Evolutionary trees are frequently used as the underlying model in the design of algorithms, optimization criteria and software packages for multiple sequence alignment (MSA). In this paper , we reexamine the suitability of trees as a universal model for MSA in light of the broad range of biological questions that MSA's are used to address. A tree model consists of a tree topology and a model of...

Gentian violet (GV) is a cationic triphenylmethane dye, with potent antifungal and antibacterial activity. We recently reported that in vitro GV suppresses the differentiation of bone resorbing osteoclasts while stimulating the differentiation and activity of bone forming osteoblasts. Breast cancer is highly metastatic to bone and drives bone turnover that further promotes cancer engraftment an...

BACKGROUND Resistance to microtubule-stabilizing agents is a major hurdle for successful cancer therapy. We investigated combined treatment of microtubule-stabilizing agents (MSAs) with inhibitors of angiogenesis to overcome MSA resistance. METHODS Treatment regimens of clinically relevant MSAs (patupilone and paclitaxel) and antiangiogenic agents (everolimus and bevacizumab) were investigate...

OBJECTIVE Glycemic variability (GV) is an important component of overall glycemic control for patients with diabetes mellitus. Physicians are able to recognize excessive GV from continuous glucose monitoring (CGM) plots; however, there is currently no universally agreed upon GV metric. The objective of this study was to develop a consensus perceived glycemic variability (CPGV) metric that could...

We present a dialectal Egyptian Arabic to English statistical machine translation system that leverages dialectal to Modern Standard Arabic (MSA) adaptation. In contrast to previous work, we first narrow down the gap between Egyptian and MSA by applying an automatic characterlevel transformational model that changes Egyptian to EG′, which looks similar to MSA. The transformations include morpho...

Multiple system atrophy (MSA) is a progressive neurodegenerative disease presenting clinically with parkinsonian, cerebellar, and autonomic features. α-Synuclein (αsyn), encoded by the gene SNCA, is the main constituent of glial cytoplasmic inclusion (GCI) found in oligodendrocytes in MSA, but the methods of its accumulation have not been established. The aim of this study is to investigate alt...

Resolve onboard the x-ray satellite X-Ray Imaging and Spectroscopy Mission (XRISM) is a cryogenic instrument with an microcalorimeter in Dewar. A lid partially transparent to x-rays (called gate valve or GV) installed at top of Dewar along optical axis. Because observations will be made through GV for first few months, transmission calibration crucial initial scientific outcomes. We present res...

We present an application of ABS algorithms for multiple sequence alignment (MSA). The Markov decision process (MDP) based model leads to a linear programming problem (LPP), whose solution is linked to a suggested alignment. The important features of our work include the facility of alignment of multiple sequences simultaneously and no limit for the length of the sequences. Our goal here is to ...

Defined over sets of truth values V which are closed subsets of [0, 1] containing both 0 and 1, Gödel logics GV are prominent examples of many-valued logics. We investigate a first-order fragment of GV extended with ∆ that is powerful enough to formalize important properties of fuzzy rule-based systems. The satisfiability problem in this fragment is shown to be NP-complete for all GV , also in ...

Many filamentous fungi produce polyketide molecules with great significance as human pharmaceuticals; these molecules include the cholesterol-lowering compound lovastatin, which was originally isolated from Aspergillus terreus. The chemical diversity and potential uses of these compounds are virtually unlimited, and it is thus of great interest to develop a well-described microbial production p...