gebhart/patrepeval huggingface dataset:
On the use of energy in LPC-based recognition of isolated words (1982)

Recognition of isolated words by encoding speech into Linear Predictive Coefficients (LPC) is well known and widely accepted as one of the better methods for speech recognition. One of the drawbacks in relying entirely on LPC for recognition, however, is that the energy information in the speech is removed during the LPC analysis. This talk discusses problems involved in combining energy pattern information with the LPC pattern information and presents results of recognition experiments with one method. The method is general and applicable to the addition of any new feature to the recognition feature set. The energy information and LPC information are combined linearly in the frame-by-frame manner utilizing the dynamic time warping (DTW) method of Itakura. The Itakura distance function, which determines the spectral difference between two frames of speech, does not lend itself to direct statistical analysis in multiple dimensions. The method for obtaining the weighting for the linear combination involves an iterative minimization of a probability of error function. The combined energy and LPC distance function was tested using a 129-word “airline” vocabulary which was designed for speaker independent, isolated word recognition. The inclusion of energy information in the recognition feature space reduces recognition error rates by an average of about 3% as compared to LPC alone.
The Development of an Internally-Worn Vocal Prosthesis (1979)

The design, construction, and evaluation of an internally worn laryngeal prosthesis for laryngectomized patients is presented. Existing speech rehabilitation techniques were analyzed. The reed-fistula technique was adopted as having the most potential for effective design improvement. Its deficiencies were explored, and an alternative strategy for an internal prosthesis was formulated. Prosthetic mechanisms which met the design criteria were developed, and their performance was evaluated both in vitro and in vivo. In this modified technique, the prosthesis is worm internally at the end of a surgically constructed fistula leading to the base of the patient's vocal tract. Exhaled air powers a miniature vibratory mechanism, whose output enters the vocal tract directly and supplies both a voiced and a voiceless sould source. Two patients using the new mechanism have regained a reasonable, usable speech with a minimum amount of effort and practice. An intelligibility test rated one patient's speech clearly superior over electronic and conventional reed-fistula speech.
Mitochondrial disease genetic diagnostics: optimized whole-exome analysis for all MitoCarta nuclear genes and the mitochondrial genome. (2012)

Discovering causative genetic variants in individual cases of suspected mitochondrial disease requires interrogation of both the mitochondrial (mtDNA) and nuclear genomes. Whole-exome sequencing can support simultaneous dual-genome analysis, although currently available capture kits do not target the mtDNA genome and provide insufficient capture for some nuclear-encoded mitochondrial genes. To optimize interrogation of nuclear and mtDNA genes relevant to mitochondrial biology and disease, a custom SureSelect "Mito-Plus" whole-exome library was formulated by blending RNA "baits" from three separate designs: (A) Agilent Technologies SureSelectXT 50 Mb All Exon PLUS Targeted Enrichment Kit, (B) 16-gene nuclear panel targeting sequences for known MitoCarta proteins not included in the 50 Mb All Exon design, and (C) sequences targeting the entire mtDNA genome. The final custom formulations consisted of a 1:1 ratio of nuclear baits to which a 1 to 1,000-fold diluted ratio of mtDNA genome baits were blended. Patient sample capture libraries were paired-end sequenced on an Illumina HiSeq 2000 system using v3.0 SBS chemistry. mtDNA genome coverage varied depending on the mtDNA:nuclear blend ratio, where a 1:100 ratio provided optimal dual-genome coverage with 10X coverage for over 97.5% of all targeted nuclear regions and 1,000X coverage for 99.8% of the mtDNA genome. mtDNA mutations were reliably detected to at least an 8% heteroplasmy level, as discriminated both from sequencing errors and potential contamination from nuclear mtDNA transcripts (Numts). The "1:100 Mito-Plus Whole-Exome" Agilent capture kit offers an optimized tool for whole-exome analysis of nuclear and mtDNA genes relevant to the diagnostic evaluation of mitochondrial disease.
Synthetic RNAi triggers and their use in chronic hepatitis B therapies with curative intent (2015)

Current therapies for chronic hepatitis B virus infection (CHB) - nucleos(t)ide analogue reverse transcriptase inhibitors and interferons - result in low rates of functional cure defined as sustained off-therapy seroclearance of hepatitis B surface antigen (HBsAg). One likely reason is the inability of these therapies to consistently and substantially reduce the levels of viral antigen production. Accumulated evidence suggests that high serum levels of HBsAg result in exhaustion of the host immune system, rendering it unable to mount the effective antiviral response required for HBsAg clearance. New mechanistic approaches are required to produce high rates of HBsAg seroclearance in order to greatly reduce off-treatment disease progression. Already shown to be a clinically viable means of reducing gene expression in a number of other diseases, therapies based on RNA interference (RNAi) can directly target hepatitis B virus transcripts with high specificity, profoundly reducing the production of viral proteins. The fact that the viral RNA transcripts contain overlapping sequences means that a single RNAi trigger can result in the degradation of all viral transcripts, including all messenger RNAs and pregenomic RNA. Advances in the design of RNAi triggers have increased resistance to degradation and reduced nonspecific innate immune stimulation. Additionally, new methods to effectively deliver the trigger to liver hepatocytes, and specifically to the cytoplasmic compartment, have resulted in increased efficacy and tolerability. An RNAi-based drug currently in clinical trials is ARC-520, a dynamic polyconjugate in which the RNAi trigger is conjugated to cholesterol, which is coinjected with a hepatocyte-targeted, membrane-active peptide. Phase 2a clinical trial results indicate that ARC-520 was well tolerated and resulted in significant, dose-dependent reduction in HBsAg for up to 57days in CHB patients. RNAi-based therapies may play an important role in future therapeutic regimes aimed at improving HBsAg seroclearance and eliminating the need for lifelong therapy. This paper forms part of a symposium in Antiviral Research on "An unfinished story: from the discovery of the Australia antigen to the development of new curative therapies for hepatitis B."
MAGIX: Model Agnostic Globally Interpretable Explanations (2017)

Explaining the behavior of a black box machine learning model at the instance level is useful for building trust. However, it is also important to understand how the model behaves globally. Such an understanding provides insight into both the data on which the model was trained and the patterns that it learned. We present here an approach that learns if-then rules to globally explain the behavior of black box machine learning models that have been used to solve classification problems. The approach works by first extracting conditions that were important at the instance level and then evolving rules through a genetic algorithm with an appropriate fitness function. Collectively, these rules represent the patterns followed by the model for decisioning and are useful for understanding its behavior. We demonstrate the validity and usefulness of the approach by interpreting black box models created using publicly available data sets as well as a private digital marketing data set.
A Motion-Compensated Interframe Coding Scheme for NTSC Color Television Signals (1984)

A motion-compensated interframe coding system for an NTSC color television signal has been developed. The output of a local decoder is used in the form of a <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y/C</tex> separated signal. Motion vectors are detected using the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y</tex> signal, and the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y</tex> signal and both baseband components of the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</tex> signal are motion-compensated. The motion-compensated signals are reencoded into an NTSC signal to provide a motion-compensation interframe prediction in the NTSC format. Real-time experimental hardware has been built. The sampling frequency and bit rate of this system are 10.7 MHz and 1.6 bits/ sample, respectively. This value includes all overhead information such as motion vectors and other control information. An assessment has been made of the picture quality of coded/decoded pictures taken from a variety of broadcast television programs. The quality was good for almost all the programs. A subjective test of picture quality was performed under stringent conditigns. The lowest value for the picture quality of the most difficult scenes at 1.6 bits/sample was 3.3 on a five-grade impairment scale.
Patterning Vascular Networks <i>In Vivo</i> for Tissue Engineering Applications (2014)

The ultimate design of functionally therapeutic engineered tissues and organs will rely on our ability to engineer vasculature that can meet tissue-specific metabolic needs. We recently introduced an approach for patterning the formation of functional spatially organized vascular architectures within engineered tissues in vivo. Here, we now explore the design parameters of this approach and how they impact the vascularization of an engineered tissue construct after implantation. We used micropatterning techniques to organize endothelial cells (ECs) into geometrically defined "cords," which in turn acted as a template after implantation for the guided formation of patterned capillaries integrated with the host tissue. We demonstrated that the diameter of the cords before implantation impacts the location and density of the resultant capillary network. Inclusion of mural cells to the vascularization response appears primarily to impact the dynamics of vascularization. We established that clinically relevant endothelial sources such as induced pluripotent stem cell-derived ECs and human microvascular endothelial cells can drive vascularization within this system. Finally, we demonstrated the ability to control the juxtaposition of parenchyma with perfused vasculature by implanting cords containing a mixture of both a parenchymal cell type (hepatocytes) and ECs. These findings define important characteristics that will ultimately impact the design of vasculature structures that meet tissue-specific needs.
Cascaded Fabry-Pérot lasers for coherent expansion of wavelength tunable gain switched comb (2014)

We propose a simple potentially integrable configuration for expanding a wavelength tunable comb by cascading gain switched Fabry-Pérot lasers. A 10GHz spaced comb, exhibiting 13 coherent low-linewidth tones within a 3 dB window, and tunable over 20 nm is demonstrated.
Study of high dynamic range video quality assessment (2015)

In recent years, High Dynamic Range (HDR) imaging has attracted significant attention from industry and academia. As a result, there are currently several on-going efforts towards standardization and benchmarking of existing tools for HDR image and video, and one of the key aspects is that of video quality measurement (both subjective and objective approaches). Therefore, this paper aims to identify few key challenges in the said area and then discuss existing solutions. Specifically, we first discuss a few important practical aspects that make HDR video quality measurement potentially challenging. Second, we report our recent efforts towards developing HDR video datasets that have been subjectively annotated for visual quality. Finally, we analyze and compare the effectiveness of existing solutions for objective quality prediction.
Robust Echo Control Using a Simple Echo Path Model (2006)

In handsfree tele or video conferencing acoustic echoes arise due to the coupling between the loudspeaker and microphone. Usually an acoustic echo canceler (AEC) is used for eliminating the undesired echoes. The weaknesses of AEC are that it is relatively complex and that it is not robust against non-linearities occurring when using low-end components such as small loudspeakers. We are describing an algorithm which models the acoustic echo path by means of an overall delay and a coloration effect filter. The echo is removed by means of short-time spectral modification. The algorithm design aims at low computational complexity and high robustness. The effect of echo path changes and non-linearities on the performance of this algorithm are investigated.
Interaction of Polyphemusin I and Structural Analogs with Bacterial Membranes, Lipopolysaccharide, and Lipid Monolayers (2000)

Three structural variants (PV5, PV7, and PV8) of the horseshoe crab cationic antimicrobial peptide polyphemusin I were designed with improved amphipathic profiles. Circular dichroism spectroscopy analysis indicated that in phosphate buffer polyphemusin I, PV7, and PV8 displayed the spectrum of a type II beta-turn-rich structure, but, like polyphemusin I, all three variants adopted a typical beta-sheet structure in an anionic lipid environment. Both polyphemusin I and variants were potent broad spectrum antimicrobials that were clearly bactericidal at their minimal inhibitory concentrations. The variants were moderately less active in vitro but more effective in animal models. Moreover, these variants exhibited delayed bacterial killing, whereas polyphemusin I killed Escherichia coli UB1005 within 5 min at 2.5 microg/mL. All the peptides showed similar abilities to bind to bacterial lipopolysaccharide (LPS) and permeabilize bacterial outer membranes. Consistent with this was the observation that all peptides significantly inhibited cytokine production by LPS-stimulated macrophages and penetrated polyanionic LPS monolayers to similar extents. None of the peptides had affinity for neutral lipids as evident from both tryptophan fluorescence spectroscopy and Langmuir monolayer analysis. As compared to polyphemusin I, all variants showed reduced ability to interact with anionic lipids, and the hemolytic activity of the variants was decreased by 2-4-fold. In contrast, polyphemusin I efficiently depolarized the cytoplasmic membrane of E. coli, as assessed using a membrane potential sensitive fluorescent dye 3,3-dipropylthiacarbocyanine (diSC(3)5) assay, but the variants showed a substantially delayed and decreased depolarizing ability. The coincident assessment of cell viability indicated that depolarization of the bacterial cytoplasmic membrane potential by polyphemusin I occurred prior to lethal damage to cells. Our data suggest that increase of amphipathicity of beta-sheet polyphemusin I generally resulted in variants with decreased activity for membranes. Interestingly, all variants showed an improved ability to protect mice both against infection by Pseudomonas aeruginosa and from endotoxaemia.
A Three Monoclonal Antibody Combination Potently Neutralizes Multiple Botulinum Neurotoxin Serotype E Subtypes (2018)

Human botulism is most commonly caused by botulinum neurotoxin (BoNT) serotypes A, B, and E. For this work, we sought to develop a human monoclonal antibody (mAb)-based antitoxin capable of binding and neutralizing multiple subtypes of BoNT/E. Libraries of yeast-displayed single chain Fv (scFv) antibodies were created from the heavy and light chain variable region genes of humans immunized with pentavalent-toxoid- and BoNT/E-binding scFv isolated by Fluorescence-Activated Cell Sorting (FACS). A total of 10 scFv were isolated that bound one or more BoNT/E subtypes with nanomolar-level equilibrium dissociation constants (K<sub>D</sub>). By diversifying the V-regions of the lead mAbs and selecting for cross-reactivity, we generated three scFv that bound all four BoNT/E subtypes tested at three non-overlapping epitopes. The scFvs were converted to IgG that had K<sub>D</sub> values for the different BoNT/E subtypes ranging from 9.7 nM to 2.28 pM. An equimolar combination of the three mAbs was able to potently neutralize BoNT/E1, BoNT/E3, and BoNT/E4 in a mouse neutralization assay. The mAbs have potential utility as therapeutics and as diagnostics capable of recognizing multiple BoNT/E subtypes. A derivative of the three-antibody combination (NTM-1633) is in pre-clinical development with an investigational new drug (IND) application filing expected in 2018.
Perianal Crohnʼs Disease is Associated with Distal Colonic Disease, Stricturing Disease Behavior, IBD-Associated Serologies and Genetic Variation in the JAK-STAT Pathway (2016)

We have identified associations between pCD, more distal colonic inflammation, Crohn's disease-associated serologies, and genetic variation in the JAK-Stat pathway.
Design, Manufacture, and Testing of the Easycuff™ Pressure Measuring Syringe (2012)

A pressure measuring syringe, known as the EasyCuff™, has been designed and manufactured to provide physicians with a tool to accurately measure the pressure inside the distal cuff of endotracheal tube tubes (ETTs). The syringe, identical in size to a standard 10 cc syringe, has four components: a seal, a plunger, a barrel, and a silicone-rubber bellows (the pressure measuring component). A finite-element model of the bellows was created using ADINA™; silicone rubber bellows were then produced and shown to correlate linearly with the model to within ±5% up to a load equivalent to an internal pressure of 200 cm H2O. 20 of these bellows were then assembled into EasyCuff™ syringes and tested to assess their accuracy and repeatability. The experimental setup used a currently-available manometer, which the EasyCuff™ is designed to replace, as a reference tool. The data show that the relationship between measured pressure and bellows deflection is linear, with a correlation factor of R2 = 0.99; additionally, environmental testing showed that the EasyCuff™ is unaffected by temperature cycling between −15 °F and +170 °F.
Significance of the minor i and t determinants of hepatitis B virus in hepatocellular carcinoma (1998)

Stored sera from asymptomatic hepatitis B virus (HBV) carriers and hepatitis B virus surface antigen-positive hepatocellular carcinoma (HCC) patients were tested for HBV subtypes, such as subtype determinants d, y, w, r and also antigenic determinants isoleucine (i) and threonine (t) by direct S gene nucleotide sequencing. Significant changes in minor i and t determinants in hepatocellular carcinoma patients with adr hepatitis B carriers were seen. The adr subtype with t determinant was present in 14/25 (56%) of HCC patients compared with only two of 28 (7%) in asymptomatic hepatitis B carriers (P<0.001). However, the adr subtype with i determinant was present in nine of 25 (36%) of the HCC patients and also present in 24/28 (86%) of asymptomatic carriers (P<0.001). No significant changes were seen with the adw subtypes. These results show that i and t minor determinant changes are more common with adr subtypes associated with HCC than with the adw subtype. Whether these subtle changes are pathologically relevant or only a polymorphism of hepatitis B genotypes will depend on subsequent follow-up studies.
HTS sensors for NQR spectroscopy (2004)

Using a high temperature superconductor (HTS) sensor, we have detected a /sup 14/N nuclear quadrupole resonance (NQR) signal from a room temperature sodium nitrite (NaNO/sub 2/) sample. This demonstrates the feasibility of using such sensors for the NQR detection of contraband, e.g. explosives. The sensor is composed of two high Q-value, self-resonant HTS devices strongly coupled to each other that detect the induced magnetization of the target compound. We briefly describe our techniques for making, adjusting the resonant frequency and spoiling the Q-value of the HTS sensors.
Design of Self-Organized Robust Wise Control Systems Based on Quantum Fuzzy Inference (2006)

This report presents a generalized design strategy of intelligent robust control systems based on quantum/soft computing technologies that enhance robustness of fuzzy controllers by supplying a self-organizing capability. It is demonstrated that fuzzy controllers prepared to maintain control object in the prescribed conditions are often fail to control when such a conditions are dramatically changed. We propose the solution of such kind of problems by introducing a generalization of strategies in fuzzy inference from a set of pre-defined fuzzy controllers by new Quantum Fuzzy Inference based systems. We stress our attention on the robustness features of intelligent control systems.
Immunoprecipitation assay for autoantibodies to steroid 21-hydroxylase in autoimmune adrenal diseases (1995)

Adrenal autoantibodies characteristic of autoimmune Addison disease are directed towards steroid 21-hydroxylase (21-OH; EC 1.14.99.10). We describe a new assay to measure 21-OH autoantibodies (21-OH Abs), based on immunoprecipitation by the antibodies of 35S-labeled human 21-OH. Using this immunoprecipitation assay (IPA), we detected 21-OH Abs in 42 of 64 (66%) patients with Addison disease and in 14 of 19 (74%) patients with autoimmune polyendocrine syndromes type I and type II. No 21-OH Abs were detected by the IPA in any patients with Addison disease attributable to tuberculosis (n = 9) or adrenoleukodystrophy (n = 9) or in patients with autoimmune thyroid disease (n = 28), systemic lupus erythematosus (n = 10), myasthenia gravis (n = 10), rheumatoid arthritis (n = 10), or insulin-dependent diabetes mellitus (n = 12). None of the 26 sera from healthy normal blood donors was positive for 21-OH Abs by the assay. We found good agreement between 21-OH Abs measured by IPA and by Western blotting (r = 0.83, n = 123, P < 0.001). The inter- and intraassay CVs for IPA were well < 10% at high, medium, and low concentrations of 21-OH Abs. Overall, our studies indicate that the IPA provides a specific, sensitive, and convenient system for measuring 21-OH Abs.
A Self-Stabilizing Distributed Clock Synchronization Protocol for Arbitrary Digraphs (2011)

This report presents a self-stabilizing distributed clock synchronization protocol in the absence of faults in the system. It is focused on the distributed clock synchronization of an arbitrary, non-partitioned digraph ranging from fully connected to 1-connected networks of nodes while allowing for differences in the network elements. This protocol does not rely on assumptions about the initial state of the system, other than the presence of at least one node, and no central clock or a centrally generated signal, pulse, or message is used. Nodes are anonymous, i.e., they do not have unique identities. There is no theoretical limit on the maximum number of participating nodes. The only constraint on the behavior of the node is that the interactions with other nodes are restricted to defined links and interfaces. We present an outline of a deductive proof of the correctness of the protocol. A model of the protocol was mechanically verified using the Symbolic Model Verifier (SMV) for a variety of topologies. Results of the mechanical proof of the correctness of the protocol are provided. The model checking results have verified the correctness of the protocol as they apply to the networks with unidirectional and bidirectional links. In addition, the results confirm the claims of determinism and linear convergence. As a result, we conjecture that the protocol solves the general case of this problem. We also present several variations of the protocol and discuss that this synchronization protocol is indeed an emergent system.