Gauging Correct Relative Rankings For Similarity Search

© 2015 ACM.One of the important tasks in link analysis is to quantify the similarity between two objects based on hyperlink structure. SimRank is an attractive similarity measure of this type. Existing work mainly focuses on absolute SimRank scores, and often harnesses an iterative paradigm to compute them. While these iterative scores converge to exact ones with the increasing number of iterations, it is still notoriously difficult to determine how well the relative orders of these iterative scores can be preserved for a given iteration. In this paper, we propose efficient ranking criteria that can secure correct relative orders of node-pairs with respect to SimRank scores when they are computed in an iterative fashion. Moreover, we show the superiority of our criteria in harvesting top-K SimRank scores and bucket orders from a full ranking list. Finally, viable empirical studies verify the usefulness of our techniques for SimRank top-K ranking and bucket ordering

A New Technique for Reachability of States in Concatenation Automata

We present a new technique for demonstrating the reachability of states in deterministic finite automata representing the concatenation of two languages. Such demonstrations are a necessary step in establishing the state complexity of the concatenation of two languages, and thus in establishing the state complexity of concatenation as an operation. Typically, ad-hoc induction arguments are used to show particular states are reachable in concatenation automata. We prove some results that seem to capture the essence of many of these induction arguments. Using these results, reachability proofs in concatenation automata can often be done more simply and without using induction directly.Comment: 23 pages, 1 table. Added missing affiliation/funding informatio

Pseudomonas aeruginosa bacteremia in patients undergoing liver transplantation: An emerging problem

In our institution, Pseudomonas aeruginosa bacteremia appeared to occur with increasing frequency in patients undergoing liver transplantation. We thus conducted a prospective study to define risk factors and outcome in these patients. Over a 19-month period 6% of liver transplants were followed by Pseudomonas bacteremia. The mean age was 46 years (range, 24 to 67 years). The interval between transplantation and onset of bacteremia was 3 to 372 days (mean, 80). The incidence of Pseudomonas bacteremia in liver transplants was three times that of other transplants (heart, lung, kidney). Ninety one percent of infections were nosocomial. Polymicrobial bacteremia occurred in 30% of episodes. The portal of entry was respiratory in 30%, abdominal in 35%, and biliary in 13%. Four patients had recurrent Pseudomonas bacteremia: liver abscess (1), biliary obstruction (2), subhepatic abscess (1). Survival at 14 days was 70%. Survival rates were significantly lower for patients with hypotension, on mechanical ventilators, and increasing severity of illness (p < 0.05). Survival was higher when bacteremia occurred within the first 30 days after transplantation compared to after 30 days. A large number (43.4%) of Pseudomonas bacteremias occurred after transplant surgery or biliary tract manipulation, while the patient was receiving a prophylactic regimen of cefotaxime and ampicillin. P. aeruginosa is an important pathogen in the liver transplant recipient; prevention may be possible for a subgroup of patients with the use of prophylactic antibiotics with activity against P. aeruginosa

Complexity of Left-Ideal, Suffix-Closed and Suffix-Free Regular Languages

A language $L$ over an alphabet $\Sigma$ is suffix-convex if, for any words $x,y,z\in\Sigma^*$, whenever $z$ and $xyz$ are in $L$, then so is $yz$. Suffix-convex languages include three special cases: left-ideal, suffix-closed, and suffix-free languages. We examine complexity properties of these three special classes of suffix-convex regular languages. In particular, we study the quotient/state complexity of boolean operations, product (concatenation), star, and reversal on these languages, as well as the size of their syntactic semigroups, and the quotient complexity of their atoms.Comment: 20 pages, 11 figures, 1 table. arXiv admin note: text overlap with arXiv:1605.0669

Most Complex Non-Returning Regular Languages

A regular language $L$ is non-returning if in the minimal deterministic finite automaton accepting it there are no transitions into the initial state. Eom, Han and Jir\'askov\'a derived upper bounds on the state complexity of boolean operations and Kleene star, and proved that these bounds are tight using two different binary witnesses. They derived upper bounds for concatenation and reversal using three different ternary witnesses. These five witnesses use a total of six different transformations. We show that for each $n\ge 4$ there exists a ternary witness of state complexity $n$ that meets the bound for reversal and that at least three letters are needed to meet this bound. Moreover, the restrictions of this witness to binary alphabets meet the bounds for product, star, and boolean operations. We also derive tight upper bounds on the state complexity of binary operations that take arguments with different alphabets. We prove that the maximal syntactic semigroup of a non-returning language has $(n-1)^n$ elements and requires at least $\binom{n}{2}$ generators. We find the maximal state complexities of atoms of non-returning languages. Finally, we show that there exists a most complex non-returning language that meets the bounds for all these complexity measures.Comment: 22 pages, 6 figure

An acidic fibroblast growth factor protein generated by alternate splicing acts like an antagonist.

Polymerase chain reaction amplification of cDNA for acidic fibroblast growth factor in several lines of cultured human cells revealed two forms of mRNA. The novel smaller mRNA lacks the entire second coding exon of the acidic fibroblast growth factor gene, whereas the previously identified mRNA consists of three coding exons. The truncated variant of acidic fibroblast growth factor (aFGF') is only 60 amino acids long with an apparent molecular mass of 6.7 kD on sodium dodecyl sulfate gels in contrast to 18 kD for the full-length acidic fibroblast growth factor. aFGF' elicits only minimal fibroblast proliferation and antagonizes the effects of acidic fibroblast growth factor when added exogenously to or when coexpressed with aFGF in BALB/c/3T3 fibroblasts. Thus, the truncated variant of acidic fibroblast growth factor may provide fibroblasts with a unique mechanism for endogenous regulation of their responses to acidic fibroblast growth factor

Nucleic acid aptamers against aggrecanases: a novel method for Degenerative Disc Disease Therapy

Track: Pharmaceutical BiotechnologyPoster PresentationAptamers are short, single-stranded oligonucleotides, which bind to their targets through 3D conformational complementarity. Aptamers are frequently called 'chemical antibodies' because of their high specificity and affinity. More than 20 aptamers for the treatment of various diseases are evaluated in clinical trials. Role of intervertebral disc is to absorb shock and transmit load, allowing the spine to bend and move. Disc degeneration may cause serious low back pain and affect daily life. Aggrecanases ADAMTS-4 and -5 are critical proteins involved in the development of degenerative disc disease (DDD) and osteoarthritis. They have been used as targets for inhibitor selection against DDD in recent studies both in vitro and in silico. Small molecules targeted on catalytic domain of aggrecanases have been developed but have broad inhibitory activity which may cause serious side effects. Nucleic acid aptamers can potentially solve this problem. Recent studies on aggrecanases have also been restrained by the low expression level and low solubility of the catalytic domain. Our studies have developed new ways to express, refold and purify human ADAMTS-4 and ADAMTS-5. ADAMTS-4 and ADAMTS-5 catalytic domain incorporating with disintegrin domain and thrombospondin motif are expressed and purified from E. coli with high yield for the first time. Specific aptamers will then be tailor selected against each aggrecanase through a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). Selected aptamers will then be characterized and evaluated as a foundation for further DDD therapeutic development.published_or_final_versio

High quality SimRank-based similarity search

SimRank is an influential link-based similarity measure that has been used in many fields of Web search and sociometry. The best-of-breed method by Kusumoto et al. [7], however, does not always deliver high-quality results, since it fails to accurately obtain its diagonal correction matrix D. Besides, SimRank is also limited by an unwanted“connectivity trait”: increasing the number of paths between nodes a and b often incurs a decrease in score s(a, b). The best-known solution, SimRank++ [1], cannot resolve this problem, since a revised score will be zero if a and b have no common in-neighbors. In this paper, we consider high-quality similarity search. Our scheme, SR#, is efficient and semantically meaningful: (1) We first formulate the exact D, and devise a “varied-D” method to accurately compute SimRank in linear memory. Moreover, by grouping computation, we also reduce the time of [7] from quadratic to linear in the number of iterations. (2) We design a “kernel-based”model to improve the quality of SimRank, and circumvent the “connectivity trait” issue. (3) We give mathematical insights to the semantic difference between SimRank and its variant, and correct an argument in [7]: “if D is replaced by a scaled identity matrix (1−γ)I, top-K rankings will not be affected much”. The experiments confirm that SR# can accurately extract high-quality scores, and is much faster than the state-of-the-art competitors

Optical Gas Sensors Using Terahertz Waves in the Layered Media

Terahertz (THz) wave propagation in the layered media is presented based on the waveguide and artificial-material configurations to sense the gas molecules. The single dielectric layer with a cylindrical conformation works as a pipe waveguide in the wave frequency of 0.1–1 THz. For a long-distance propagation over 10 cm of the pipe, resonant modes are characterized from the transmission power dips. The pipe-waveguide resonator works for a THz refractive-index sensor when the resonance frequency is monitored to sense vapor molecules inside the pipe core. Besides of the waveguide configuration, a multilayer microporous polymer structure (MPS) is considered an artificial material to transmit THz waves for sensing gaseous molecules. The MPS is not only transparent to THz waves but also enhances the detection resolution of THz absorption for the vapor molecules. The porous structure provides a large hydrophilic surface area and numerous micropores to adsorb or fill vapors, thereby leading to greatly enhanced wave-analyte interaction with an apparent THz signal change. Different concentrations of toxic methanol adulterated in alcoholic aqueous solutions are thus identified in their vapor phases by using the MPS-based THz sensor

Combinatorial Pharyngeal Taste Coding for Feeding Avoidance in Adult Drosophila.

Taste drives appropriate food preference and intake. In Drosophila, taste neurons are housed in both external and internal organs, but the latter have been relatively underexplored. Here, we report that Poxn mutants with a minimal taste system of pharyngeal neurons can avoid many aversive tastants, including bitter compounds, acid, and salt, suggesting that pharyngeal taste is sufficient for rejecting intake of aversive compounds. Optogenetic activation of selected pharyngeal bitter neurons during feeding events elicits changes in feeding parameters that can suppress intake. Functional dissection experiments indicate that multiple classes of pharyngeal neurons are involved in achieving behavioral avoidance, by virtue of being inhibited or activated by aversive tastants. Tracing second-order pharyngeal circuits reveals two main relay centers for processing pharyngeal taste inputs. Together, our results suggest that the pharynx can control the ingestion of harmful compounds by integrating taste input from different classes of pharyngeal neurons