Nonlinear Shear-free Radiative Collapse

We study realistic models of relativistic radiating stars undergoing gravitational collapse which have vanishing Weyl tensor components. Previous investigations are generalised by retaining the inherent nonlinearity at the boundary. We transform the boundary condition to an Abel equation of the first kind. A variety of nonlinear solutions are generated all of which can be written explicitly. Several classes of infinite solutions exist.Comment: 13 pages, To appear in Math. Meth. Appl. Sc

Comparing Differentiated Rod And Cone Transcriptomes Reveals Rax As A Controller Of A Defined Cone Gene Regulatory Program

PurposeRods and cones convert light stimuli into signaling information for brain- mediated visual perception. Specific gene mutations primarily affecting both photoreceptor (PRs) types lead to retinal dystrophies, including rod-cone (retinitis pigmentosa) and cone-rod degeneration. Rods and cones are generated from common precursor cells and their differentiation program is strongly regulated by transcription factors (TFs) that control gene networks during development transitions and in the adult to maintain their identity and function. The aim of this thesis was to investigate post-mitotic transcriptional regulation of rod- and cone-specific gene regulatory networks (GRNs). Specifically, retrieving transcription factor sets has biological relevance and may be instrumental for designing somatic gene transfer methodologies for both gene-based and regenerative therapeutic strategies. Methods We developed an Adeno-associated viral (AAV) vector-based transfer method to isolate rods and cones by fluorescence-based sorting. To isolate “pure” rod and cone populations from the same retinal samples we designed a double expression cassette (“double fluo”) encoding mCherry under the transcriptional control of the human G-protein coupled receptor Kinase 1 (GRK1) gene rods and cones-specific promoter elements of, and eGFP under the transcriptional control of rod-specific human Guanine Nucleotide Binding Protein Alpha Transducing (GNAT1) promoter elements. Porcine (Sus scrofa) retinae were injected with AAV 2/8 GRK1-mCherry_hGNAT1-eGFP, at the dose of 1x1012 genome copies (GC) per eye (n=3). The animals were sacrificed 15 days after injection to evaluate fluorescence reporter based rod and cone photoreceptor identities by histological and FACS analysis. We evaluated, on sorted populations, rods and cone specific transcriptomes by RNA sequencing (RNA- seq) using Illumina Hiseq 1500 (n=3). Moreover, after overexpression of human Retina And Anterior Neural Fold Homeobox (RAX), using subretinal injection of AAV2/8 hGNAT1-hRAX2aeGFP at a dose of 5 x 1011gc/eye we studied the GRN associated with RAX, by a second round of RNA-seq. Electroretinography (ERG) was used to correlate RAX-specific GRN with retina function. Results Histological analysis showed unambiguous expression of both mCherry and eGFP in rods, whereas cones showed exclusive expression of mCherry. Furthermore, cone arrestin (CAR) showed exclusive co-localization with the mCherry signal (cones), which was absent in red-green cells (rods). Photoreceptors specifically labeled were positive for both mCherry and eGFP (rods) or mCherry-only (cones) expressing Rhodopsin (RHO), Neural retina leucin zipper (NRL), Guanine Nucleotide Binding Protein Alpha Transducine 1 (GNAT1) (rod markers) and Short wavelength cone opsin (S-opsin), Medium wavelength cone opsin (M-opsin), Guanine Nucleotide Binding Protein Alpha Transducing 2 (GNAT2) (cone markers), respectively. RNA-seq differential expression analysis (DEA) showed 198 differential expressed genes (DEGs), of which 68 genes were up-regulated and 128 genes down-regulated in rod versus cone analysis. Furthermore, 8 TFs were found differentially expressed in rods and 8 in cones. In the cone-specific TFs set, out of 3 known TFs (Rax, Sall3 and Six6), Rax was selected for further analysis. Rax was ectopically expressed in rods (Rax-rod) to reconstruct its GRN. Differential expression analysis identified 386 DEGs, of which 224 genes (58%) were up- and 162 (42%) down regulated. Clustering for biological processes gene ontology (BP-GO), showed enrichment in action potential genes. Furthermore, ERG showed a different light response of the hRax-treated retina. In particular, a decrease of the mesopic (dark adapted) and an increase of the photopic (light adapted) responses were found. Conclusion We showed that the “double fluo” provided a robust method to isolate and cross-compare rod and cone photoreceptors in the adult porcine retina upon photoreceptor somatic gene transfer via AAV vectors. Furthermore, RNA-seq data set analysis showed that the cone and rod specific transcriptome differs quantitatively by about 200 transcripts and that 8 TFs are photoreceptor specific In addition, the data show that post-mitotic rods are able to express cone genes upon Rax ectopic expression. Furthermore the data support a role of Rax in controlling cone-specific action potential gene set

MHC-I genotype drives early immune selection of oncogenic mutations.

MHC-I exposes the intracellular contents to immune cells for surveillance of cellular health. Due to high genomic variation, individuals' immune systems differ in their ability to expose and eliminate cancer-causing mutations. These personalized immune blind spots create specific oncogenic mutation predispositions within patients and influence their prevalence across populations

An investigation of some key physico-chemical water quality parameters of an Integrated Multi-Trophic Aquaculture (IMTA) system operating recirculation methodology in the Western Cape of South Africa

Over the last few decades, Integrated Multi-Trophic Aquaculture (IMTA) in South Africa has developed from early experimental designs to large scale, commercially operating farms. This was in response to uncertainty regarding food availability for stock (primarily kelp in the case of abalone farms) and a desire to recirculate water whilst reducing the environmental footprint of the abalone farms. The growing prevalence of IMTA as a commercially viable activity has brought about a need for an expansion of the knowledge pool regarding the physico-chemical processes at work in such systems. Of particular interest to researchers are mechanisms and dynamics of nutrient transfer between components of the system and how these could be manipulated to increase efficiency and reduce running cost of farms. This work was conducted to try and quantify some of the changes in some physical and chemical characteristics of the water stream on a large-scale IMTA farm cultivating seaweed of the genus Ulva (Ulva rigida) and the locally named perlemoen abalone (Haliotis midae) on the south west coast of South Africa (Viking Abalone Farm at Buffeljagsbaai, Western Cape, South Africa) (34.7550° S, 19.6154° E). Experiment one was a three-day experiment taking place in December of 2018, there was no particular reason for the choice of month, analyses of this nature are potentially useful on any given day of any given month as although the literature contains plenty of gaps, there is no single identifiable data gap sufficient to encourage the use of particular timeframes. The sampling regime involved single sample point testing of three modular clusters each operating a different rate of water recirculation (50%, 75% and 100%) with 50% recirculation being standard farm operation, 75% and 100% tested to gauge effect of increasing recirculation, 75% tested as a potential standard farm operation to reduce load on pumps and reduce volumes of water pumped in, 100% tested in case of emergency situation which requires farm to be isolated from the inbound water stream arriving from the immediate coastal water, ambient conditions were also tested for reference and comparison. Parameters tested were those which the farmers already tested periodically to gauge changes in water quality which may effect the abalone or seaweed, though slightly different methods were used for the testing of ammonia. On the farm the standard method is the Nesler photometric test (Lovibond photometer), whereas this research was conducted using a calibrated indophenol blue spectrophotometric technique (Modified Grasshoff, 1976). Results showed no statistically significant differences (Mood's Median Test, p>0.05) between the 50% and 75% recirculation cluster for temperature, pH, Total Ammonia Nitrogen (TAN) or Free Ammonia Nitrogen NH3 (FAN). At 100% recirculation, statistically significant differences (Mood's Median Test, p0.05) occurred for temperature. At 100% recirculation, TAN and FAN increased rapidly, though the commensurate rapid and considerable decrease in pH meant the FAN increase was not as high in magnitude as it would be at 4 a normal seawater pH of around 8.2. Abalone suffered no mortalities at 100% recirculation for three days and later reports from the farmers suggested no noticeable drop in growth rate that could be attributed to this test in the months following the experiment. From the regulatory perspective, the TAN levels breached WWF guideline maximum effluent concentrations for abalone aquaculture (600µM/l) only in the 100% recirculation cluster, and only then during three of the thirteen sampling runs. The TAN concentrations in 50% and 75% recirculation treatments were far below the WWF guideline maximum effluent concentration with maximum concentrations of 7.15 µM/l in 50% and 13.46 µM/l at 75%, the increase in maximum concentration was large but not egregious and resulted from a more pronounced build-up of ammonia as residence time of water in the cluster increases at 75% recirculation. Experiment two was an intensive 24-hour sampling run; the primary aim was to test the effectiveness of the seaweed biofilter in an Integrated Multi-Trophic Aquaculture (IMTA) farm culturing perlemoen abalone and a green macroalga. Parameters tested were temperature, pH, dissolved oxygen, salinity, TAN, nitrate and nitrite as these are relevant parameters for the farmer and the necessary equipment to test them was available. Samples were stored in a freezer for this experiment due to intensity of sampling regime, and spiked standards were prepared to check shifts in concentration of TAN, nitrate and nitrite that may have resulted from the freezing and thawing processes. Spike recoveries were good in the case of TAN (87%-98%) and nitrite (92%-96%), but random and widely dispersed in the case of nitrate. As such, nitrate and nitrite were removed from the analysis as nitrite values only really held value if taken in conjunction with nitrate values. Minimal and non-useful variation in salinity observations meant that salinity was also discounted from the analysis. Temperatures varied minimally between sampling points during the experiment, though they rose in all sampling points during daytime as would be expected. pH was higher in abalone inbound and Ulva effluent water compared to the abalone effluent water. Total ammonia nitrogen percentage removal across the seaweed biofilters ranged from 65%-85% with the mean and median at 73% and 71% respectively. Free ammonia nitrogen percentage removal across the seaweed biofilters ranged from 41%-80% with the mean and median removals at 63% and 66% respectively. A regression analysis demonstrates a strong positive linear relationship between TAN removal and TAN load to the seaweed biofilter (r2= 0.90). Principal component analysis revealed a strong negative correlation between FAN removal and pH, as pH increased across the seaweed biofilters, the level of FAN removal decreased. This suggests that the perceived benefit of increasing pH in seaweed biofilters during the day-time may have some negative repercussions

Catastrophic Faults in Reconfigurable Linear Arrays of Processors

In regular architectures of identical processing elements, a widely used technique to improve the reconfigurability of the system consists of providing redundant processing elements and mechanisms of reconfiguration. In this paper we consider linear arrays of processing elements, with unidirectional bypass links of length g. We count the number of particular sets of faulty processing elements. We show that the number of catastrophic faults of g elements is equal to the (g-1)-th Catalan number. We also provide algorithms to rank and unrank all catastrophic sets of g faults. Finally, we describe a linear time algorithm that generate all such sets of faults

Optimal Colored Threshold Visual Cryptography Schemes

Visual cryptography schemes allow the encoding of a secret image into n shares which are distributed to the participants. The shares are such that only qualified subsets of participants can visually recover the secret image. Usually the secret image consist of black and white pixels. In colored threshold visual cryptography schemes the secret image is composed of pixels taken from a given set of c colors. The pixels expansion and the contrast of a scheme are two measures of the goodness of the scheme. In this paper, we study c-color (k,n)-threshold visual cryptography schemes and provide a characterization of contrast-optimal schemes. More specifically we prove that there exists a contrast-optimal scheme that is a member of a special set of schemes, which we call canonical schemes, and that satisfy strong symmetry properties. Then we use canonical schemes to provide a constructive proof of optimality, with respect to the pixel expansion, of c-color (n,n)-threshold visual cryptography schemes. Finally, we provide constructions of c-color (2,n)-threshold schemes whose pixels expansion improves on previously proposed schemes

Minimal Path Length of Trees with Known Fringe

In this paper we continue the study of the path length of trees with known fringe as initiated by [1] and [2]. We compute the path length of the minimal tree with given number of leaves N and fringe ∆ for the case ∆ ≥ N/2. This complements the result of [2] that studied the case ∆ ≤ N/2. Our methods also yields a linear time algorithm for constructing the minimal tree when ∆ ≥ N/2

A Differential Evolution Algorithm Assisted by ANFIS for Music Fingering

Music fingering is a cognitive process whose goal is to map each note of a music score to a fingering on some instrument. A fingering specifies the fingers of the hands that the player should use to play the notes. This problem arises for many instruments and it can be quite different from instrument to instrument; guitar fingering, for example, is different from piano fingering. Previous work focuses on specific instruments, in particular the guitar, and evolutionary algorithms have been used. In this paper, we propose a differential evolution (DE) algorithm designed for general music fingering (any kind of music instruments). The algorithm uses an Adaptive Neuro-Fuzzy Inference System (ANFIS) engine that learns the fingering from music already fingered. The algorithm follows the basic DE strategy but exploits also some customizations specific to the fingering problem. We have implemented the DE algorithm in Java and we have used the ANFIS network in Matlab. The two systems communicate by using the MatlabControl library. Several tests have been performed to evaluate its efficacy

The power of verification for one-parameter agents

We initiate the study of mechanisms with verification for one-parameter agents. We give an algorithmic characterization of such mechanisms and show that they are provably better than mechanisms without verification, i.e., those previously considered in the literature. These results are obtained for a number of optimization problems motivated by the Internet and recently studied in the algorithmic mechanism design literature. The characterization can be regarded as an alternative approach to existing techniques to design truthful mechanisms. The construction of such mechanisms reduces to the construction of an algorithm satisfying certain “monotonicity” conditions which, for the case of verification, are much less stringent. In other words, verification makes the construction easier and the algorithm more efficient (both computationally and in terms of approximability)