Augmenting graphs to minimize the diameter

We study the problem of augmenting a weighted graph by inserting edges of bounded total cost while minimizing the diameter of the augmented graph. Our main result is an FPT 4-approximation algorithm for the problem.Comment: 15 pages, 3 figure

Diameter Minimization by Shortcutting with Degree Constraints

We consider the problem of adding a fixed number of new edges to an undirected graph in order to minimize the diameter of the augmented graph, and under the constraint that the number of edges added for each vertex is bounded by an integer. The problem is motivated by network-design applications, where we want to minimize the worst case communication in the network without excessively increasing the degree of any single vertex, so as to avoid additional overload. We present three algorithms for this task, each with their own merits. The special case of a matching augmentation, when every vertex can be incident to at most one new edge, is of particular interest, for which we show an inapproximability result, and provide bounds on the smallest achievable diameter when these edges are added to a path. Finally, we empirically evaluate and compare our algorithms on several real-life networks of varying types.Comment: A shorter version of this work has been accepted at the IEEE ICDM 2022 conferenc

Inelastic Neutron Scattering of Hydrogen in Palladium Studied by Semiclassical Dynamics

Inelastic neutron scattering (INS) spectra of hydrogen in face-centered cubic palladium have been calculated considering nuclear quantum effects (NQE) at finite temperatures. The calculations were performed using semiclassical Brownian chain molecular dynamics (MD) [Shiga, J. Comput. Chem. 43, 1864 (2022)] and artificial neural network potentials with an accuracy of generalized gradient approximation of density functional theory. The calculated spectra are in good agreement with experimental spectra with respect to the peak positions and intensities corresponding to the fundamental tone and the first overtone of the vibrational excitation of hydrogen atoms. These results differ significantly from those of classical MD, indicating that NQE plays an essential role in the correct estimation of the INS spectrum. Importantly, the NQE acts as a blue-shift of the INS spectrum for hydrogen in the octahedral site, due to strong anharmonic vibrations of hydrogen on the potential surface with even symmetry. The calculated peak shifts associated with Pd lattice distortion were also in agreement with experimental results

Immunophenotypic characterization of normal blood CD56+lo versus CD56+hi NK‐cell subsets and its impact on the understanding of their tissue distribution and functional properties

Blood Cells Mol Dis. 2001 Jul-Aug;27(4):731-43. Immunophenotypic characterization of normal blood CD56+lo versus CD56+hi NK-cell subsets and its impact on the understanding of their tissue distribution and functional properties. Lima M, Teixeira MA, Queirós ML, Leite M, Santos AH, Justiça B, Orfão A. Service of Clinical Hematology, Unit of Cytometry, Hospital Geral de Santo António, Porto, Portugal. [email protected] Abstract In the present study we have compared the immunophenotypic characteristics of the CD56+lo and CD56+hi NK-cell subsets in a group of normal healthy adults. Our results show that CD56+hi NK-cells display greater light-scatter properties than CD56+lo NK-cells at the same time they have higher levels of CD25 and CD122 IL-2 chains, together with a higher reactivity for HLA-DR and CD45RO and lower levels of CD45RA, supporting that, as opposed to the majority of the CD56+lo population, CD56+hi NK-cells might correspond to a subset of activated circulating NK-lymphocytes. Higher expression of the CD2 and CD7 costimulatory molecules found for the CD56+hi NK-cells would support their greater ability to respond to various stimuli. In addition, CD56+hi NK-cells expressed higher levels of several adhesion molecules such as CD2, CD11c, CD44, CD56, and CD62L compared to CD56+lo NK-cells, supporting a particular ability of these cells to migrate from blood to tissues and/or a potential advantage to form conjugates with target cells. Interestingly, CD56+lo and CD56+hi NK-cells showed a different pattern of expression of killer receptors that might determine different activation requirements for each of these NK-cell subsets. For instance, absence or low levels of CD16 expression might explain the lower antibody-dependent cytotoxicity activity of CD56+hi NK-cells. On the other hand, the virtual absence of expression of the CD158a and NKB1 immunoglobulin-like and the greater reactivity for the CD94 lectin-like killer receptors on CD56+hi in comparison to CD56+lo NK-cells might determine different MHC-class I specificities for both NK-cell subsets, a possibility that deserves further studies to be confirmed. PMID: 11778657 [PubMed - indexed for MEDLINE

WeBCMD: A cross-platform interface for the BCMD modelling framework

Multimodal monitoring of the brain generates a great quantity of data, providing the potential for great insight into both healthy and injured cerebral dynamics. In particular, near-infrared spectroscopy can be used to measure various physiological variables of interest, such as haemoglobin oxygenation and the redox state of cytochrome-c-oxidase, alongside systemic signals, such as blood pressure. Interpreting these measurements is a complex endeavour, and much work has been done to develop mathematical models that can help to provide understanding of the underlying processes that contribute to the overall dynamics. BCMD is a software framework that was developed to run such models. However, obtaining, installing and running this software is no simple task. Here we present WeBCMD, an online environment that attempts to make the process simpler and much more accessible. By leveraging modern web technologies, an extensible and cross-platform package has been created that can also be accessed remotely from the cloud. WeBCMD is available as a Docker image and an online service

In-silico investigation of the neonatal brain physiology using a systems biology approach: modelling birth asphyxia and neuroprotective strategies

Hypoxic ischaemic encephelopathy (HIE), often resulting from intrapartum hypoxic-ischemic injury, is a significant cause of death and morbidity before, during and after birth. In order to identify and monitor HIE, clinicians use non-invasive techniques including magnetic resonance spectroscopy (MRS) and near-infrared spectroscopy (NIRS). However, interpretation of these signals, particularly to determine the effectiveness of treatment and the severity of injury, is a challenging and difficult task. This thesis describes an attempt to use a systems biology approach to better understand the mechanisms behind HIE and its outcomes, using mathematical and computational techniques to analyse multimodal data, including broadband near-infrared spectroscopy (bNIRS). These models incorporate submodels of cerebral blood flow, oxygen transport and metabolism into a single cohesive model that attempts to simulate the observed measurements of tissue oxygenation and metabolism. The scope of this work is to both develop a set of computational tools that can be used to better understand existing systems biology models of the brain and to develop a new model which is able to incorporate the effects of therapeutic hypothermia, a common treatment for HIE, on the underlying physiology and its dynamics. The work begins by redeveloping the existing framework used for running and analysing systems biology models as used previously, before going on to develop a Bayesian framework which allows a better and more comprehensive interpretation of the results. This framework is then used to analyse three new models that incorporate the impact of therapeutic hypothermia on the piglet brain. The model determined to be most effective is then applied to clinical data from neonates that experience spontaneous desaturations in blood oxygen whilst undergoing hypothermic treatment. In all cases data from subjects with both mild and severe injuries are compared to determine if separate parameter spaces (and therefore physiological mechanisms) can be identified for each

Augmenting Graphs to Minimize the Radius

We study the problem of augmenting a metric graph by adding k edges while minimizing the radius of the augmented graph. We give a simple 3-approximation algorithm and show that there is no polynomial-time (5/3-?)-approximation algorithm, for any ? > 0, unless P = NP. We also give two exact algorithms for the special case when the input graph is a tree, one of which is generalized to handle metric graphs with bounded treewidth