363 research outputs found
Light Spanners
A -spanner of a weighted undirected graph , is a subgraph
such that for all . The sparseness of
the spanner can be measured by its size (the number of edges) and weight (the
sum of all edge weights), both being important measures of the spanner's
quality -- in this work we focus on the latter.
Specifically, it is shown that for any parameters and ,
any weighted graph on vertices admits a
-stretch spanner of weight at most , where is the weight of a minimum
spanning tree of . Our result is obtained via a novel analysis of the
classic greedy algorithm, and improves previous work by a factor of .Comment: 10 pages, 1 figure, to appear in ICALP 201
Tight Kernel Bounds for Problems on Graphs with Small Degeneracy
In this paper we consider kernelization for problems on d-degenerate graphs,
i.e. graphs such that any subgraph contains a vertex of degree at most .
This graph class generalizes many classes of graphs for which effective
kernelization is known to exist, e.g. planar graphs, H-minor free graphs, and
H-topological-minor free graphs. We show that for several natural problems on
d-degenerate graphs the best known kernelization upper bounds are essentially
tight.Comment: Full version of ESA 201
Hardware acceleration of DNA pattern matching using analog resistive CAMs
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The remarkable growth in the size of DNA datasets has resulted in challenges in discovering DNA patterns efficiently in terms of run time and power consumption. In this paper, we propose an efficient pipelined hardware accelerator that determines the chance of the occurrence of repeat-expansion diseases using DNA pattern matching. The proposed design parallelizes the DNA pattern matching task using associative memory realized with analog content-addressable memory and implements an algorithm that returns the maximum number of consecutive occurrences of a specific pattern within a DNA sequence. We fully implement all the required hardware circuits with PTM 45-nm technology, and we evaluate the proposed architecture on a practical human DNA dataset. The results show that our design is energy-efficient and accelerates the DNA pattern matching task by more than 100× compared to the approaches described in the literature
Spanning Properties of Theta-Theta Graphs
We study the spanning properties of Theta-Theta graphs. Similar in spirit
with the Yao-Yao graphs, Theta-Theta graphs partition the space around each
vertex into a set of k cones, for some fixed integer k > 1, and select at most
one edge per cone. The difference is in the way edges are selected. Yao-Yao
graphs select an edge of minimum length, whereas Theta-Theta graphs select an
edge of minimum orthogonal projection onto the cone bisector. It has been
established that the Yao-Yao graphs with parameter k = 6k' have spanning ratio
11.67, for k' >= 6. In this paper we establish a first spanning ratio of
for Theta-Theta graphs, for the same values of . We also extend the class of
Theta-Theta spanners with parameter 6k', and establish a spanning ratio of
for k' >= 5. We surmise that these stronger results are mainly due to a
tighter analysis in this paper, rather than Theta-Theta being superior to
Yao-Yao as a spanner. We also show that the spanning ratio of Theta-Theta
graphs decreases to 4.64 as k' increases to 8. These are the first results on
the spanning properties of Theta-Theta graphs.Comment: 20 pages, 6 figures, 3 table
Ultra-tuning of nonlinear drumhead MEMS resonators by electro-thermoelastic buckling
Nonlinear micro-electro-mechanical systems (MEMS) resonators open new
opportunities in sensing and signal manipulation compared to their linear
counterparts by enabling frequency tuning and increased bandwidth. Here, we
design, fabricate and study drumhead resonators exhibiting strongly nonlinear
dynamics and develop a reduced order model (ROM) to capture their response
accurately. The resonators undergo electrostatically-mediated thermoelastic
buckling which tunes their natural frequency from 4.7 to 11.3 MHz, a factor of
2.4x tunability. Moreover, the imposed buckling switches the nonlinearity of
the resonators between purely stiffening, purely softening, and even
softening-to-stiffening. Accessing these exotic dynamics requires precise
control of the temperature and the DC electrostatic forces near the resonator's
critical-buckling point. To explain the observed tunability, we develop a
one-dimensional physics-based ROM that predicts the linear and nonlinear
response of the fundamental bending mode of these drumhead resonators. The ROM
captures the dynamic effects of the internal stresses resulting from three
sources: The residual stresses from the fabrication process, the mismatch in
thermal expansion between the constituent layers, and lastly, the applied
electrostatic forces. The ROM replicates the observed tunability of linear
(within 5.5% error) and nonlinear responses even near the states of critical
buckling. These remarkable nonlinear and large tunability of the natural
frequency are valuable features for on-chip acoustic devices in broad
applications such as signal manipulation, filtering, and MEMS waveguides
Folding and unfolding phylogenetic trees and networks
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network can be "unfolded" to obtain a MUL-tree and, conversely, a MUL-tree can in certain circumstances be "folded" to obtain a phylogenetic network that exhibits . In this paper, we study properties of the operations and in more detail. In particular, we introduce the class of stable networks, phylogenetic networks for which is isomorphic to , characterise such networks, and show that they are related to the well-known class of tree-sibling networks.We also explore how the concept of displaying a tree in a network can be related to displaying the tree in the MUL-tree . To do this, we develop a phylogenetic analogue of graph fibrations. This allows us to view as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in and reconcilingphylogenetic trees with networks
A Note on Encodings of Phylogenetic Networks of Bounded Level
Driven by the need for better models that allow one to shed light into the
question how life's diversity has evolved, phylogenetic networks have now
joined phylogenetic trees in the center of phylogenetics research. Like
phylogenetic trees, such networks canonically induce collections of
phylogenetic trees, clusters, and triplets, respectively. Thus it is not
surprising that many network approaches aim to reconstruct a phylogenetic
network from such collections. Related to the well-studied perfect phylogeny
problem, the following question is of fundamental importance in this context:
When does one of the above collections encode (i.e. uniquely describe) the
network that induces it? In this note, we present a complete answer to this
question for the special case of a level-1 (phylogenetic) network by
characterizing those level-1 networks for which an encoding in terms of one (or
equivalently all) of the above collections exists. Given that this type of
network forms the first layer of the rich hierarchy of level-k networks, k a
non-negative integer, it is natural to wonder whether our arguments could be
extended to members of that hierarchy for higher values for k. By giving
examples, we show that this is not the case
Promoting cross-regional collaboration in antimicrobial stewardship: Findings of an infectious diseases working group survey in Arab countries of the Middle East.
Abstract Background Antimicrobial resistance is a significant global issue that presents an increasing threat to patients' wellbeing. Although a global concern, the emergence of multi-drug resistant organisms is of particular significance in the Middle East. In recent years, this region has seen an alarming increase in antimicrobial resistance presenting a major challenge to physicians managing various infectious diseases. Methods A Working Group comprising experts in infectious diseases from Arab countries of Middle East assembled to review similarities and differences in antimicrobial practices and management of multi-drug resistant organisms across the region and assess the barriers to achieving cross-regional collaboration. The Working Group conducted an anonymous online survey to evaluate current practice and understanding of management of multi-drug resistant organisms across the region. Results A total of 122 physicians from Arab countries of the Middle East responded to the survey. Their responses demonstrated heterogeneity between countries in awareness of local epidemiology, management of multi-drug resistant organisms and antimicrobial stewardship practices. The Working Group recognized similarities and differences in the management of multi-drug resistant organisms across the region, and these were validated by the data collected in the survey. Overall, the similarities across the region reflect several key issues that can have an impact on the management of multi-drug resistant organisms and the prevention of antimicrobial resistance. Conclusions This paper highlights the urgency of addressing antimicrobial resistance in Arab countries of the Middle East. The Working Group identified key barriers to effective management which may guide the development of future coherent strategies to promote effective antimicrobial stewardship in the region. Here, we outline a call to action for the region, with a need to focus on training and education, capacity building, infrastructure, regional research, and regional surveillance
Unmasking the interplay between mTOR and Nox4: novel insights into the mechanism connecting diabetes and cancer
Cancer was recently annexed to diabetic complications. Furthermore, recent studies suggest that cancer can increase the risk of diabetes. Consequently, diabetes and cancer share many risk factors, but the cellular and molecular pathways correlating diabetes and colon and rectal cancer (CRC) remain far from understood. In this study, we assess the effect of hyperglycemia on cancer cell aggressiveness in human colon epithelial adenocarcinoma cells in vitro and in an experimental animal model of CRC. Our results show that Nox (NADPH oxidase enzyme) 4-induced reactive oxygen species (ROS) production is deregulated in both diabetes and CRC. This is paralleled by inactivation of the AMPK and activation of the mammalian target of rapamycin (mTOR) C1 signaling pathways, resulting in 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) accumulation, induction of DNA damage, and exacerbation of cancer cell aggressiveness, thus contributing to the genomic instability and predisposition to increased tumorigenesis in the diabetic milieu. Pharmacologic activation of AMPK, inhibition of mTORC1, or blockade of Nox4 reduce ROS production, restore the homeostatic signaling of 8-oxoguanine DNA glycosylase/8-oxodG, and lessen the progression of CRC malignancy in a diabetic milieu. Taken together, our results identify the AMPK/mTORC1/Nox4 signaling axis as a molecular switch correlating diabetes and CRC. Modulating this pathway may be a strategic target of therapeutic potential aimed at reversing or slowing the progression of CRC in patients with or without diabetes.-Mroueh, F. M., Noureldein, M., Zeidan, Y. H., Boutary, S., Irani, S. A. M., Eid, S., Haddad, M., Barakat, R., Harb, F., Costantine, J., Kanj, R., Sauleau, E.-A., Ouhtit, A., Azar, S. T., Eid, A. H., Eid, A. A. Unmasking the interplay between mTOR and Nox4: novel insights into the mechanism connecting diabetes and cancer.Scopu
Early appropriate diagnostics and treatment of MDR Gram-negative infections
The term difficult-to-treat resistance has been recently coined to identify Gram-negative bacteria exhibiting resistance to all fluoroquinolones and all β-lactam categories, including carbapenems. Such bacteria are posing serious challenges to clinicians trying to identify the best therapeutic option for any given patient. Delayed appropriate therapy has been associated with worse outcomes including increase in length of stay, increase in total in-hospital costs and ∼20% increase in the risk of in-hospital mortality. In addition, time to appropriate antibiotic therapy has been shown to be an independent predictor of 30 day mortality in patients with resistant organisms. Improving and anticipating aetiological diagnosis through optimizing not only the identification of phenotypic resistance to antibiotic classes/agents, but also the identification of specific resistance mechanisms, would have a major impact on reducing the frequency and duration of inappropriate early antibiotic therapy. In light of these considerations, the present paper reviews the increasing need for rapid diagnosis of bacterial infections and efficient laboratory workflows to confirm diagnoses and facilitate prompt de-escalation to targeted therapy, in line with antimicrobial stewardship principles. Rapid diagnostic tests currently available and future perspectives for their use are discussed. Early appropriate diagnostics and treatment of MDR Gram-negative infections require a multidisciplinary approach that includes multiple different diagnostic methods and further consensus of algorithms, protocols and guidelines to select the optimal antibiotic therapy
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