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PubMed1991

Cloning and sequence determination of the Schizosaccharomyces pombe rpb1 gene encoding the largest subunit of RNA polymerase II.

The gene, rpb1, encoding the largest subunit of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB1, of Saccharomyces cerevisiae as a cross-hybridization probe. We have determined the complete sequence of this gene, and parts of PCR-amplified rpb1 cDNA. The predicted coding sequence, interrupted by six introns, encodes a polypeptide of 1,752 amino acid residues in length with a molecular weight of 194 kilodaltons. This polypeptide contains eight conserved structural domains characteristic of the largest subunit of RNA polymerases from other eukaryotes and, in addition, 29 repetitions of the C-terminal heptapeptide found in all the eukaryotic RNA polymerase II largest subunits so far examined.

Amino Acid Sequence↗
PubMed1990

Ground distribution patterns of selected radioactive, chemical, and physical contaminants from dispersion of U mill tailings.

Ground concentrations of 226Ra and total alpha activity as a function of soil depth and distance from an acidic U mill tailings pile were measured, as well as soil pH, sulfate, chloride, and conductivity. Contamination decreased with increasing soil depth and distance from the source. Most of the measured parameters were indistinguishable from background after a distance of 3.3 km from the tailings impoundment. The highest concentrations of all contaminants were contained in the particles less than 0.045 mm in diameter at the soil surface (0-0.6 cm). This fraction represents only 4% to 10% of the total soil mass. Surface soil particles greater than 2.0 mm contained higher concentrations of all contaminants than the intermediate-size (0.045-2.0 mm) fraction. Aggregate formation of the greater than 2.0-mm fraction from small particles or preferential erosion and transport of the tailings sand fractions were proposed as possible explanations. The significant correlations between various measurements were soil 226Ra vs. total alpha activity, sulfate concentration, and conductivity. The latter two parameters are indicative of sulfuric acid leached tailings. The sulfate concentration appeared to be a sensitive and easily measured indicator of tailings contamination and migration into the soil profile. Furthermore, sulfate may be used to delineate acidic U tailings from other sources of contamination (U ore dust, yellowcake, naturally elevated U and Ra) in the environment. Actual site measurements for surface 226Ra concentration were approximately twice the MILDOS computer code prediction.

Chlorides↗
PubMed1992

Detection of laryngeal function using speech and electroglottographic data.

The purpose of this research was to develop quantitative measures for the assessment of laryngeal function using speech and electroglottographic (EGG) data. We developed two procedures for the detection of laryngeal pathology: 1) a spectral distortion measure using pitch synchronous and asynchronous methods with linear predictive coding (LPC) vectors and vector quantization (VQ) and 2) analysis of the EGG signal using time interval and amplitude difference measures. The VQ procedure was conjectured to offer the possibility of circumventing the need to estimate the glottal volume velocity wave-form by inverse filtering techniques. The EGG procedure was to evaluate data that was "nearly" a direct measure of vocal fold vibratory motion and thus was conjectured to offer the potential for providing an excellent assessment of laryngeal function. A threshold based procedure gave 75.9 and 69.0% probability of pathological detection using procedures 1) and 2), respectively, for 29 patients with pathological voices and 52 normal subjects. The false alarm probability was 9.6% for the normal subjects.

Adult↗
PubMed1989

Algorithms, hardware, and software for a digital signal processor microcomputer-based speech processor in a multielectrode cochlear implant system.

Software and hardware have been developed to create a powerful, inexpensive, compact digital signal processing system which in real-time extracts a low-bit rate linear predictive coding (LPC) speech system model. The model parameters derived include accurate spectral envelope, formant, pitch, and amplitude information. The system is based on the Texas Instruments TMS320 family, and the most compact realization requires only three chips (TMS320E17, A/D-D/A, op-amp), consuming a total of less than 0.5 W. The processor is part of programmable cochlear implant system under development by a multiuniversity Canadian team, but also has other applications in aids to the hearing handicapped.

Algorithms↗
PubMedDate not supplied

Effect of tissue inhomogeneity on dose distribution of point sources of low-energy electrons.

Perturbation in dose distributions of point sources of low-energy electrons at planar interfaces of cortical bone (CB) and red marrow (RM) was investigated experimentally and by Monte Carlo codes EGS and the TIGER series. Ultrathin LiF thermoluminescent dosimeters were used to measure the dose distributions of point sources of 204Tl and 147Pm in RM. When the point sources were at 12 mg/cm2 from a planar interface of CB and RM equivalent plastics, dose enhancement ratios in RM averaged over the region 0-12 mg/cm2 from the interface were measured to be 1.08 +/- 0.03 (SE) and 1.03 +/- 0.03 (SE) for 204Tl and 147Pm, respectively. The Monte Carlo codes predicted 1.05 +/- 0.02 and 1.01 +/- 0.02 for the two nuclides, respectively. However, EGS gave consistently 3% higher dose in the dose scoring region than the TIGER series when point sources of monoenergetic electrons up to 0.75 MeV energy were considered in the homogeneous RM situation or in the CB and RM heterogeneous situation. By means of the TIGER series, it was demonstrated that aluminum, which is normally assumed to be equivalent to CB in radiation dosimetry, leads to an overestimation of backscattering of low-energy electrons in soft tissue at a CB-soft-tissue interface by as much as a factor of 2.

Bone Marrow↗
PubMed1978

Acoustic determinants of phrase boundary perception.

How three supersegmental variables (amplitude, pitch contour, and duration pattern) influence phrase boundary perception was investigated in two studies. Listeners located the phrase boundary in ambiguous algebraic expressions, such as "(A plus E) times O" and A plus (E times O)." In one experiment, two values of each of three variables (appropriate or neutral) were orthogonally varied, using linear predictive coding analysis-synthesis procedures. There was a total of eight manipulations for each expression. In the other, the three suprasegmental variables were exchanged between the two alternative meanings of an expression, yielding a total of eight manipulations for each expression. Results from the two studies were consistent in showing that listeners use all three cues, and just these three to parse such utterances. That is, it was possible to completely shift the meaning of an expression uttered with one meaning into its alternate meaning by exchanging all three variables. In both studies, the effects of duration pattern and pitch contour were additive in total proportion correct. Possible models of how listeners process pitch and duration information independently in making a parsing decision are discussed.

Adolescent↗
PubMed1989

Perceptual differences between vowels located in a limited phonetic space.

The perception of subphonemic differences between vowels was investigated using multidimensional scaling techniques. Three experiments were conducted with natural-sounding synthetic stimuli generated by linear predictive coding (LPC) formant synthesizers. In the first experiment, vowel sets near the pairs (i-I), (epsilon-ae), or (u-U) were synthesized containing 11 vowels each. Listeners judged the dissimilarities between all pairs of vowels within a set several times. These perceptual differences were mapped into distances between the vowels in an n-dimensional space using two-way multidimensional scaling. Results for each vowel set showed that the physical stimulus space, which was specified by the two parameters F1 and F2, was always mapped into a two-dimensional perceptual space. The best metric for modeling the perceptual distances was the Euclidean distance between F1 and F2 in barks. The second experiment investigated the perception of the same vowels from the first experiment, but embedded in a consonantal context. Following the same procedures as experiment 1, listeners' perception of the (bv) dissimilarities was not different from their perception of the isolated vowel dissimilarities. The third experiment investigated dissimilarity judgments for the three vowels (ae-alpha-lambda) located symmetrically in the F1 X F2 vowel space. While the perceptual space was again two dimensional, the influence of phonetic identity on vowel difference judgments was observed. Implications for determining metrics for subphonemic vowel differences using multidimensional scaling are discussed.

Adult↗
PubMed1989

Comments on "Effects of Noise on Speech Production: Acoustic and Perceptual Analyses" [J. Acoust. Soc. Am. 84, 917-928 (1988)].

The effect of background noise on speech production is an important issue, both from the practical standpoint of developing speech recognition algorithms and from the theoretical standpoint of understanding how speech is tuned to the environment in which it is spoken. Summers et al. [J. Acoust. Soc. Am. 84, 917-928 (1988]) address this issue by experimentally manipulating the level of noise delivered through headphones to two talkers and making several kinds of acoustic measurements on the resulting speech. They indicate that they have replicated effects on amplitude, duration, and pitch and have found effects on spectral tilt and first-formant frequency (F1). The authors regard these acoustic changes as effects in themselves rather than as consequences of a change in vocal effort, and thus treat equally the change in spectral tilt and the change in F1. In fact, the change in spectral tilt is a well-documented and understood consequence of the change in the glottal waveform, which is known to occur with increased effort. The situation with F1 is less clear and is made difficult by measurement problems. The bias in linear predictive coding (LPC) techniques related to two of the other changes-fundamental frequency and spectral tilt-is discussed.

Humans↗
PubMed1989

An addendum to "Effects of Noise on Speech Production: Acoustic and Perceptual Analyses" [J. Acoust. Soc. Am. 84, 917-928 (1988)].

The authors respond to Fitch's comments [H. Fitch, J. Acoust. Soc. Am. 86, 2017-2019 (1989)] on an earlier paper. New analyses are presented to address the question of whether F1 differences observed in the original report are an artifact of linear predictive coding (LPC) analysis techniques. Contrary to Fitch's claims, the results suggest that the F1 differences originally reported are, in fact, due to changes in vocal tract resonance characteristics. It is concluded that there are important acoustic-phonetic differences in speech when talkers speak in noise. These differences reflect changes in both glottal and supraglottal events that are designed to maintain speech intelligibility under adverse conditions.

Humans↗
PubMed2004

The Burkholderia cepacia epidemic strain marker is part of a novel genomic island encoding both virulence and metabolism-associated genes in Burkholderia cenocepacia.

The Burkholderia cepacia epidemic strain marker (BCESM) is a useful epidemiological marker for virulent B. cenocepacia strains that infect patients with cystic fibrosis. However, there was no evidence that the original marker, identified by random amplified polymorphic DNA fingerprinting, contributed to pathogenicity. Here we demonstrate that the BCESM is part of a novel genomic island encoding genes linked to both virulence and metabolism. The BCESM was present on a 31.7-kb low-GC-content island that encoded 35 predicted coding sequences (CDSs): an N-acyl homoserine lactone (AHL) synthase gene (cciI) and corresponding transcriptional regulator (cciR), representing the first time cell signaling genes have been found on a genomic island; fatty acid biosynthesis genes; an IS66 family transposase; transcriptional regulator CDSs; amino acid metabolism genes; and a group of hypothetical genes. Mutagenesis of the AHL synthase, amidase (amiI), and porin (opcI) genes on the island was carried out. Testing of the isogenic mutants in a rat model of chronic lung infection demonstrated that the amidase played a role in persistence, while the AHL synthase and porin were both involved in virulence. The island, designated the B. cenocepacia island (cci), is the first genomic island to be defined in the B. cepacia complex and its discovery validates the original epidemiological correlation of the BCESM with virulent CF strains. The features of the cci, which overlap both pathogenicity and metabolism, expand the concept of bacterial pathogenicity islands and illustrate the diversity of accessory functions that can be acquired by lateral gene transfer in bacteria.

Amidohydrolases↗
PubMed1990

Structure and expression of the vaccinia virus gene which prevents virus-induced breakdown of RNA.

Three noncomplementing vaccinia virus temperature-sensitive mutants, ts4, ts22, and ts23, exhibit an abortive late phenotype characterized by the simultaneous cessation of protein synthesis, the breakdown of rRNA and viral mRNA, and an increase in intracellular concentrations of 2'-5'-linked oligoadenylates late during infection at the nonpermissive temperature (R.F. Pacha and R.C. Condit, J. Virol. 56:395-403, 1985; R.J. Cohrs, R.C. Condit, R.F. Pacha, C.L. Thompson, and O.K. Sharma, J. Virol. 63:948-951, 1989). We have identified the virus gene affected by the abortive late mutants, determined its DNA sequence, and analyzed its transcription. The gene resides in the HindIII A DNA fragment, it has a predicted coding capacity of 57 kilodaltons, and it is transcribed both early and late during infection. The early transcript of the abortive late gene is unusual; it contains a 426-nucleotide 5' untranslated region, and it must be synthesized by transcription through an early transcription termination signal which is located in the middle of the gene in a hairpin loop structure. DNA sequence and transcription analysis of two flanking genes is also presented.

Amino Acid Sequence↗
PubMed1987

Identification and characterization of cDNA clones encoding two homologous proteins that are part of the asialoglycoprotein receptor.

The asialoglycoprotein receptor (ASGP-R) from rat liver contains the following three distinct protein species when it is analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis: RHL1 (42 kilodaltons), RHL2 (49 kilodaltons), and RHL3 (54 kilodaltons). In this paper we describe the isolation of cDNA clones encoding RHL1 and RHL2 from a cDNA library constructed from rat liver mRNA. A comparison of the predicted coding sequence for RHL2 with that for RHL1 showed that these sequences are highly homologous. The library also contained numerous cDNA clones for both RHL1 and RHL2 that were derived from unspliced precursor mRNAs. Differential splicing at the 5' end of the RHL1 transcript was inferred from the finding that two different types of RHL1 cDNA were identified, each having a different 5' terminus.

Amino Acid Sequence↗
PubMed1989

[Prosthetic application of digital processing of speech signals].

The purpose of this study was to investigate the acoustic characteristics of the nine sounds, /sa/, /si/, /ka/, /ki/, /ci/, /hi/ and /ri/, which were reported affected by wearing complete denture, through the acoustic analysis of speech samples uttered by nine male subjects. Spectrum analysis was done within the frequency range of 0 to 10 KHz according to the auto-correlation method of liner predictive coding (LPC) analysis. Results 1. The consonant parts of /sa/, /si/, /ci/ and /hi/ wee characterized by the spectrum envelopes and their peak frequencies derived from the LPC analysis of order 5. 2. The consonant parts of /ka/ and /ki/ were characterized by their first spectrum peak frequencies derived from the LPC analysis of order 10. 3. The consonant part of /ri/ was characterized by the spectrum envelope derived from the LPC analysis of order 24, and the sound waveform. 4. The frequencies of the formants (F 1, F 2, F 3) of the following vowels /i/ were derived from the LPC analysis of order 24. They were influenced by individual variations and preceding consonants. 5. Each sound had its own characteristics in the duration of the consonant and of the closure interval and the time from the end of preceding vowel to the beginning of the following vowel.

Analog-Digital Conversion↗
PubMed1992

Two types of murine CD34 mRNA generated by alternative splicing.

To characterize and clarify the function of CD34 antigen experimentally, we isolated two types of CD34 mRNA from a cDNA library of murine stromal cell line, PA-6 stimulated with lipopolysaccharide (LPS) and 12-o-tetra-decanoylphorbol 13-acetate (TPA) using a human CD34 probe. In addition to the clone (open reading frame [ORF]:1149bp) reported by Brown et al, a novel clone (ORF:978 bp) was obtained. The difference between the two clones was in the cytoplasmic portion of CD34; the former has 73 amino acids, while the latter has 16. We investigated the genomic sequence of cytoplasmic portion and found conserved nucleotide sequences at the exon-intron junction (GT ... AG). Thus, it was concluded that alternative splicing gave two types of CD34 mRNA. A novel clone contains the longer cDNA, including a insert of 156 bp, but results in a shorter predicted coding sequence because of the introduction of an inframe stop codon. Northern blot analysis using a murine cDNA probe (HindIII fragment, 900 bp) showed that CD34 was highly expressed in the brain and testis, and moderately in the thymus, spleen, and bone marrow, but not in adult liver. However, day 12 to 14 fetal liver cells showed significant expression of CD34. Quantitative reverse transcription polymerase chain reaction showed that spleen, thymus, bone marrow, and testis RNA gave two bands of almost equal intensity, but in the brain a novel clone was expressed three times more than the other clone. Furthermore, Northern blot analysis using a probe (156 bp) specific for the spliced intracellular region confirmed the significant mRNA expression of a novel clone. Although the biologic significance of alternative splicing remains to be elucidated, it is suggested that a different carboxyterminal tail causes a change in signal transduction.

Amino Acid Sequence↗
PubMed1989

Nucleotide sequence of the rat Bmyc gene.

We have cloned and sequenced the rat Bmyc gene. The rat Bmyc gene contains sequences related to the central part of c-myc, namely the first intron, the second exon, and the noncoding part of the third exon. The homology drops in the 3' part of the c-myc second exon, but continues in the noncoding part of the third exon. We have sequenced the total predicted coding region of the Bmyc. The longest open reading frame in Bmyc suggests a protein of 178 amino acids, which is only 41% of the c-myc protein size. To confirm the putative open reading frame, we have produced a trpE-Bmyc protein that is detected with a pan-myc antibody. We discuss these findings in the context of potential functional domains and the possibility of overlapping and distinct activities of myc-family proteins.

Amino Acid Sequence↗
PubMed1985

Design verification on a speech synthesizer using electron beam testing techniques.

The use of Electron Beam Testing (EBT) techniques in the verification both of the circuit and of electric simulation tools turns out to be very powerful and promises to improve the reliability and performance of VLSI circuit design by providing an effective feedback from measurements to circuit design. That is true within the traditional design environment and, more effectively, in a standard cell design approach, characterized by a fast development and update time. In the latter case it is really possible to take strong advantage of tools and circuit improvements. The design tool taken into account is the world-wide used electrical simulator SPICE. The EBT system used, allows in sampling mode 1 ns time resolution and applies an oscilloscope with programmable digitizer to display the acquired waveforms. The actual example is carried out on a 2-phase generator inside a VLSI circuit: a speech synthesizer (Linear Predicting Code technique) designed in CSELT and implemented in a N-MOS 4 micron process by SGS-ATES.

Communication Devices for People with Disabilities↗