On Online Labeling with Polynomially Many Labels

In the online labeling problem with parameters n and m we are presented with a sequence of n keys from a totally ordered universe U and must assign each arriving key a label from the label set {1,2,...,m} so that the order of labels (strictly) respects the ordering on U. As new keys arrive it may be necessary to change the labels of some items; such changes may be done at any time at unit cost for each change. The goal is to minimize the total cost. An alternative formulation of this problem is the file maintenance problem, in which the items, instead of being labeled, are maintained in sorted order in an array of length m, and we pay unit cost for moving an item. For the case m=cn for constant c>1, there are known algorithms that use at most O(n log(n)^2) relabelings in total [Itai, Konheim, Rodeh, 1981], and it was shown recently that this is asymptotically optimal [Bul\'anek, Kouck\'y, Saks, 2012]. For the case of m={\Theta}(n^C) for C>1, algorithms are known that use O(n log n) relabelings. A matching lower bound was claimed in [Dietz, Seiferas, Zhang, 2004]. That proof involved two distinct steps: a lower bound for a problem they call prefix bucketing and a reduction from prefix bucketing to online labeling. The reduction seems to be incorrect, leaving a (seemingly significant) gap in the proof. In this paper we close the gap by presenting a correct reduction to prefix bucketing. Furthermore we give a simplified and improved analysis of the prefix bucketing lower bound. This improvement allows us to extend the lower bounds for online labeling to the case where the number m of labels is superpolynomial in n. In particular, for superpolynomial m we get an asymptotically optimal lower bound {\Omega}((n log n) / (log log m - log log n)).Comment: 15 pages, Presented at European Symposium on Algorithms 201

Cross-Document Pattern Matching

We study a new variant of the string matching problem called cross-document string matching, which is the problem of indexing a collection of documents to support an efficient search for a pattern in a selected document, where the pattern itself is a substring of another document. Several variants of this problem are considered, and efficient linear-space solutions are proposed with query time bounds that either do not depend at all on the pattern size or depend on it in a very limited way (doubly logarithmic). As a side result, we propose an improved solution to the weighted level ancestor problem

A symmetry invariant integral on kappa-deformed spacetime

In this note we present an approach using both constructive and Hopf algebraic methods to contribute to the not yet fully satisfactory definition of an integral on kappa-deformed spacetime. The integral presented here is based on the inner product of differential forms and it is shown that this integral is explicitly invariant under the deformed symmetry structure.Comment: 16 page

Comparative proteomics of exosomes secreted by tumoral jurkat t cells and normal human t cell blasts unravels a potential tumorigenic role for valosin-containing protein

We have previously characterized that FasL and Apo2L/TRAIL are stored in their bioactive form inside human T cell blasts in intraluminal vesicles present in multivesicular bodies. These vesicles are rapidly released to the supernatant in the form of exosomes upon re-activation of T cells. In this study we have compared for the first time proteomics of exosomes produced by normal human T cell blasts with those produced by tumoral Jurkat cells, with the objective of identify proteins associated with tumoral exosomes that could have a previously unrecognized role in malignancy. We have identified 359 and 418 proteins in exosomes from T cell blasts and Jurkat cells, respectively. Interestingly, only 145 (around a 40%) are common. The major proteins in both cases are actin and tubulin isoforms and the common interaction nodes correspond to these cytoskeleton and related proteins, as well as to ribosomal and mRNA granule proteins. We detected 14 membrane proteins that were especially enriched in exosomes from Jurkat cells as compared with T cell blasts. The most abundant of these proteins was valosin-containing protein (VCP), a membrane ATPase involved in ER homeostasis and ubiquitination. In this work, we also show that leukemic cells are more sensitive to cell death induced by the VCP inhibitor DBeQ than normal T cells. Furthermore, VCP inhibition prevents functional exosome secretion only in Jurkat cells, but not in T cell blasts. These results suggest VCP targeting as a new selective pathway to exploit in cancer treatment to prevent tumoral exosome secretion

Species composition influences soil nutrient depletion and plantphysiology in prairie agroenergy feedstocks

High-diversity mixtures of perennial tallgrass prairie vegetation could be useful biomass feed-stocks for marginal farmland in the Midwestern United States. These agroenergy crops can help meet cel-lulosic agrofuel targets while also enhancing other ecosystem services on the landscape. One proposedadvantage of high-diversity prairie biomass feedstocks is that they should become nutrient limited at aslower rate than monoculture feedstocks. In this study, we examine rates of soil nutrient depletion and thephysiology and performance of a focal species (switchgrass,Panicum virgatumL.) in four prairie agroen-ergy feedstocks with different species composition and diversity. The feedstocks in this study were a1-species switchgrass monoculture, a 5-species mixture of C4grasses, a 16-species mixture of C3and C4grasses, forbs, and legumes, and a 32-species mixture of C3and C4grasses, forbs, legumes, and sedges. Toassess feedstock effects on soil, we measured changes in soil N/P/K over afive-year period. We also per-formed a greenhouse study, in which we grew switchgrass plants infield soil conditioned by each feed-stock. To assess feedstock effects on plant function, we measured four physiological traits (photosyntheticrate, chlorophyll concentration, leafflorescence, leaf N concentration) on switchgrass plants within eachfeedstock in thefield. In the soil analysis, we found that the 5-species feedstock displayed higher rates ofsoil N/P/K depletion than other feedstocks. In the greenhouse analysis, we found that switchgrass plantsgrown in soil conditioned by the 5-species feedstock were smaller than plants grown in soil conditionedby other feedstocks. In the physiological analysis, we found that switchgrass plants in the 5-species feed-stock had lower leaf N, photosynthesis, chlorophyll concentration, and higherflorescence than switchgrassplants growing in other feedstocks. Collectively, our results show that prairie agroenergy feedstocks withdifferent species composition and diversity have different rates of soil nutrient depletion, which influencesthe physiology and performance of plants within the feedstock. These differences would ultimately impactthe ecosystem services (e.g., biomass production, need for fertilizer) that these prairie agroenergyfeedstocks provide

Compressed Subsequence Matching and Packed Tree Coloring

We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses $O(n+\frac{n\sigma}{w})$ space and $O(n+\frac{n\sigma}{w}+m\log N\log w\cdot occ)$ or $O(n+\frac{n\sigma}{w}\log w+m\log N\cdot occ)$ time. Here $w$ is the word size and $occ$ is the number of occurrences of the pattern. Our algorithm uses less space than previous algorithms and is also faster for $occ=o(\frac{n}{\log N})$ occurrences. The algorithm uses a new data structure that allows us to efficiently find the next occurrence of a given character after a given position in a compressed string. This data structure in turn is based on a new data structure for the tree color problem, where the node colors are packed in bit strings.Comment: To appear at CPM '1

Stable isotope food-web analysis and mercury biomagnification in polar bears ( Ursus maritimus )

Mercury (Hg) biomagnification occurs in many ecosystems, resulting in a greater potential for toxicological effects in higher-level trophic feeders. However, Hg transport pathways through different food-web channels are not well known, particularly in high-latitude systems affected by the atmospheric Hg deposition associated with snow and ice. Here, we report on stable carbon and nitrogen isotope ratios, and Hg concentrations, determined for 26, late 19th and early 20th century, polar bear ( Ursus maritimus ) hair specimens, collected from catalogued museum collections. These data elucidate relationships between the high-latitude marine food-web structure and Hg concentrations in polar bears. The carbon isotope compositions of polar bear hairs suggest that polar bears derive nutrition from coupled food-web channels, based in pelagic and sympagic primary producers, whereas the nitrogen isotope compositions indicate that polar bears occupy > fourth-level trophic positions. Our results show a positive correlation between polar bear hair Hg concentrations and δ 15 N. Interpretation of the stable isotope data in combination with Hg concentrations tentatively suggests that polar bears participating in predominantly pelagic food webs exhibit higher mercury concentrations than polar bears participating in predominantly sympagic food webs.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73930/1/j.1751-8369.2009.00114.x.pd

Effect of time to diagnostic testing for breast, cervical, and colorectal cancer screening abnormalities on screening efficacy: A modeling study

Background: Patients who receive an abnormal cancer screening result require follow-up for diagnostic testing, but the time to follow-up varies across patients and practices. Methods: We used a simulation study to estimate the change in lifetime screening benefits when time to follow-up for breast, cervical, and colorectal cancers was increased. Estimates were based on four independently developed microsimulation models that each simulated the life course of adults eligible for breast (women ages 50–74 years), cervical (women ages 21–65 years), or colorectal (adults ages 50–75 years) cancer screening. We assumed screening based on biennial mammography for breast cancer, triennial Papanicolaou testing for cervical cancer, and annual fecal immunochemical testing for colorectal cancer. For each cancer type, we simulated diagnostic testing immediately and at 3, 6, and 12 months after an abnormal screening exam. Results: We found declines in screening benefit with longer times to diagnostic testing, particularly for breast cancer screening. Compared to immediate diagnostic testing, testing at 3 months resulted in reduced screening benefit, with fewer undiscounted life years gained per 1,000 screened (breast: 17.3%, cervical: 0.8%, colorectal: 2.0% and 2.7%, from two colorectal cancer models), fewer cancers prevented (cervical: 1.4% fewer, colorectal: 0.5% and 1.7% fewer, respectively), and, for breast and colorectal cancer, a less favorable stage distribution. Conclusions: Longer times to diagnostic testing after an abnormal screening test can decrease screening effectiveness, but the impact varies substantially by cancer type. Impact: Understanding the impact of time to diagnostic testing on screening effectiveness can help inform quality improvement efforts. Cancer Epidemiol Biomarkers Prev; 27(2); 158–64. 2017 AACR