Mutually Uncorrelated Primers for DNA-Based Data Storage

We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and for synchronization of communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized and cyclic codes.Comment: 14 pages, 3 figures, 1 Table. arXiv admin note: text overlap with arXiv:1601.0817

Set-Codes with Small Intersections and Small Discrepancies

We are concerned with the problem of designing large families of subsets over a common labeled ground set that have small pairwise intersections and the property that the maximum discrepancy of the label values within each of the sets is less than or equal to one. Our results, based on transversal designs, factorizations of packings and Latin rectangles, show that by jointly constructing the sets and labeling scheme, one can achieve optimal family sizes for many parameter choices. Probabilistic arguments akin to those used for pseudorandom generators lead to significantly suboptimal results when compared to the proposed combinatorial methods. The design problem considered is motivated by applications in molecular data storage and theoretical computer science

Bestrophin 1 is indispensable for volume regulation in human retinal pigment epithelium cells

In response to cell swelling, volume-regulated anion channels (VRACs) participate in a process known as regulatory volume decrease (RVD). Only recently, first insight into the molecular identity of mammalian VRACs was obtained by the discovery of the leucine-rich repeats containing 8A (LRRC8A) gene. Here, we show that bestrophin 1 (BEST1) but not LRRC8A is crucial for volume regulation in human retinal pigment epithelium (RPE) cells. Whole-cell patch-clamp recordings in RPE derived from human-induced pluripotent stem cells (hiPSC) exhibit an outwardly rectifying chloride current with characteristic functional properties of VRACs. This current is severely reduced in hiPSC-RPE cells derived from macular dystrophy patients with pathologic BEST1 mutations. Disruption of the orthologous mouse gene (Best1−/−) does not result in obvious retinal pathology but leads to a severe subfertility phenotype in agreement with minor endogenous expression of Best1 in murine RPE but highly abundant expression in mouse testis. Sperm from Best1−/− mice showed reduced motility and abnormal sperm morphology, indicating an inability in RVD. Together, our data suggest that the molecular identity of VRACs is more complex—that is, instead of a single ubiquitous channel, VRACs could be formed by cell type- or tissue-specific subunit composition. Our findings provide the basis to further examine VRAC diversity in normal and diseased cell physiology, which is key to exploring novel therapeutic approaches in VRAC-associated pathologies

Covariation Among Vowel Height Effects on Acoustic Measures

Covariation among vowel height effects on vowel intrinsic fundamental frequency (IF0), voice onset time (VOT), and voiceless interval duration (VID) is analyzed to assess the plausibility of a common physiological mechanism underlying variation in these measures. Phrases spoken by 20 young adults, containing words composed of initial voiceless stops or /s/ and high or low vowels, were produced in habitual and voluntarily increased F0 conditions. High vowels were associated with increased IF0 and longer VIDs. VOT and VID exhibited significant covariation with IF0 only for males at habitua

Immobilization of Co-60 and Sr-90 Ions Using Red Mud from Aluminum Industry

The removal of Co-60 and Sr-90 from the aqueous phase was tested using red mud - the fine grained residue from bauxite ore processing. This industrial waste represents a mixture of numerous minerals, mainly oxides and hydroxides of Fe, Al, Si, and Ti. Experiments were conducted as a function of contact time, pH, and pollutant concentrations. Kinetic data were well fitted with a pseudo-second order equation. The calculated rate constants and initial sorption rates indicated faster sorption of Sr2+ ions. Removal of both cations rapidly increased with the initial pH increase from 2.5 to 3.5. With the further increase of pH, Co2+ sorption was nearly constant (98%-100%), whereas Sr2+ removal remained at the same level to initial pH similar to 8 and gradually increased to 100% at pH 12. Equilibrium sorption data followed the Langmuir model, with the maximum sorption capacities of 0.52 mmol/g for Co2+ and 0.31 mmol/g for Sr2+. Sorbed cations exhibited high stability in distilled water. Desorption of Co2+ was also negligible in the presence of the competing Ca2+ cation, while 42%-25% of Sr2+ ions were desorbed depending on the previously sorbed amount. The results indicate that red mud is of potential significance as Co2+ and Sr2+ immobilization agent due to its high efficiency, abundance, and low-cost