PRISE2: software for designing sequence-selective PCR primers and probes.

BackgroundPRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines.ResultsPRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays.ConclusionsPRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays

Phenotype-based and Self-learning Inter-individual Sleep Apnea Screening with a Level IV Monitoring System

Purpose: We propose a phenotype-based artificial intelligence system that can self-learn and is accurate for screening purposes, and test it on a Level IV monitoring system. Methods: Based on the physiological knowledge, we hypothesize that the phenotype information will allow us to find subjects from a well-annotated database that share similar sleep apnea patterns. Therefore, for a new-arriving subject, we can establish a prediction model from the existing database that is adaptive to the subject. We test the proposed algorithm on a database consisting of 62 subjects with the signals recorded from a Level IV wearable device measuring the thoracic and abdominal movements and the SpO2. Results: With the leave-one cross validation, the accuracy of the proposed algorithm to screen subjects with an apnea-hypopnea index greater or equal to 15 is 93.6%, the positive likelihood ratio is 6.8, and the negative likelihood ratio is 0.03. Conclusion: The results confirm the hypothesis and show that the proposed algorithm has great potential to screen patients with SAS

Learning Multi-Level Information for Dialogue Response Selection by Highway Recurrent Transformer

With the increasing research interest in dialogue response generation, there is an emerging branch formulating this task as selecting next sentences, where given the partial dialogue contexts, the goal is to determine the most probable next sentence. Following the recent success of the Transformer model, this paper proposes (1) a new variant of attention mechanism based on multi-head attention, called highway attention, and (2) a recurrent model based on transformer and the proposed highway attention, so-called Highway Recurrent Transformer. Experiments on the response selection task in the seventh Dialog System Technology Challenge (DSTC7) show the capability of the proposed model of modeling both utterance-level and dialogue-level information; the effectiveness of each module is further analyzed as well

Synthesis of thioesters through copper-catalyzed coupling of aldehydeswith thiols in water

Copper-catalyzed C–S bond formation between aldehydes and thiols in the presence of TBHP as an oxidant is described. Functional groups including chloro, trifluoromethyl, bromo, iodo, nitrile, ester and thiophene are all tolerated by the reaction conditions employed. This reaction is performed in water without the use of a surfactant. Both aryl and alkyl aldehydes couple suitably with aryl- and alkyl thiols, affording the corresponding thioesters in moderate to good yields