The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD—taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites

BDEF : the behavioral design data exchange format

BDDB is a Behavioral Design Data Base that manages the design data produced and consumed by different behavioral synthesis tools. These different design tools retrieve design data from BDDB, manipulate the data, and then store the results back into the data base. BDDB thus needs to address the following two issues: (1) a design data exchange approach and (2) customized design data interfaces. To address the first issue, we have developed a textual description format for describing design data objects and relationships. This language, referred to as the Behavioral Design Data Exchange Format (BDEF), is used as common format for exchanging design data between BDDB and the design tools in the behavioral synthesis environment. To address the second issue, we have developed a behavioral object type description language (generally referred to as schema definition language) for describing the global data structures required by design tools as well as the desired design subviews of this global BDDB design information. One design view class, namely, BDEF, is the topic of this report.In this report we give a formal definition of the BDEF format. Then we describe a comprehensive example of applying BDEF to the behavioral synthesis domain. That is, we present the complete BDEF syntax for the Extended Control/Data Flow Graph Model (ECDFG), which is the design representation model used by most behavioral synthesis tools in the UCI CADLAB synthesis system. We also present several example descriptions of designs using this ECDFG model. A parser/graph compiler from BDEF into the generalized ECDFG design representation as well as a BDEF generator from the ECDFG data structures into the BDEF format have been implemented

Rapidly quantifying the relative distention of a human bladder

A device and method was developed to rapidly quantify the relative distention of the bladder of a human subject. An ultrasonic transducer is positioned on the human subject near the bladder. A microprocessor controlled pulser excites the transducer by sending an acoustic wave into the human subject. This wave interacts with the bladder walls and is reflected back to the ultrasonic transducer where it is received, amplified, and processed by the receiver. The resulting signal is digitized by an analog to digital converter, controlled by the microprocessor again, and is stored in data memory. The software in the microprocessor determines the relative distention of the bladder as a function of the propagated ultrasonic energy. Based on programmed scientific measurements and the human subject's past history as contained in program memory, the microprocessor sends out a signal to turn on any or all of the available alarms. The alarm system includes and audible alarm, the visible alarm, the tactile alarm, and the remote wireless alarm

Towards responsive Sensitive Artificial Listeners

This paper describes work in the recently started project SEMAINE, which aims to build a set of Sensitive Artificial Listeners – conversational agents designed to sustain an interaction with a human user despite limited verbal skills, through robust recognition and generation of non-verbal behaviour in real-time, both when the agent is speaking and listening. We report on data collection and on the design of a system architecture in view of real-time responsiveness