me of tau = 15 ns in alcohol solutions at room temperature, which should be compared to a lifetime of tau = 0.25 ns for [Ru(tpy)(2)](2+). The X-ray structure of the new complex indeed shows a more octahedral geometry than that of [Ru(tpy)(2)](2+). Most importantly, the high excited-state energy was retained, and thus, so was the potential high reactivity of the excited complex, which has not been the case with previously published strategies based on bistridentate complexes.
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| 7. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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The human gut microbiome as a transporter of antibiotic resistance genes between continents
- 2015
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Ingår i: Antimicrobial Agents and Chemotherapy. - 0066-4804 .- 1098-6596. ; 59:10, s. 6551-6560
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies of antibiotic resistance dissemination by travel have, by targeting only a select number of cultivable bacterial species, omitted most of the human microbiome. Here, we used explorative shotgun metagenomic sequencing to address the abundance of >300 antibiotic resistance genes in fecal specimens from 35 Swedish students taken before and after exchange programs on the Indian peninsula or in Central Africa. All specimens were additionally cultured for extended-spectrum beta-lactamase (ESBL)-producing enterobacteria, and the isolates obtained were genome sequenced. The overall taxonomic diversity and composition of the gut microbiome remained stable before and after travel, but there was an increasing abundance of Proteobacteria in 25/35 students. The relative abundance of antibiotic resistance genes increased, most prominently for genes encoding resistance to sulfonamide (2.6-fold increase), trimethoprim (7.7-fold), and beta-lactams (2.6-fold). Importantly, the increase observed occurred without any antibiotic intake. Of 18 students visiting the Indian peninsula, 12 acquired ESBL-producing Escherichia coli, while none returning from Africa were positive. Despite deep sequencing efforts, the sensitivity of metagenomics was not sufficient to detect acquisition of the low-abundant genes responsible for the observed ESBL phenotype. In conclusion, metagenomic sequencing of the intestinal microbiome of Swedish students returning from exchange programs in Central Africa or the Indian peninsula showed increased abundance of genes encoding resistance to widely used antibiotics.
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| 8. |
- Berglund, Erik, et al.
(författare)
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Distributed Newton Method Over Graphs : Can Sharing of Second-Order Information Eliminate the Condition Number Dependence?
- 2021
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Ingår i: IEEE Signal Processing Letters. - : Institute of Electrical and Electronics Engineers (IEEE). - 1070-9908 .- 1558-2361. ; 28, s. 1180-1184
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Tidskriftsartikel (refereegranskat)abstract
- One of the main advantages of second-order methods in a centralized setting is that they are insensitive to the condition number of the objective function's Hessian. For applications such as regression analysis, this means that less pre-processing of the data is required for the algorithm to work well, as the ill-conditioning caused by highly correlated variables will not be as problematic. Similar condition number independence has not yet been established for distributed methods. In this paper, we analyze the performance of a simple distributed second-order algorithm on quadratic problems and show that its convergence depends only logarithmically on the condition number. Our empirical results indicate that the use of second-order information can yield large efficiency improvements over first-order methods, both in terms of iterations and communications, when the condition number is of the same order of magnitude as the problem dimension.
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| 9. |
- Berglund, Erik, et al.
(författare)
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Revisiting the Curvature-aided IAG : Improved Theory and Reduced Complexity
- 2023
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Ingår i: IFAC-PapersOnLine. - : Elsevier BV. - 2405-8963. ; 56:2, s. 5221-5226, s. 5221-5226
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Tidskriftsartikel (refereegranskat)abstract
- The curvature-aided IAG (CIAG) algorithm is an efficient asynchronous optimization method that accelerates IAG using a delay compensation technique. However, existing step-size rules for CIAG are conservative and hard to implement, and the Hessian computation in CIAG is often computationally expensive. To alleviate these issues, we first provide an easy-to-implement and less conservative step-size rule for CIAG. Next, we propose a modified CIAG algorithm that reduces the computational complexity by approximating the Hessian with a constant matrix. Convergence results are derived for each algorithm on both convex and strongly convex problems, and numerical experiments on logistic regression demonstrate their effectiveness in practice.
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| 10. |
- Branca, Rui M. M., et al.
(författare)
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HiRIEF LC-MSMS enables deep proteome coverage and unbiased proteogenomics
- 2014
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Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 11:1, s. 59-
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Tidskriftsartikel (refereegranskat)abstract
- We present a liquid chromatography-mass spectrometry (LC-MSMS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.
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