AUTOMORPHIC LEFSCHETZ PROPERTIES FOR NONCOMPACT ARITHMETIC MANIFOLDS

We prove the injectivity of Oda-type restriction maps for the cohomology of noncompact congruence quotients of symmetric spaces. This includes results for restriction between (1) congruence real hyperbolic manifolds, (2) congruence complex hyperbolic manifolds, and (3) orthogonal Shimura varieties. These results generalize results for compact congruence quotients by Bergeron and Clozel [Quelques conséquences des travaux d’Arthur pour le spectre et la topologie des variétés hyperboliques, Invent. Math.192 (2013), 505–532] and Venkataramana [Cohomology of compact locally symmetric spaces, Compos. Math.125 (2001), 221–253]. The proofs combine techniques of mixed Hodge theory and methods involving automorphic forms.

Finding Overlapping Rmaps via Gaussian Mixture Model Clustering

Optical mapping is a method for creating high resolution restriction maps of an entire genome. Optical mapping has been largely automated, and first produces single molecule restriction maps, called Rmaps, which are assembled to generate genome wide optical maps. Since the location and orientation of each Rmap is unknown, the first problem in the analysis of this data is finding related Rmaps, i.e., pairs of Rmaps that share the same orientation and have significant overlap in their genomic location. Although heuristics for identifying related Rmaps exist, they all require quantization of the data which leads to a loss in the precision. In this paper, we propose a Gaussian mixture modelling clustering based method, which we refer to as OMclust, that finds overlapping Rmaps without quantization. Using both simulated and real datasets, we show that OMclust substantially improves the precision (from 48.3% to 73.3%) over the state-of-the art methods while also reducing CPU time and memory consumption. Further, we integrated OMclust into the error correction methods (Elmeri and cOMet) to demonstrate the increase in the performance of these methods. When OMclust was combined with cOMet to error correct Rmap data generated from human DNA, it was able to error correct close to 3x more Rmaps, and reduced the CPU time by more than 35x. Our software is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/OMclust

Molecular Identification of Five Multidrug-resistant Salmonella Enterica Serovars Isolated from Egyptian Poultry Farms

Salmonella spp is the main cause of foodborne salmonellosis that is considered a public health threat all over the world. The robust usage of antibiotics in Egyptian poultry farms resulted in increasing the prevalence of multi-drug resistant Salmonella enterica. In this study, the authors identify five multi-drug resistant Salmonella enterica serovars. Multidrug-resistant characteristics of these isolates were detected. The taxonomic evidence of these isolates was investigated based on 16S rRNA gene sequence and pairwise sequence alignment between the isolates' sequence and the nearest sequences in the database. In silico restriction maps and phylogenetic trees were also constructed. The obtained sequences were deposited in the database under accession numbers MW311328.1, MW311371.1, MN820824.1, MN822653.1 and MW310702.1 for Salmonella enterica subsp. enterica serovar Enteritidis strains EG.SmE1, EG.SmE2 and Salmonella enterica subsp. enterica serovar Typhimurium strains EG.SmT1, EG.SmT2, EG.SmT3, respectively. The five Salmonella isolates in this study showed multi-drug resistant characteristics. Salmonella Typhimurium isolate EG.SmT3 revealed resistance to more than five antibiotics. Results of pairwise sequence alignment, restriction maps and phylogenetic tree confirmed the close relationship between S. enteritidis isolates (EG.SmE1, EG. SmE2) and S. typhimurium isolates (EG.SmT1, EG.SmT2). However, the other S. typhimurium isolate (EG.SmT3) revealed the lowest identity ratio (98.6%) with the nearest sequence. The relative divergence of this isolate could be attributed to proposed mutations as a result of the vigorous use of antibiotics in Egyptian poultry farms.

Linear Maps in Minimal Free Resolutions of Stanley-Reisner Rings

In this short note we give an elementary description of the linear part of the minimal free resolution of a Stanley-Reisner ring of a simplicial complex Δ . Indeed, the differentials in the linear part are simply a compilation of restriction maps in the simplicial cohomology of induced subcomplexes of Δ . Along the way, we also show that if a monomial ideal has at least one generator of degree 2, then the linear strand of its minimal free resolution can be written using only ± 1 coefficients.

FN-Identify: Novel Restriction Enzymes-Based Method for Bacterial Identification in Absence of Genome Sequencing

Sequencing and restriction analysis of genes like 16S rRNA and HSP60 are intensively used for molecular identification in the microbial communities. With aid of the rapid progress in bioinformatics, genome sequencing became the method of choice for bacterial identification. However, the genome sequencing technology is still out of reach in the developing countries. In this paper, we propose FN-Identify, a sequencing-free method for bacterial identification. FN-Identify exploits the gene sequences data available in GenBank and other databases and the two algorithms that we developed, CreateScheme and GeneIdentify, to create a restriction enzyme-based identification scheme. FN-Identify was tested using three different and diverse bacterial populations (members of Lactobacillus, Pseudomonas, and Mycobacterium groups) in an in silico analysis using restriction enzymes and sequences of 16S rRNA gene. The analysis of the restriction maps of the members of three groups using the fragment numbers information only or along with fragments sizes successfully identified all of the members of the three groups using a minimum of four and maximum of eight restriction enzymes. Our results demonstrate the utility and accuracy of FN-Identify method and its two algorithms as an alternative method that uses the standard microbiology laboratories techniques when the genome sequencing is not available.

Continuity of the Restriction Maps on Smirnov Classes

We prove the restriction maps define continuous linear operators on the Smirnov classes for some certain domain with analytic boundary.