DEVELOPMENT OF NOVEL METHODS TO MINIMIZE THE IMPACT OF SEQUENCING ERRORS IN THE NEXT-GENERATION SEQUENCING DATA ANALYSIS

Next-generation sequencing (NGS) technology has become a prominent tool in biological and biomedical research. However, NGS data analysis, such as de novo assembly, mapping and variants detection is far from maturity, and the high sequencing error-rate is one of the major problems. . To minimize the impact of sequencing errors, we developed a highly robust and efficient method, MTM, to correct the errors in NGS reads. We demonstrated the effectiveness of MTM on both single-cell data with highly non-uniform coverage and normal data with uniformly high coverage, reflecting that MTM’s performance does not rely on the coverage of the sequencing reads. MTM was also compared with Hammer and Quake, the best methods for correcting non-uniform and uniform data respectively. For non-uniform data, MTM outperformed both Hammer and Quake. For uniform data, MTM showed better performance than Quake and comparable results to Hammer. By making better error correction with MTM, the quality of downstream analysis, such as mapping and SNP detection, was improved. SNP calling is a major application of NGS technologies. However, the existence of sequencing errors complicates this process, especially for the low coverage (

Improving disclosure of medical errors: Including patients and family members in the disclosure process

Over the last decade, adverse events and medical errors have become a main focus of interest for the standards of quality and safety in the U.S. healthcare system (Weinstein & Henderson, 2009). Particularly when a medical error occurs, the disclosure of medical errors and its practices have become a focal point of the healthcare process. Patients and family members who have experienced a medical error might be able to provide knowledge and insight on how to improve the disclose process. However, patient and family member are not typically involved in the disclosure process, thus their experiences go unnoticed. ^ The purpose of this research was to explore how best to include patients and family members in the disclosure process regarding a medical error. The research consisted of 28 qualitative interviews from three stakeholder groups: Hospital Administrators, Clinical Service Providers, and Patients and Family Members. They were asked for their ideas and suggestions on how best to include patients and family members in the disclosure process. Framework Analysis was used to analyze this data and find prevalent themes based on the primary research question. A secondary aim was to index categories created based on the interviews that were collected. Data was used from the Texas Disclosure and Compensation Study with Dr. Eric Thomas as the Principal Investigator. Full acknowledgement of access to this data is given to Dr. Thomas. ^ The themes from the research revealed that each stakeholder group was interested and open to including patients and family members in the disclosure process and that the disclosure process should not be a "one-way" avenue. The themes gave many suggestions regarding how to best include patients and family members in the disclosure process of a medical error. Secondary aims revealed several ways to assess the ideas and suggestion given by the stakeholders. Overall, acceptability of getting the perspective of patients and family members was the most common theme. Comparison of each stakeholder group revealed that including patients and family members would be beneficial to improving hospital disclosure practices. ^ Conclusions included a list of recommendations and measureable appropriate strategies that could provide hospital with key stakeholders insights on how to improve their disclosure process. Sharing patients and family members experience with healthcare providers can encourage a shift in culture where patients are valued and active in participating in hospital practices. To my knowledge, this research is the very first of its kind and moves the disclosure process conversation forward in a patient-family member inclusion direction that will assist in improving disclosure practices. Future research should implement and evaluate the success of the various inclusion strategies.^

Standard Errors for the Blinder-Oaxaca Decomposition

The decomposition technique introduced by Blinder (1973) and Oaxaca (1973) is widely used to study outcome differences between groups. For example, the technique is commonly applied to the analysis of the gender wage gap. However, despite the procedure's frequent use, very little attention has been paid to the issue of estimating the sampling variances of the decomposition components. We therefore suggest an approach that introduces consistent variance estimators for several variants of the decomposition. The accuracy of the new estimators under ideal conditions is illustrated with the results of a Monte Carlo simulation. As a second check, the estimators are compared to bootstrap results obtained using real data. In contrast to previously proposed statistics, the new method takes into account the extra variation imposed by stochastic regressors.

Reduction of truncation errors in planar, cylindrical and partial spherical near-field antenna measurements

A method to reduce truncation errors in near-field antenna measurements is presented. The method is based on the Gerchberg-Papoulis iterative algorithm used to extrapolate band-limited functions and it is able to extend the valid region of the calculated far-field pattern up to the whole forward hemisphere. The extension of the valid region is achieved by the iterative application of a transformation between two different domains. After each transformation, a filtering process that is based on known information at each domain is applied. The first domain is the spectral domain in which the plane wave spectrum (PWS) is reliable only within a known region. The second domain is the field distribution over the antenna under test (AUT) plane in which the desired field is assumed to be concentrated on the antenna aperture. The method can be applied to any scanning geometry, but in this paper, only the planar, cylindrical, and partial spherical near-field measurements are considered. Several simulation and measurement examples are presented to verify the effectiveness of the method.

Correction of systematic errors in Wide Area Multilateration

This work presents a method to estimate and correct slow time-dependent position errors due to non perfect ground station synchronization and tropospheric propagation. It uses opportunity traffic emissions, i.e. signals transmitted from the aircrafts within the coverage zone. This method is used to overcome the difficulty of installing reference beacons simultaneously visible by all the base stations in a given Wide Area Multilateration (WAM) system.

Evaluating a Speech Communication System for deaf people

This paper describes the development of an Advanced Speech Communication System for Deaf People and its field evaluation in a real application domain: the renewal of Driver’s License. The system is composed of two modules. The first one is a Spanish into Spanish Sign Language (LSE: Lengua de Signos Española) translation module made up of a speech recognizer, a natural language translator (for converting a word sequence into a sequence of signs), and a 3D avatar animation module (for playing back the signs). The second module is a Spoken Spanish generator from sign-writing composed of a visual interface (for specifying a sequence of signs), a language translator (for generating the sequence of words in Spanish), and finally, a text to speech converter. For language translation, the system integrates three technologies: an example-based strategy, a rule-based translation method and a statistical translator. This paper also includes a detailed description of the evaluation carried out in the Local Traffic Office in the city of Toledo (Spain) involving real government employees and deaf people. This evaluation includes objective measurements from the system and subjective information from questionnaires. Finally, the paper reports an analysis of the main problems and a discussion about possible solutions.

Speaker Diarization Features: The UPM Contribution to the RT09 Evaluation

Two new features have been proposed and used in the Rich Transcription Evaluation 2009 by the Universidad Politécnica de Madrid, which outperform the results of the baseline system. One of the features is the intensity channel contribution, a feature related to the location of the speaker. The second feature is the logarithm of the interpolated fundamental frequency. It is the first time that both features are applied to the clustering stage of multiple distant microphone meetings diarization. It is shown that the inclusion of both features improves the baseline results by 15.36% and 16.71% relative to the development set and the RT 09 set, respectively. If we consider speaker errors only, the relative improvement is 23% and 32.83% on the development set and the RT09 set, respectively.

Review of Research on Speech Technology: Main Contributions From Spanish Research Groups

In the last two decades, there has been an important increase in research on speech technology in Spain, mainly due to a higher level of funding from European, Spanish and local institutions and also due to a growing interest in these technologies for developing new services and applications. This paper provides a review of the main areas of speech technology addressed by research groups in Spain, their main contributions in the recent years and the main focus of interest these days. This description is classified in five main areas: audio processing including speech, speaker characterization, speech and language processing, text to speech conversion and spoken language applications. This paper also introduces the Spanish Network of Speech Technologies (RTTH. Red Temática en Tecnologías del Habla) as the research network that includes almost all the researchers working in this area, presenting some figures, its objectives and its main activities developed in the last years.

A speech interface for air traffic control terminals

Several issues concerning the current use of speech interfaces are discussed and the design and development of a speech interface that enables air traffic controllers to command and control their terminals by voice is presented. A special emphasis is made in the comparison between laboratory experiments and field experiments in which a set of ergonomics-related effects are detected that cannot be observed in the controlled laboratory experiments. The paper presents both objective and subjective performance obtained in field evaluation of the system with student controllers at an air traffic control (ATC) training facility. The system exhibits high word recognition test rates (0.4% error in Spanish and 1.5% in English) and low command error (6% error in Spanish and 10.6% error in English in the field tests). Subjective impression has also been positive, encouraging future development and integration phases in the Spanish ATC terminals designed by Aeropuertos Españoles y Navegación Aérea (AENA).

Exploring differences between phonetic classes in Sleep Apnoea Syndrome Patients using automatic speech processing techniques

This work is part of an on-going collaborative project between the medical and signal processing communities to promote new research efforts on automatic OSA (Obstructive Apnea Syndrome) diagnosis. In this paper, we explore the differences noted in phonetic classes (interphoneme) across groups (control/apnoea) and analyze their utility for OSA detection

Improving Speech Interaction in Vehicles Using Context-Aware Information through A SCXML Framework

Speech Technologies can provide important benefits for the development of more usable and safe in-vehicle human-machine interactive systems (HMIs). However mainly due robustness issues, the use of spoken interaction can entail important distractions to the driver. In this challenging scenario, while speech technologies are evolving, further research is necessary to explore how they can be complemented with both other modalities (multimodality) and information from the increasing number of available sensors (context-awareness). The perceived quality of speech technologies can significantly be increased by implementing such policies, which simply try to make the best use of all the available resources; and the in vehicle scenario is an excellent test-bed for this kind of initiatives. In this contribution we propose an event-based HMI design framework which combines context modelling and multimodal interaction using a W3C XML language known as SCXML. SCXML provides a general process control mechanism that is being considered by W3C to improve both voice interaction (VoiceXML) and multimodal interaction (MMI). In our approach we try to anticipate and extend these initiatives presenting a flexible SCXML-based approach for the design of a wide range of multimodal context-aware HMI in-vehicle interfaces. The proposed framework for HMI design and specification has been implemented in an automotive OSGi service platform, and it is being used and tested in the Spanish research project MARTA for the development of several in-vehicle interactive applications.

A New Method to Reduce Truncation Errors in Partial Spherical Near-Field Measurements

A new and effective method for reduction of truncation errors in partial spherical near-field (SNF) measurements is proposed. The method is useful when measuring electrically large antennas, where the measurement time with the classical SNF technique is prohibitively long and an acquisition over the whole spherical surface is not practical. Therefore, to reduce the data acquisition time, partial sphere measurement is usually made, taking samples over a portion of the spherical surface in the direction of the main beam. But in this case, the radiation pattern is not known outside the measured angular sector as well as a truncation error is present in the calculated far-field pattern within this sector. The method is based on the Gerchberg-Papoulis algorithm used to extrapolate functions and it is able to extend the valid region of the calculated far-field pattern up to the whole forward hemisphere. To verify the effectiveness of the method, several examples are presented using both simulated and measured truncated near-field data.

New methods to reduce leakage errors in planar near-field measurements

This paper describes two methods to cancel the effect of two kinds of leakage signals which may be presented when an antenna is measured in a planar near-field range. One method tries to reduce leakage bias errors from the receiver¿s quadrature detector and it is based on estimating the bias constant added to every near-field data sample. Then, that constant is subtracted from the data, removing its undesired effect on the far-field pattern. The estimation is performed by back-propagating the field from the scan plane to the antenna under test plane (AUT) and averaging all the data located outside the AUT aperture. The second method is able to cancel the effect of the leakage from faulty transmission lines, connectors or rotary joints. The basis of this method is also a reconstruction process to determine the field distribution on the AUT plane. Once this distribution is known, a spatial filtering is applied to cancel the contribution due to those faulty elements. After that, a near-field-to-far-field transformation is applied, obtaining a new radiation pattern where the leakage effects have disappeared. To verify the effectiveness of both methods, several examples are presented.