Scale-Invariant Random Spatial Networks

Real-world road networks have an approximate scale-invariance property; can one devise mathematical models of random networks whose distributions are {\em exactly} invariant under Euclidean scaling? This requires working in the continuum plane. We introduce an axiomatization of a class of processes we call {\em scale-invariant random spatial networks}, whose primitives are routes between each pair of points in the plane. We prove that one concrete model, based on minimum-time routes in a binary hierarchy of roads with different speed limits, satisfies the axioms, and note informally that two other constructions (based on Poisson line processes and on dynamic proximity graphs) are expected also to satisfy the axioms. We initiate study of structure theory and summary statistics for general processes in this class.Comment: 56 page

Transit Node Routing Reconsidered

Transit Node Routing (TNR) is a fast and exact distance oracle for road networks. We show several new results for TNR. First, we give a surprisingly simple implementation fully based on Contraction Hierarchies that speeds up preprocessing by an order of magnitude approaching the time for just finding a CH (which alone has two orders of magnitude larger query time). We also develop a very effective purely graph theoretical locality filter without any compromise in query times. Finally, we show that a specialization to the online many-to-one (or one-to-many) shortest path further speeds up query time by an order of magnitude. This variant even has better query time than the fastest known previous methods which need much more space.Comment: 19 pages, submitted to SEA'201

{EpiExplorer}: {Live} Exploration and Global Analysis of Large Epigenomic Datasets

ABSTRACT: Epigenome mapping consortia are generating resources of tremendous value for studying epigenetic regulation. To maximize their utility and impact, new tools are needed that facilitate interactive analysis of epigenome datasets. Here we describe EpiExplorer, a web tool for exploring genome and epigenome data on a genomic scale. We demonstrate EpiExplorer's utility by describing a hypothesis-generating analysis of DNA hydroxymethylation in relation to public reference maps of the human epigenome. All EpiExplorer analyses are performed dynamically within seconds, using an efficient and versatile text indexing scheme that we introduce to bioinformatics. EpiExplorer is available at http://epiexplorer.mpi-inf.mpg.de

Sex-biased gene expression is repeatedly masculinized in asexual females.

Males and females feature strikingly different phenotypes, despite sharing most of their genome. A resolution of this apparent paradox is through differential gene expression, whereby genes are expressed at different levels in each sex. This resolution, however, is likely to be incomplete, leading to conflict between males and females over the optimal expression of genes. Here we test the hypothesis that gene expression in females is constrained from evolving to its optimum level due to sexually antagonistic selection on males, by examining changes in sex-biased gene expression in five obligate asexual species of stick insect, which do not produce males. We predicted that the transcriptome of asexual females would be feminized as asexual females do not experience any sexual conflict. Contrary to our prediction we find that asexual females feature masculinized gene expression, and hypothesise that this is due to shifts in female optimal gene expression levels following the suppression of sex

Morpho-molecular assessment of Acetabularia jalakanyakae Sp. Nov. (Dasycladales, Chlorophyta) - a new species from Andaman and Nicobar Islands, India

701-708Acetabularia (Dasycladales) is an extant genus of a single-celled green alga. There are four species of this genus reported from India, three reported from Andaman and Nicobar Islands. For this study, Acetabularia isolate was collected from a rocky intertidal habitat in the Andaman and Nicobar Islands. Light microscopy and Scanning Electron Microscopy were used for the morphological characterization. The distinct traits of caps of the thalli were prioritized because, traditionally, species delimitations in Acetabularia mainly were based on cap morphology. Our isolate showed morphological similarity with Acetabularia crenulata. However, the number of hairs in the inner ring of lobes of caps and the stalk length were observed to be different from A. crenulata and other closely related species. The phylogenetic tree constructed for partial 18S rDNA using the Maximum Likelihood (ML) method revealed the evolutionary affinity of this new species with Acetabularia dentata. Based on morphological and molecular synapomorphy, a new species of Acetabularia, Acetabularia jalakanyakae is formally proposed herein, and the further implications of this species discovery are discussed

Morpho-molecular assessment of Acetabularia jalakanyakae Sp. Nov. (Dasycladales, Chlorophyta) - a new species from Andaman and Nicobar Islands, India

Acetabularia (Dasycladales) is an extant genus of a single-celled green alga. There are four species of this genus reported from India, three reported from Andaman and Nicobar Islands. For this study, Acetabularia isolate was collected from a rocky intertidal habitat in the Andaman and Nicobar Islands. Light microscopy and Scanning Electron Microscopy were used for the morphological characterization. The distinct traits of caps of the thalli were prioritized because, traditionally, species delimitations in Acetabularia mainly were based on cap morphology. Our isolate showed morphological similarity with Acetabularia crenulata. However, the number of hairs in the inner ring of lobes of caps and the stalk length were observed to be different from A. crenulata and other closely related species. The phylogenetic tree constructed for partial 18S rDNA using the Maximum Likelihood (ML) method revealed the evolutionary affinity of this new species with Acetabularia dentata. Based on morphological and molecular synapomorphy, a new species of Acetabularia, Acetabularia jalakanyakae is formally proposed herein, and the further implications of this species discovery are discussed

Silk sericin-polylactide protein-polymer conjugates as biodegradable amphiphilic material and its application in drug release systems

Silk sericin (SS) is a byproduct of silk production. In order to transform it into value-added products, sericin can be used as a biodegradable and pH-responsive building block in drug delivery materials. To this end, amphiphilic substances were synthesized via the conjugation of hydrophobic polylactide (PLA) to the hydrophilic sericin using a bis-aryl hydrazone linker. PLA was esterified with a terephthalaldehydic acid to obtain aromatic aldehyde terminated PLA (PLA-CHO). In addition, lysine groups of SS were modified with the linker succinimidyl-6-hydrazino-nicotinamide (S-HyNic). Then, both macromolecules were mixed to form the amphipilic protein-polymer conjugate in buffer-DMF solution. The formation of bis-aryl hydrazone linkages was confirmed and quantified by UV-vis spectroscopy. SS-PLA conjugates self-assembled in water into spherical multicompartment micelles with a diameter of around 100 nm. Doxorubicin (DOX) was selected as a model drug for studying the pH-dependent drug release from SS-PLA nanoparticles. The release rate of the encapsulated drug was slower than that of the free drug and dependent on pH, faster at pH 5.0, and it resulted in a larger cumulative amount of drug released than at physiological pH of 7.4. The SS-PLA conjugate of high PLA branches showed smaller particle size and lower loading capacity than the one with low PLA branches. Both SS-PLA conjugates had negligible cytotoxicity, whereas after loading with DOX, the SS-PLA micelles were highly toxic for the human liver carcinoma immortalized cell line HepG2. Therefore, the SS-based biodegradable amphiphilic material showed great potential as a drug carrier for cancer therapy

Exploring the Immunoproteome for Ovarian Cancer Biomarker Discovery

Most scientific efforts towards early detection of ovarian cancer are commonly focused on the discovery of tumour-associated antigens (TAA). Autologous antibodies against TAA, however, may serve as more sensitive diagnostic markers. They circulate in the blood before TAA and are usually more abundant than the TAAs themselves as a result of amplification through the humoral immune response. Accumulating evidence also suggests that a humoral response already exists during malignant transformation when aberrant gene expression is translated into premalignant cellular changes. This article reviews the current knowledge about autoantibodies against TAA in ovarian cancer and presents current immunoproteomic approaches for their detection

Pelvic mass associated with raised CA 125 for benign condition: a case report

<p>Abstract</p> <p>Background</p> <p>Raised CA 125 with associated pelvic mass is highly suggestive of ovarian malignancy, but there are various other benign conditions that can be associated with pelvic mass and a raised CA 125.</p> <p>Case presentation</p> <p>We present a case of 19 year old, Caucasian British woman who presented initially with sudden onset right sided iliac fossa pain and on imaging was found to have 9.8 × 4.5 cm complex cystic mass in right adnexa with a raised CA 125 of 657, which was initially thought to be highly suspicious of cancer but was subsequently found to be due to pelvic inflammatory disease on histology.</p> <p>Conclusion</p> <p>This case highlights the fact that though a pelvic mass with raised CA 125 is highly suggestive of malignancy, pelvic inflammatory disease should always be considered as a differential diagnosis especially in a young patient and a thorough sexual history and screening for pelvic infection should always be carried out in these patients.</p