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

Towards Precision Dermatology: Emerging Role of Proteomic Analysis of the Skin

Background: The skin is the largest organ in the human body and serves as a multilayered protective shield from the environment as well as a sensor and thermal regulator. However, despite its importance, many details about skin structure and function at the molecular level remain incompletely understood. Recent advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics have enabled the quantification and characterization of the proteomes of a number of clinical samples, including normal and diseased skin. Summary: Here, we review the current state of the art in proteomic analysis of the skin. We provide a brief overview of the technique and skin sample collection methodologies as well as a number of recent examples to illustrate the utility of this strategy for advancing a broader understanding of the pathology of diseases as well as new therapeutic options. Key Messages: Proteomic studies of healthy skin and skin diseases can identify potential molecular biomarkers for improved diagnosis and patient stratification as well as potential targets for drug development. Collectively, efforts such as the Human Skinatlas offer improved opportunities for enhancing clinical practice and patient outcomes

Dynamic Range Majority Data Structures

Given a set $P$ of coloured points on the real line, we study the problem of answering range $\alpha$-majority (or "heavy hitter") queries on $P$. More specifically, for a query range $Q$, we want to return each colour that is assigned to more than an $\alpha$-fraction of the points contained in $Q$. We present a new data structure for answering range $\alpha$-majority queries on a dynamic set of points, where $\alpha \in (0,1)$. Our data structure uses O(n) space, supports queries in $O((\lg n) / \alpha)$ time, and updates in $O((\lg n) / \alpha)$ amortized time. If the coordinates of the points are integers, then the query time can be improved to $O(\lg n / (\alpha \lg \lg n) + (\lg(1/\alpha))/\alpha))$. For constant values of $\alpha$, this improved query time matches an existing lower bound, for any data structure with polylogarithmic update time. We also generalize our data structure to handle sets of points in d-dimensions, for $d \ge 2$, as well as dynamic arrays, in which each entry is a colour.Comment: 16 pages, Preliminary version appeared in ISAAC 201

Optimal Color Range Reporting in One Dimension

Color (or categorical) range reporting is a variant of the orthogonal range reporting problem in which every point in the input is assigned a \emph{color}. While the answer to an orthogonal point reporting query contains all points in the query range $Q$, the answer to a color reporting query contains only distinct colors of points in $Q$. In this paper we describe an O(N)-space data structure that answers one-dimensional color reporting queries in optimal $O(k+1)$ time, where $k$ is the number of colors in the answer and $N$ is the number of points in the data structure. Our result can be also dynamized and extended to the external memory model

Caregiving, Metabolic Syndrome Indicators, and 1-year Decline in Walking Speed: Results of Caregiver-SOF

BACKGROUND Chronic stress may lead to health decline through metabolic syndrome. Thus, persons in stressful caregiving situations who also have more indicators of metabolic syndrome may experience more decline than other caregivers or noncaregivers. METHODS The sample included 921 women (338 caregivers and 583 noncaregivers) from the Caregiver-Study of Osteoporotic Fractures study. Participants had home-based baseline and 1-year follow-up interviews between 1999 and 2003. At baseline, caregivers were categorized as long term (³4 years) versus short term (<4 years), and caring for someone with Alzheimer's disease/dementia or not. A metabolic risk composite score was the sum of four indicators: body mass index ³30, and diagnosis or using medications for hypertension, diabetes, or high cholesterol. Walking speed (m/second) was measured at both interviews. RESULTS Walking speed declined for the total sample (adjusted mean = −0.005 m/second, ±0.16) over an average of 1.04 years (±0.16). Overall, caregiving was not associated with decline. Increasing metabolic risk score was associated with greater decline for the total sample and long-term and dementia caregivers, but not other caregivers or noncaregivers. Metabolic risk score modified the adjusted associations between years of caregiving and dementia caregiving with walking speed decline (p values for interaction terms were 0.039 and 0.057, respectively). The biggest declines were in long-term caregivers and dementia caregivers who also had 3–4 metabolic indicators (−0.10 m/second and −0.155 m/second, respectively). CONCLUSIONS Walking speed declined the most among older women who had both stressful caregiving situations and more metabolic syndrome indicators, suggesting these caregiver subgroups may have increased risk of health decline.AG18037, AG05407, AR35582, AG05394, AR35584, and AR3558

Lower bounds for fully dynamic connectivity problems in graphs

We prove lower bounds on the complexity of maintaining fully dynamic k-edge or k-vertex connectivity in plane graphs and in (k - 1)-vertex connected graphs. We show an amortized lower bound of _0_(log n/k(log log n + log b)) per edge insertion, deletion, or query operation in the cell probe model, where b is the word size of the machine and n is the number of vertices in G. We also show an amortized lower bound of _0_(log n/(log log n + log b)) per operation for fully dynamic planarity testing in embedded graphs. These are the first lower bounds for fully dynamic connectivity problems

Parameterized searching with mismatches for run-length encoded strings

Parameterized matching between two strings occurs when it is possible to reduce the first one to the second by a renaming of the alphabet symbols. We present an algorithm for searching for parameterized occurrences of a patten in a textstring when both are given in run-length encoded form. The proposed method extends to alphabets of arbitrary yet constant size with O(| rp|×| rt|) time bounds, previously achieved only with binary alphabets. Here rp and rt denote the number of runs in the corresponding encodings for p and t. For general alphabets, the time bound obtained by the present method exhibits a polynomial dependency on the alphabet size. Such a performance is better than applying convolution to the cleartext, but leaves the problem still open of designing an alphabet independent O(| rp|×| rt|) time algorithm for this problem. © 2012 Elsevier B.V. All rights reserved

On dualization in products of forests, in

Abstract. Let P = P1 ×...×Pn be the product of n partially ordered sets, each with an acyclic precedence graph in which either the in-degree or the out-degree of each element is bounded. Given a subset A⊆P,it is shown that the set of maximal independent elements of A in P can be incrementally generated in quasi-polynomial time. We discuss some applications in data mining related to this dualization problem

Rumination and impaired prospective memory

Prospective memory (PM), remembering to remember, is crucial to everyday functioning. Understanding factors associated with PM impairments is thus important. One likely factor is rumination: a common cognitive process comprising repetitive self-focused thoughts. We investigated whether rumination is associated with impaired PM, and whether any associated impairment is exacerbated with negative stimuli. A sentence-rating task with sentences varying in valence was used with embedded PM cues in a non-clinical sample (N = 60). State rumination, two trait rumination subtypes (reflective pondering and brooding), and mood were measured in relation to PM cue detection and response times. Results showed that state rumination was associated with impaired PM cue detection and slower response times to PM cues embedded in negative sentences (not positive or neutral). Trait brooding (not reflective pondering) was associated with slower PM response times. These findings indicate that state rumination and trait brooding are associated with dissociable PM impairments

Employing BAC-reporter constructs in the sea anemone Nematostella vectensis

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Integrative and Comparative Biology 53 (2013): 832-846, doi:10.1093/icb/ict091.Changes in the expression and function of genes drive evolutionary change. Comparing how genes are regulated in different species is therefore becoming an important part of evo-devo studies. A key tool for investigating the regulation of genes is represented by Bacterial Artificial Chromosomes-reporter constructs (BAC). BACs are large insert libraries, often >>100 kb, which thus capture the genomic sequences surrounding a gene of interest, including all, or nearly all, of the elements underpinning regulation. Recombinant BACs, containing a reporter gene in place of the endogenous coding sequence of genes, can be utilized to drive the expression of reporter genes under the regulatory control of the gene of interest while still embedded within its genomic context. Systematic deletions within the BAC reporter construct can be used to identify the minimal reporter in an unbiased way, avoiding the risk of overlooking regulatory elements that may be many kilobases away from the transcription start-site. Nematostella vectensis (Edwardsiidae, Anthozoa, Cnidaria) has become an important model in regenerative biology, ecology, and especially in studies of evo-devo and gene-regulatory networks due to its interesting phylogenetic position and amenability to molecular techniques. The increasing interest in this rising model system also led to a demand for methods that can be used to study the regulation of genes in Nematostella. Here we present our progress in employing BAC reporter constructs to visualize gene-expression in Nematostella. Using a new Nematostella-specific recombination cassette, we made nine different BAC reporter constructs. Although five BAC recombinants gave variable effects, three constructs, namely Nv-bra:eGFP::L10 BAC, Nv-dpp:eGFP::L10 BAC, and Nv-grm:eGFP::L10 BAC, delivered promising results. We show that these three constructs express the reporter gene eGFP in 10.4% – 17.2% of all analyzed larvae, out of which 26.2 – 41.9% express GFP in a mosaic fashion within the expected domain. In addition to the expression within the known domains, we also observed cases of misexpression of eGFP and examples that could represent actual expression outside the described domain. Furthermore, we deep-sequenced and assembled five different BACs containing Nv-chordin, Nv-foxa, Nv-dpp, Nv-wnta, and Nvwnt1, to improve assembly around these genes. The use of BAC reporter constructs will foster cis-regulatory analyses in Nematostella and thus help to improve our understanding of the regulatory network in this cnidarian system. Ultimately, this will advance the comparison of gene-regulation across species and lead to a much better understanding of evolutionary changes and novelties.2014-08-1