Synchronization Strings: Channel Simulations and Interactive Coding for Insertions and Deletions

We present many new results related to reliable (interactive) communication over insertion-deletion channels. Synchronization errors, such as insertions and deletions, strictly generalize the usual symbol corruption errors and are much harder to protect against. We show how to hide the complications of synchronization errors in many applications by introducing very general channel simulations which efficiently transform an insertion-deletion channel into a regular symbol corruption channel with an error rate larger by a constant factor and a slightly smaller alphabet. We utilize and generalize synchronization string based methods which were recently introduced as a tool to design essentially optimal error correcting codes for insertion-deletion channels. Our channel simulations depend on the fact that, at the cost of increasing the error rate by a constant factor, synchronization strings can be decoded in a streaming manner that preserves linearity of time. Interestingly, we provide a lower bound showing that this constant factor cannot be improved to 1+epsilon, in contrast to what is achievable for error correcting codes. Our channel simulations drastically and cleanly generalize the applicability of synchronization strings. We provide new interactive coding schemes which simulate any interactive two-party protocol over an insertion-deletion channel. Our results improve over the interactive coding schemes of Braverman et al. [TransInf `17] and Sherstov and Wu [FOCS `17] which achieve a small constant rate and require exponential time computations with respect to computational and communication complexities. We provide the first computationally efficient interactive coding schemes for synchronization errors, the first coding scheme with a rate approaching one for small noise rates, and also the first coding scheme that works over arbitrarily small alphabet sizes. We also show tight connections between synchronization strings and edit-distance tree codes which allow us to transfer results from tree codes directly to edit-distance tree codes. Finally, using on our channel simulations, we provide an explicit low-rate binary insertion-deletion code that improves over the state-of-the-art codes by Guruswami and Wang [TransInf `17] in terms of rate-distance trade-off

The Most Temperature-Adapted Corals Have an Achilles\u27 Heel

The corals of the Persian/Arabian Gulf are better adapted to temperature fluctuations than elsewhere in the Indo-Pacific. The Gulf is an extreme marine environment displaying the highest known summer water temperatures for any reef area. The small and shallow sea can be considered a good analogue to future conditions for the rest of the world’s oceans under global warming. The fact that corals can persist in such a demanding environment indicates that they have been able to acclimatize and selectively adapt to elevated temperature. The implication being that colonies elsewhere may be able to follow suit. This in turn provides hope that corals may, given sufficient time, similarly adapt to survive even in an impoverished form, under conditions of acidification-driven lowering of CaCO3 saturation state, a further consequence of raised atmospheric CO2. This paper demonstrates, however, that the uniquely adapted corals of the Gulf may, within the next three centuries, be threatened by a chronic habitat shortage brought about by the dissolution of the lithified seabed on which they rely for colonisation. This will occur due to modifications in the chemical composition of the Gulf waters due to climate change

Synthesis, Characterization and Solution Chemistry of trans-Indazoliumtetrachlorobis(Indazole)Ruthenate(III), a New Anticancer Ruthenium Complex. IR, UV, NMR, HPLC Investigations and Antitumor Activity. Crystal Structures of trans-1-Methyl-Indazoliumtetrachlorobis-(1-Methylindazole)Ruthenate(III) and its Hydrolysis Product trans-Monoaquatrichlorobis-(1-Methylindazole)-Ruthenate(III)

Besides intensive studies into the synthesis of the complex trans-Hlnd[RuCl4(ind)2] (Ind = indazole) 1, which differs remarkably from the usual method for the complexes of the HL[RuCl4L2] - type, competitive products and hydrolysis of this species are described. Stability and pseudo-first-order rate constant under physiological conditions of complex 1 in comparison with the analogous imidazole complex trans-Hlm[RuCl4im2] (Im = imidaZole) ICR were examined by means of HPLC, UV and conductivity measurements (Kobs.(1) = 1.55 × 10-4 s-1; Kobs.(ICR) = 9.10 × 10-4 s-1). An attempt was made to elucidate the bonding conditions in 1 by studying the reactions of Ru(lll) and the two N-methyl isomers of indazole. It can be expected that bonding in the unsubstituted ligand should occur via the N2 nitrogen. The molecular structures of the complex trans-H(1-Melnd)[RuCl4(1-Melnd)2] × 1H2O (1-Melnd = 1-methylindazole) 6 and its hydrolysis product in aqueous solution [RuCl4(H2O)(1-Melnd)2] 7 were determined crystallographically. After anisotropic refinement of F values by least squares, R is 0.053 for 6 and 0.059 for 7. Both complexes crystallize with four molecules in a unit cell of monoclinic symmetry. The space group is P2.1/n for 6 with cell dimensions a = 10.511Å, b = 13.87Å, c = 19.93Å, and β = 98.17° and C2/c for 7 with a = 19.90Å, b = 10.94Å, c = 8.490Å and β = 96.74 ° The fact that the aqua species 7 could be isolated after dissolving 6 in a water/acetone solution confirmed the theory of many Ru(lll) complexes being initially transformed, under physiological conditions, into aqua complexes in a first and often rate-determining hydrolysis step. Compounds 1 and ICR are potent antitumor agents which exhibit activity against a variety of tumor cells and experimental tumor models in animals, including autochthonous colorectal tumors. Clinical studies with 1 are in preparation

Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins

Background: The deep-sea hypersaline anoxic basins (DHABs) of the Mediterranean (water depth similar to 3500 m) are some of the most extreme oceanic habitats known. Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB haloclines and brines, loriciferans are the only metazoan reported to inhabit the anoxic DHAB brines. Our goal was to further investigate metazoan communities in DHAB haloclines and brines. Results: We report observations from sediments of three DHAB (Urania, Discovery, L'Atalante) haloclines, comparing these to observations from sediments underlying normoxic waters of typical Mediterranean salinity. Due to technical difficulties, sampling of the brines was not possible. Morphotype analysis indicates nematodes are the most abundant taxon; crustaceans, loriciferans and bryozoans were also noted. Among nematodes, Daptonema was the most abundant genus; three morphotypes were noted with a degree of endemicity. The majority of rRNA sequences were from planktonic taxa, suggesting that at least some individual metazoans were preserved and inactive. Nematode abundance data, in some cases determined from direct counts of sediments incubated in situ with CellTracker (TM) Green, was patchy but generally indicates the highest abundances in either normoxic control samples or in upper halocline samples; nematodes were absent or very rare in lower halocline samples. Ultrastructural analysis indicates the nematodes in L'Atalante normoxic control sediments were fit, while specimens from L'Atalante upper halocline were healthy or had only recently died and those from the lower halocline had no identifiable organelles. Loriciferans, which were only rarely encountered, were found in both normoxic control samples as well as in Discovery and L'Atalante haloclines. It is not clear how a metazoan taxon could remain viable under this wide range of conditions. Conclusions: We document a community of living nematodes in normoxic, normal saline deep-sea Mediterranean sediments and in the upper halocline portions of the DHABs. Occurrences of nematodes in mid-halocline and lower halocline samples did not provide compelling evidence of a living community in those zones. The possibility of a viable metazoan community in brines of DHABs is not supported by our data at this time

Acute and Sub-Acute Toxicity of the Polycyclic Aromatic Hydrocarbon 1-Methylnaphthalene to the Shallow-Water Coral Porites divaricata: Application of a Novel Exposure Protocol

Previous research evaluating hydrocarbon toxicity to corals and coral reefs has generally focused on community-level effects, and results often are not comparable between studies because of variability in hydrocarbon exposure characterization and evaluation of coral health and mortality during exposure. Toxicity of the polycyclic aromatic hydrocarbon 1-methylnaphthalene to the coral Porites divaricata was assessed in a constant exposure toxicity test utilizing a novel toxicity testing protocol uniquely applicable to shallow-water corals, which considered multiple assessment metrics and evaluated the potential for post-exposure mortality and/or recovery. Acute and subacute effects (gross morphological changes, photosynthetic efficiency, mortality, and histologic cellular changes) were evaluated during pre-exposure (4 wk), exposure (48 h), and post-exposure recovery (4 wk) periods. Coral condition scores were used to determine a 48-h median effective concentration of 7442 μg/L. Significant physical and histological changes resulted from exposure to 640 μg/L and 5427 μg/L 1-methylnaphthalene, with a 1-d to 3-d delay in photosynthetic efficiency effects (ΔF/Fm). Pigmented granular amoebocyte area was found to be a potentially useful sublethal endpoint for this species. Coral mortality was used to estimate a 48-h median lethal concentration of 12 123 μg/L

Short-Term Toxicity of 1-Methylnaphthalene to Americamysis bahia and 5 Deep-Sea Crustaceans

There are few studies that have evaluated hydrocarbon toxicity to vertically migrating deep-sea micronekton. Crustaceans were collected alive using a 9-m2 Tucker trawl with a thermally insulated cod end and returned to the laboratory in 10 °C seawater. Toxicity of the polycyclic aromatic hydrocarbon 1-methylnaphthalene to Americamysis bahia, Janicella spinacauda, Systellaspis debilis, Sergestes sp., Sergia sp., and a euphausiid species was assessed in a constant exposure toxicity test utilizing a novel passive dosing toxicity testing protocol. The endpoint of the median lethal concentration tests was mortality, and the results revealed high sensitivity of the deep-sea micronekton compared with other species for which these data are available. Threshold concentrations were also used to calculate critical target lipid body burdens using the target lipid model

Molluscan mega-hemocyanin: an ancient oxygen carrier tuned by a ~550 kDa polypeptide

<p>Abstract</p> <p>Background</p> <p>The allosteric respiratory protein hemocyanin occurs in gastropods as tubular di-, tri- and multimers of a 35 × 18 nm, ring-like decamer with a collar complex at one opening. The decamer comprises five subunit dimers. The subunit, a 400 kDa polypeptide, is a concatenation of eight paralogous functional units. Their exact topology within the quaternary structure has recently been solved by 3D electron microscopy, providing a molecular model of an entire didecamer (two conjoined decamers). Here we study keyhole limpet hemocyanin (KLH2) tridecamers to unravel the exact association mode of the third decamer. Moreover, we introduce and describe a more complex type of hemocyanin tridecamer discovered in fresh/brackish-water cerithioid snails (<it>Leptoxis</it>, <it>Melanoides</it>, <it>Terebralia</it>).</p> <p>Results</p> <p>The "typical" KLH2 tridecamer is partially hollow, whereas the cerithioid tridecamer is almost completely filled with material; it was therefore termed "mega-hemocyanin". In both types, the staggering angle between adjoining decamers is 36°. The cerithioid tridecamer comprises two typical decamers based on the canonical 400 kDa subunit, flanking a central "mega-decamer" composed of ten unique ~550 kDa subunits. The additional ~150 kDa per subunit substantially enlarge the internal collar complex. Preliminary oxygen binding measurements indicate a moderate hemocyanin oxygen affinity in <it>Leptoxis </it>(p50 ~9 mmHg), and a very high affinity in <it>Melanoides </it>(~3 mmHg) and <it>Terebralia </it>(~2 mmHg). Species-specific and individual variation in the proportions of the two subunit types was also observed, leading to differences in the oligomeric states found in the hemolymph.</p> <p>Conclusions</p> <p>In cerithioid hemocyanin tridecamers ("mega-hemocyanin") the collar complex of the central decamer is substantially enlarged and modified. The preliminary O₂binding curves indicate that there are species-specific functional differences in the cerithioid mega-hemocyanins which might reflect different physiological tolerances of these gill-breathing animals. The observed differential expression of the two subunit types of mega-hemocyanin might allow individual respiratory acclimatization. We hypothesize that mega-hemocyanin is a key character supporting the adaptive radiation and invasive capacity of cerithioid snails.</p

Seasonal, interannual and spatial patterns of bacterial taxonomy and genetic functions in the Arctic Ocean

Bacterial diversity and function across time and space in the Arctic Ocean, including the Polar Night, remain virtually unknown. In the FRAM Observatory, we study microbial composition and genetic potential in ice-covered and ice-free regions of the Fram Strait, the major gateway between the Arctic and Atlantic Oceans. A continuous amplicon time-series, derived from moored autonomous samplers, revealed marked taxonomic and functional seasonality among bacterial communities in the ice-free West Spitsbergen Current, with distinct succession of taxonomic modules. PacBio long-read metagenomes showed peaks of proteorhodopsin- and DMSP-utilizing genes in late summer, whereas winter mixing of the water column covaried with ammonia- and nitrite-metabolizing bacterial genes. In the ice-covered East Greenland Current, taxonomic and functional diversity varied less with seasons, with prominent influence of ice cover and polar water masses. For instance, high-ice conditions coincided with higher number of peptidoglycan-utilizing genes. Continuous observations were contextualized with five-year amplicon data from summertime samples collected across Fram Strait, integrating seasonal and interannual patterns of bacterial community dynamics. This fundamental baseline information helps understanding ecological and biogeochemical processes in a marine region severely affected by climate change

The Grizzly, January 28, 2010

Ursinus Students Celebrate MLK Jr. Day • Recyclemania: Ursinus to Get in the Game • Bisphenol-A: Focus of Ursinus Professor\u27s Research • Ursinus is Top 100 • Making the Landscape at the Berman • Spring Dancing Brings Fundraising and Events • Bouncing Souls Celebrate • Opinion: Liberal Arts Education in the Real World • UC Women\u27s Swimming Makes Big Splash in Conference Poolhttps://digitalcommons.ursinus.edu/grizzlynews/1803/thumbnail.jp

Tickborne Encephalitis in Naturally Exposed Monkey (Macaca sylvanus)

We describe tickborne encephalitis (TBE) in a monkey (Macaca sylvanus) after natural exposure in an area at risk for TBE. TBE virus was present in the brain and could be identified as closely related to the European subtype, strain Neudoerfl