Evidence for low homology between mammalian leptin and chicken leptin-like gene sequences

Leptin is a 167-amino acid hormone produced chiefly by adipocytes. It plays an important role in regulation of food intake, energy metabolism and reproduction in mammals. However, a leptin gene homologue has yet to be cloned in a non-mammalian vertebrate. The aim of this thesis was to establish the existence of a leptin gene homologue in the domestic chicken (Gallus gallus) genome, and to determine the degree of sequence identity with mammalian leptin genes, and with a putative chicken leptin sequence published during the course of the thesis work. An initial attempt was made to clone the chicken leptin gene by heterologous RT-PCR using degenerate primers to conserved regions of mammalian leptin sequences. However, no leptin-like products were amplified from chicken adipose tissue and liver cDNAs,or from genomic DNA. RTPCR was also used to test the existence of a published chicken leptin cDNA sequence that shares 95% identity with mouse leptin at the nucleotide level. When PCR primers identical to the mouse and published chicken leptin sequences were used, no PCR product sharing close similarity to the mouse leptin sequence were generated from any chicken templates, whereas amplification of mouse leptin leptin sequences was consistently obtained from control mouse templates. Following the failure to clone the chicken leptin by RT-PCR, evidence for the existence of a mammalian-like leptin in the chicken genome was sought by Southern analysis. Southern blots under low stringency hybridization and washing conditions revealed hybridization of a mouse leptin probe to chicken genomic DNA. With high stringency washing, the chicken signal disappeared, while those from sheep and mouse genomic DNA remained. Screening of a chicken adipose tissue cDNA library, and chicken genomic DNA and cosmid libraries with the same mouse probe failed to isolate a chicken leptin homologue. Collectively, these results indicate that if a chicken leptin homologue exists in the chicken genome, it is likely to be of low homology to mammalian leptin sequences. The results do not support the existence of a mouse-like leptin sequence in the chicken genome, an assertion supported by theoretical analysis of the molecular evolution of leptin based on the rate of synonymous substitution. This analysis indicated that the probability that the chicken and mouse leptin sequences are 95% identical, is less than one in a million

Derandomized Graph Product Results using the Low Degree Long Code

In this paper, we address the question of whether the recent derandomization results obtained by the use of the low-degree long code can be extended to other product settings. We consider two settings: (1) the graph product results of Alon, Dinur, Friedgut and Sudakov [GAFA, 2004] and (2) the "majority is stablest" type of result obtained by Dinur, Mossel and Regev [SICOMP, 2009] and Dinur and Shinkar [In Proc. APPROX, 2010] while studying the hardness of approximate graph coloring. In our first result, we show that there exists a considerably smaller subgraph of $K_3^{\otimes R}$ which exhibits the following property (shown for $K_3^{\otimes R}$ by Alon et al.): independent sets close in size to the maximum independent set are well approximated by dictators. The "majority is stablest" type of result of Dinur et al. and Dinur and Shinkar shows that if there exist two sets of vertices $A$ and $B$ in $K_3^{\otimes R}$ with very few edges with one endpoint in $A$ and another in $B$, then it must be the case that the two sets $A$ and $B$ share a single influential coordinate. In our second result, we show that a similar "majority is stablest" statement holds good for a considerably smaller subgraph of $K_3^{\otimes R}$. Furthermore using this result, we give a more efficient reduction from Unique Games to the graph coloring problem, leading to improved hardness of approximation results for coloring

Streaming algorithms for language recognition problems

We study the complexity of the following problems in the streaming model. Membership testing for \DLIN We show that every language in \DLIN\ can be recognised by a randomized one-pass $O(\log n)$ space algorithm with inverse polynomial one-sided error, and by a deterministic p-pass $O(n/p)$ space algorithm. We show that these algorithms are optimal. Membership testing for \LL$(k)$ For languages generated by \LL$(k)$ grammars with a bound of $r$ on the number of nonterminals at any stage in the left-most derivation, we show that membership can be tested by a randomized one-pass $O(r\log n)$ space algorithm with inverse polynomial (in $n$) one-sided error. Membership testing for \DCFL We show that randomized algorithms as efficient as the ones described above for \DLIN\ and \LL(k) (which are subclasses of \DCFL) cannot exist for all of \DCFL: there is a language in \VPL\ (a subclass of \DCFL) for which any randomized p-pass algorithm with error bounded by $\epsilon < 1/2$ must use $\Omega(n/p)$ space. Degree sequence problem We study the problem of determining, given a sequence $d_1, d_2,..., d_n$ and a graph $G$, whether the degree sequence of $G$ is precisely $d_1, d_2,..., d_n$. We give a randomized one-pass $O(\log n)$ space algorithm with inverse polynomial one-sided error probability. We show that our algorithms are optimal. Our randomized algorithms are based on the recent work of Magniez et al. \cite{MMN09}; our lower bounds are obtained by considering related communication complexity problems

On Fortification of Projection Games

A recent result of Moshkovitz \cite{Moshkovitz14} presented an ingenious method to provide a completely elementary proof of the Parallel Repetition Theorem for certain projection games via a construction called fortification. However, the construction used in \cite{Moshkovitz14} to fortify arbitrary label cover instances using an arbitrary extractor is insufficient to prove parallel repetition. In this paper, we provide a fix by using a stronger graph that we call fortifiers. Fortifiers are graphs that have both $\ell_1$ and $\ell_2$ guarantees on induced distributions from large subsets. We then show that an expander with sufficient spectral gap, or a bi-regular extractor with stronger parameters (the latter is also the construction used in an independent update \cite{Moshkovitz15} of \cite{Moshkovitz14} with an alternate argument), is a good fortifier. We also show that using a fortifier (in particular $\ell_2$ guarantees) is necessary for obtaining the robustness required for fortification.Comment: 19 page

Semi-Supervised Recurrent Neural Network for Adverse Drug Reaction Mention Extraction

Social media is an useful platform to share health-related information due to its vast reach. This makes it a good candidate for public-health monitoring tasks, specifically for pharmacovigilance. We study the problem of extraction of Adverse-Drug-Reaction (ADR) mentions from social media, particularly from twitter. Medical information extraction from social media is challenging, mainly due to short and highly information nature of text, as compared to more technical and formal medical reports. Current methods in ADR mention extraction relies on supervised learning methods, which suffers from labeled data scarcity problem. The State-of-the-art method uses deep neural networks, specifically a class of Recurrent Neural Network (RNN) which are Long-Short-Term-Memory networks (LSTMs) \cite{hochreiter1997long}. Deep neural networks, due to their large number of free parameters relies heavily on large annotated corpora for learning the end task. But in real-world, it is hard to get large labeled data, mainly due to heavy cost associated with manual annotation. Towards this end, we propose a novel semi-supervised learning based RNN model, which can leverage unlabeled data also present in abundance on social media. Through experiments we demonstrate the effectiveness of our method, achieving state-of-the-art performance in ADR mention extraction.Comment: Accepted at DTMBIO workshop, CIKM 2017. To appear in BMC Bioinformatics. Pls cite that versio

Super-polylogarithmic hypergraph coloring hardness via low-degree long codes

We prove improved inapproximability results for hypergraph coloring using the low-degree polynomial code (aka, the 'short code' of Barak et. al. [FOCS 2012]) and the techniques proposed by Dinur and Guruswami [FOCS 2013] to incorporate this code for inapproximability results. In particular, we prove quasi-NP-hardness of the following problems on $n$-vertex hyper-graphs: * Coloring a 2-colorable 8-uniform hypergraph with $2^{2^{\Omega(\sqrt{\log\log n})}}$ colors. * Coloring a 4-colorable 4-uniform hypergraph with $2^{2^{\Omega(\sqrt{\log\log n})}}$ colors. * Coloring a 3-colorable 3-uniform hypergraph with $(\log n)^{\Omega(1/\log\log\log n)}$ colors. In each of these cases, the hardness results obtained are (at least) exponentially stronger than what was previously known for the respective cases. In fact, prior to this result, polylog n colors was the strongest quantitative bound on the number of colors ruled out by inapproximability results for O(1)-colorable hypergraphs. The fundamental bottleneck in obtaining coloring inapproximability results using the low- degree long code was a multipartite structural restriction in the PCP construction of Dinur-Guruswami. We are able to get around this restriction by simulating the multipartite structure implicitly by querying just one partition (albeit requiring 8 queries), which yields our result for 2-colorable 8-uniform hypergraphs. The result for 4-colorable 4-uniform hypergraphs is obtained via a 'query doubling' method. For 3-colorable 3-uniform hypergraphs, we exploit the ternary domain to design a test with an additive (as opposed to multiplicative) noise function, and analyze its efficacy in killing high weight Fourier coefficients via the pseudorandom properties of an associated quadratic form.Comment: 25 page

A Characterization of Hard-to-cover CSPs

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