Differential neuroproteomic and systems biology analysis of spinal cord injury

Acute spinal cord injury (SCI) is a devastating condition with many consequences and no known effective treatment. Although it is quite easy to diagnose traumatic SCI, the assessment of injury severity and projection of disease progression or recovery are often challenging, as no consensus biomarkers have been clearly identified. Here rats were subjected to experimental moderate or severe thoracic SCI. At 24h and 7d postinjury, spinal cord segment caudal to injury center versus sham samples was harvested and subjected to differential proteomic analysis. Cationic/anionic-exchange chromatography, followed by 1D polyacrylamide gel electrophoresis, was used to reduce protein complexity. A reverse phase liquid chromatography-tandem mass spectrometry proteomic platform was then utilized to identify proteome changes associated with SCI. Twenty-two and 22 proteins were up-regulated at 24 h and 7 day after SCI, respectively; whereas 19 and 16 proteins are down-regulated at 24 h and 7 day after SCI, respectively, when compared with sham control. A subset of 12 proteins were identified as candidate SCI biomarkers - TF (Transferrin), FASN (Fatty acid synthase), NME1 (Nucleoside diphosphate kinase 1), STMN1 (Stathmin 1), EEF2 (Eukaryotic translation elongation factor 2), CTSD (Cathepsin D), ANXA1 (Annexin A1), ANXA2 (Annexin A2), PGM1 (Phosphoglucomutase 1), PEA15 (Phosphoprotein enriched in astrocytes 15), GOT2 (Glutamic-oxaloacetic transaminase 2), and TPI-1 (Triosephosphate isomerase 1), data are available via ProteomeXchange with identifier PXD003473. In addition, Transferrin, Cathepsin D, and TPI-1 and PEA15 were further verified in rat spinal cord tissue and/or CSF samples after SCI and in human CSF samples from moderate/severe SCI patients. Lastly, a systems biology approach was utilized to determine the critical biochemical pathways and interactome in the pathogenesis of SCI. Thus, SCI candidate biomarkers identified can be used to correlate with disease progression or to identify potential SCI therapeutic targets

A heuristic for the container loading problem: A tertiary-tree-based dynamic space decomposition approach

Increasing fuel costs, post-911 security concerns, and economic globalization provide a strong incentive for container carriers to use available container space more efficiently, thereby minimizing the number of container trips and reducing socio-economic vulnerability. A heuristic algorithm based on a tertiary tree model is proposed to handle the container loading problem (CLP) with weakly heterogeneous boxes. A dynamic space decomposition method based on the tertiary tree structure is developed to partition the remaining container space after a block of homogeneous rectangular boxes is loaded into a container. This decomposition approach, together with an optimal-fitting sequencing and an inner-right-corner-occupying placement rule, permits a holistic loading strategy to pack a container. Comparative studies with existing algorithms and an illustrative example demonstrate the efficiency of this algorithm

Probing Cosmology with Weak Lensing Minkowski Functionals

In this paper, we show that Minkowski Functionals (MFs) of weak gravitational lensing (WL) convergence maps contain significant non-Gaussian, cosmology-dependent information. To do this, we use a large suite of cosmological ray-tracing N-body simulations to create mock WL convergence maps, and study the cosmological information content of MFs derived from these maps. Our suite consists of 80 independent 512^3 N-body runs, covering seven different cosmologies, varying three cosmological parameters Omega_m, w, and sigma_8 one at a time, around a fiducial LambdaCDM model. In each cosmology, we use ray-tracing to create a thousand pseudo-independent 12 deg^2 convergence maps, and use these in a Monte Carlo procedure to estimate the joint confidence contours on the above three parameters. We include redshift tomography at three different source redshifts z_s=1, 1.5, 2, explore five different smoothing scales theta_G=1, 2, 3, 5, 10 arcmin, and explicitly compare and combine the MFs with the WL power spectrum. We find that the MFs capture a substantial amount of information from non-Gaussian features of convergence maps, i.e. beyond the power spectrum. The MFs are particularly well suited to break degeneracies and to constrain the dark energy equation of state parameter w (by a factor of ~ three better than from the power spectrum alone). The non-Gaussian information derives partly from the one-point function of the convergence (through V_0, the "area" MF), and partly through non-linear spatial information (through combining different smoothing scales for V_0, and through V_1 and V_2, the boundary length and genus MFs, respectively). In contrast to the power spectrum, the best constraints from the MFs are obtained only when multiple smoothing scales are combined.Comment: 19 pages, 9 figures, 5 table

Projective Ribbon Permutation Statistics: a Remnant of non-Abelian Braiding in Higher Dimensions

In a recent paper, Teo and Kane proposed a 3D model in which the defects support Majorana fermion zero modes. They argued that exchanging and twisting these defects would implement a set R of unitary transformations on the zero mode Hilbert space which is a 'ghostly' recollection of the action of the braid group on Ising anyons in 2D. In this paper, we find the group T_{2n} which governs the statistics of these defects by analyzing the topology of the space K_{2n} of configurations of 2n defects in a slowly spatially-varying gapped free fermion Hamiltonian: T_{2n}\equiv {\pi_1}(K_{2n})$. We find that the group T_{2n}= Z \times T^r_{2n}, where the 'ribbon permutation group' T^r_{2n} is a mild enhancement of the permutation group S_{2n}: T^r_{2n} \equiv \Z_2 \times E((Z_2)^{2n}\rtimes S_{2n}). Here, E((Z_2)^{2n}\rtimes S_{2n}) is the 'even part' of (Z_2)^{2n} \rtimes S_{2n}, namely those elements for which the total parity of the element in (Z_2)^{2n} added to the parity of the permutation is even. Surprisingly, R is only a projective representation of T_{2n}, a possibility proposed by Wilczek. Thus, Teo and Kane's defects realize `Projective Ribbon Permutation Statistics', which we show to be consistent with locality. We extend this phenomenon to other dimensions, co-dimensions, and symmetry classes. Since it is an essential input for our calculation, we review the topological classification of gapped free fermion systems and its relation to Bott periodicity.Comment: Missing figures added. Fixed some typos. Added a paragraph to the conclusio

Traumatic Brain Injury in the Elderly: Is it as Bad as we Think?

Traumatic brain injury in elderly patients is a neglected global disease burden. The main cause is fall, followed by motor vehicle accidents. This review article summarizes different aspects of geriatric traumatic brain injury, including epidemiology, pathology, and effects of comorbidities and pre-injury medications such as antiplatelets and anticoagulants. Functional outcome with or without surgical intervention, cognitive outcome, and psychiatric complications are discussed. Animal models are also reviewed in attempt to explain the relationship of aging and outcome, together with advances in stem cell research. Though elderly people in general did fare worse after traumatic brain injury, certain “younger elderly” people, aged 65–75 years, could have a comparable outcome to younger adults after minor to moderate head injury