Derandomized Construction of Combinatorial Batch Codes

Combinatorial Batch Codes (CBCs), replication-based variant of Batch Codes introduced by Ishai et al. in STOC 2004, abstracts the following data distribution problem: $n$ data items are to be replicated among $m$ servers in such a way that any $k$ of the $n$ data items can be retrieved by reading at most one item from each server with the total amount of storage over $m$ servers restricted to $N$. Given parameters $m, c,$ and $k$, where $c$ and $k$ are constants, one of the challenging problems is to construct $c$-uniform CBCs (CBCs where each data item is replicated among exactly $c$ servers) which maximizes the value of $n$. In this work, we present explicit construction of $c$-uniform CBCs with $\Omega(m^{c-1+{1 \over k}})$ data items. The construction has the property that the servers are almost regular, i.e., number of data items stored in each server is in the range $[{nc \over m}-\sqrt{{n\over 2}\ln (4m)}, {nc \over m}+\sqrt{{n \over 2}\ln (4m)}]$. The construction is obtained through better analysis and derandomization of the randomized construction presented by Ishai et al. Analysis reveals almost regularity of the servers, an aspect that so far has not been addressed in the literature. The derandomization leads to explicit construction for a wide range of values of $c$ (for given $m$ and $k$) where no other explicit construction with similar parameters, i.e., with $n = \Omega(m^{c-1+{1 \over k}})$, is known. Finally, we discuss possibility of parallel derandomization of the construction

Linear response functions for a vibrational configuration interaction state

Linear response functions are implemented for a vibrational configuration interaction state allowing accurate analytical calculations of pure vibrational contributions to dynamical polarizabilities. Sample calculations are presented for the pure vibrational contributions to the polarizabilities of water and formaldehyde. We discuss the convergence of the results with respect to various details of the vibrational wave function description as well as the potential and property surfaces. We also analyze the frequency dependence of the linear response function and the effect of accounting phenomenologically for the finite lifetime of the excited vibrational states. Finally, we compare the analytical response approach to a sum-over-states approac

Mutagenic and inhibitory compounds produced by fungi affect detrimentally diagnosis and phylogenetic analyses.

Microorganisms manufacture prolifically bioactive compounds. For example, fungi produce antibiotics and mycotoxins. However, many are difficult to identify and classify. Methods which rely on nucleic acid (DNA/RNA) are increasingly being used for this purpose where strains are grown in liquid or agar culture and often subjected to polymerase chain reaction (PCR) analyses. It has not been considered that self-produced mutagenic and inhibitory secondary metabolites (SM) affect DNA analysis of the target fungi. The most obvious mycotoxins and fungi to consider in this regard are aflatoxins (AFB) and Aspergillus, as AFB are the most mutagenic natural compounds. Many other fungi and SM are relevant and fungi act as a model for bacteria and plants. In fact, fungi repair damaged nucleic acid (NA) and are capable of removing toxins by employing transporter proteins. Nevertheless, these could be inhibited by bioactive metabolites. Mutagenic effects may involve inhibition of DNA stabilising enzymes. In addition, PCR is subject to false negative results. Samples of fungi with the genes of interest (e.g. a mycotoxin) may be categorized as negative and safe as a consequence. Internal amplification controls (IACs) will ameliorate the situation and need to become mandatory. These are conventionally NA that posses a sequence which will provide a PCR product (a) using the same primers employed for the target gene and (b) that will not coincide on the gel with the product of the target gene. Inhibitors and mutagens in cultures need to be minimized, and SM are an obvious source. This is a crucial issue in developing diagnostic and phylogenetic methods. The conclusions are (a) previous reports are compromised because IACs have not been employed in PCR and (b) mutagens and inhibitors may affect the very stability essential for NA analyses used in diagnostics and phylogenetics

Biofilms from a Brazilian water distribution system include filamentous fungi

Filamentous fungi in drinking water can block water pipes, can cause organoleptic biodeterioration, and are a source of pathogens. There are increasing reports of the involvement of the organisms in biofilms. This present study describes a sampling device that can be inserted directly into pipes within water distribution systems, allowing biofilm formation in situ. Calcofluor White M2R staining and fluorescent in situ hybridization with morphological analyses using epifluorescent microscopy were used to analyse biofilms for filamentous fungi, permitting direct observation of the fungi. DAPI (4=,6-diamidino-2- phenylindole) was applied to detect bacteria. Filamentous fungi were detected in biofilms after 6 months on coupons exposed to raw water, decanted water and at the entrance of the water distribution system. Algae, yeast, and bacteria were also observed. The role of filamentous fungi requires further investigations.The authors acknowledge Companhia Pernambucana de Saneamento (COMPESA) for its support in making the work by H.M.B. Oliveira possible. V.M. de Siqueira is supported by the grant SFRH/BD/43719/2008 from Fundacao para a Ciencia e Tecnologia (FCT), Portugal

Aflatoxin B1 in chilies from the Punjab region, Pakistan

The occurrence of aflatoxin B1 (AFB1) in chilies from Pakistan was determined by using HPLC in work undertaken in Pakistan.Whole (n=22) and powdered (n=22) chilies were analyzed. Sixteen (73.0%) and 19 (86.4%) samples of whole and ground chilies, respectively, were contaminated. The mean concentration in powdered chilies (32.20 μg/kg) was higher statistically than in whole chilies (24.69 μg/kg). Concentrations ranged from 0.00 to 89.56 μg/ kg for powdered chilies, compared with 0.00–96.3 μg/kg for whole chilies. The limits of detection and quantification were 0.05 μg/kg and 0.53 μg/kg, respectively. The concentrations were high in general and greater than the statutory limit set by the European Union. There is considerable scope for improvements in chili production in Pakistan.Higher Education Commission, PakistanFundação para a Ciência e a Tecnologia (FCT