gebhart/patrepeval huggingface dataset:
Background model based posterior probability for measuring confidence (2005)

Word posterior probability (WPP) computed over LVCSR word graphs has been used successfully in measuring confidence of speech recognition output. However, for certain applications the word graph is too sparse to warrant reliable WPP estimation. In this paper, we incorporate subword units as background models to generate a subword graph for estimating posterior probability. Experiments on both English and Chinese databases show that syllable background models can repopulate the dynamic hypothesis space for effective computation of confidence measure. The resultant posterior probability confidence measure achieves 94.3% and 95.2% Out-Of-Vocabulary (OOV) word detection / rejection in English and Chinese, respectively. Correspondingly, confidence error rates are at 6.0% and 6.4%, respectively.
Second Generation G-Quadruplex Stabilizing Trimethine Cyanines (2019)

G-Quadruplex DNA has been recognized as a highly appealing target for the development of new selective chemotherapeutics, which could result in markedly reduced toxicity toward normal cells. In particular, the cyanine dyes that bind selectively to G-quadruplex structures without targeting duplex DNA have attracted attention due to their high amenability to structural modifications that allows fine-tuning of their biomolecular interactions. We have previously reported pentamethine and symmetric trimethine cyanines designed to effectively bind G-quadruplexes through end stacking interactions. Herein, we are reporting a second generation of drug candidates, the asymmetric trimethine cyanines. These have been synthesized and evaluated for their quadruplex binding properties. Incorporating a benz[c,d]indolenine heterocyclic unit increased overall quadruplex binding, and elongating the alkyl length increases the quadruplex-to-duplex binding specificity.
Evaluation of modifications of the traditional patch test in assessing the chemical irritation potential of feminine hygiene products (2004)

All four protocol variations of the standard upper arm patch test can be used to assess the inherent chemical irritant properties of feminine protection products. For these products, which are inherently non-irritating, tape stripping and/or applying wet samples does not increase the sensitivity of the patch test method. Differences in irritation potential were apparent after one to three 24-h applications. Therefore, the standard patch test protocol can be shortened to three applications without compromising our ability to detect differences in the chemical irritation produced by the test materials. The patch test can be used to evaluate effectively the inherent chemical irritation potential of these types of products. However, this method is not suitable for testing the mechanical irritation due to friction that occurs during product use. There is no relationship between specific test conditions, i.e., compromised skin and/or testing wet samples and reports of perceived sensory reactions. However, there seems to be a clear relationship between sensory reactions and objective irritation scores.
Correlation of high levels of HER2 measured by multiplex mass spectrometry with increased overall survival in patients treated with anti-HER2-based therapy. (2014)

649 Background: There is evidence that increased absolute levels of the HER2 receptor in breast cancer positively correlates with a clinical benefit from anti-HER2 therapies. The current method of HER2 evaluation, immunohistochemistry (IHC), does not allow for absolute HER2 quantification and is prone to false-positives. Thus, a significant portion of patients classified as HER2-positive actually express low levels of the receptor. We quantitated absolute levels of HER2 using a mass spectrometry-based assay and correlated expression levels with the anti-HER2 therapy benefit. Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor sections were microdissected and proteins were solubilized and digested by trypsin in Liquid Tissue buffer. After digestion, internal standards were added and absolute quantitation for multiple proteins was performed using selected reaction monitoring (SRM) mass spectrometry. Results: 26 HER2-positive (IHC 3+) breast cancer samples from patients treated with anti-HER2 therapy were obtained from Vall d´Hebron Hospital. Nineteen patients were treated with trastuzumab-based therapy; six were treated with a combination of anti-Her2 therapies. HER2 quantitation by SRM revealed receptor level ranges from 283 to 12840 amol/µg. Based on the median HER2 expression of the trastuzumab-only treated patients, the patients were divided into two subgroups. The subgroup with high expression levels of HER2 protein (average of 7461 amol/µg) had an overall survival time of 82.8 months whereas the subgroup with low levels of HER2 (average of 1823 amol/µg) had a significantly shorter survival time of 55.3 months. Conclusions: We used a non-antibody based assay to quantify absolute levels of HER2 in samples from patients treated with anti-HER2 therapy. We found high variability in HER2 expression within a patient population that had been homogenously classified as 3+ by IHC. High levels of HER2 correlated with increased overall survival following anti-HER2 therapy. This study demonstrates the need for improved quantitation of HER2 protein levels prior to initiating anti-HER2 therapy.
A Fast, Compact, Accurate Model for Language Identification of Codemixed Text (2018)

We address fine-grained multilingual language identification: providing a language code for every token in a sentence, including codemixed text containing multiple languages. Such text is prevalent online, in documents, social media, and message boards. We show that a feed-forward network with a simple globally constrained decoder can accurately and rapidly label both codemixed and monolingual text in 100 languages and 100 language pairs. This model outperforms previously published multilingual approaches in terms of both accuracy and speed, yielding an 800x speed-up and a 19.5% averaged absolute gain on three codemixed datasets. It furthermore outperforms several benchmark systems on monolingual language identification.
Optimization of Phenyl Indole Inhibitors of the AAA+ ATPase p97 (2018)

Optimization of the side-chain of a phenyl indole scaffold identified from a high-throughput screening campaign for inhibitors of the AAA+ ATPase p97 is reported. The addition of an <i>N</i>-alkyl piperazine led to high potency of this series in a biochemical assay, activity in cell-based assays, and excellent pharmaceutical properties. Molecular modeling based on a subsequently obtained cryo-EM structure of p97 in complex with a phenyl indole was used to rationalize the potency of these allosteric inhibitors.
<i>In situ</i> measurement of aspect ratio dependent etch rates of polysilicon in an inductively coupled fluorine plasma (2001)

The etch rate of polysilicon in high aspect ratio structures has been studied in an inductively coupled fluorine based plasma (pure SF6). The change of the silicon etch rate with increasing aspect ratio [aspect ratio dependent etch rate or reactive ion etching (RIE) lag] has been measured in situ by interferometry. The experimental structures as well as the process conditions were chosen such that (i) the interaction of neutral fluorine atoms with the silicon surface determines the etch rate, (ii) the ion energy is minimized, (iii) the mass transport of neutrals is in a molecular flow (Knudsen) regime, and (iv) the interaction of the etch species with the sidewalls can be neglected. Under these conditions, the experimental findings indicate that the RIE lag effect is reduced for higher pressures and lower cathode temperatures, i.e., for higher fluorine atom coverages of the silicon surface. This is in agreement with the Knudsen transport model by Coburn and Winters [W. Coburn and H. F. Winters, Appl. Phys. Lett. 55, 2730 (1989)]. Probabilities for the reaction of fluorine atoms with the silicon surface between 0.03 and 0.11 can be derived when fitting the experimental data with this model. The findings reported in this work are of relevance for the formation of deep trench storage capacitors and polysilicon plugs. In particular, we show that we can control RIE lag and etch rate independently for the given process conditions.
Miniaturized time-of-flight mass spectrometer for peptide and oligonucleotide analysis (1999)

A matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometer was developed which uses a novel reflectron composed of a grounded cylinder and an adjustable endcap electrode to provide high-order kinetic energy focusing for a miniaturized mass analyzer. The nearly quadratic potential form of the reflecting field focuses ions desorbed from a source of very small dimensions formed by placing the sample probe within the centered hole of the coaxial dual channel plate detector. At the same time, the depth of the reflectron can be adjusted to accommodate a short drift length between the source/detector and the reflectron. For larger drift lengths, in particular to allow the addition of an XY stage for the analysis of sample arrays, endcap reflectron focusing can be combined with time-delayed ion extraction to achieve good mass resolution. The instrument has been used for the analysis of peptides digested with trypsin or carboxypeptidase, and also small DNA oligomers.
Low-threshold photonic crystal laser (2002)

We have fabricated photonic crystal nanocavity lasers, based on a high-quality factor design that incorporates fractional edge dislocations. Lasers with InGaAsP quantum well active material emitting at 1550 nm were optically pumped with 10 ns pulses, and lased at threshold pumping powers below 220 μW, the lowest reported for quantum-well based photonic crystal lasers, to our knowledge. Polarization characteristics and lithographic tuning properties were found to be in excellent agreement with theoretical predictions.
Discrete-Fracture Modeling of Complex Hydraulic-Fracture Geometries in Reservoir Simulators (2016)

Summary Hydraulic fracturing is a dominant technology in unconventional resources development. Recent advances in fracture-diagnostic tools and fracture-propagation models make it necessary to model fractures with complex geometries in reservoir-simulation studies. In this paper, we present an efficient method to model fractures with complex geometries with reservoir simulators. Through nonneighboring connections (NNCs), an embedded discrete-fracture modeling (EDFM) formulation is applied to reservoir simulators to properly model fractures with complex geometries such as fracture networks and nonplanar hydraulic fractures. We demonstrate the accuracy of the approach by performing a series of case studies with two commercial reservoir simulators and comparing the results with local-grid-refinement (LGR) models and a semianalytical solution. The limitations of the model are also discussed. In addition, the results show its computational efficiency as the complexity of fractures increases. We also present two numerical case studies to demonstrate the applicability of our method in naturally fractured reservoirs. The nonintrusive application of the EDFM allows insertion of the discrete fractures into the computational domain and the use of original functionalities of the simulators without having access to the source code of the simulators. It may be easily integrated into existing frameworks for unconventional reservoirs to perform sensitivity analysis, history matching, and production forecasting.
Diamond: An efficient source of soft x rays for high-resolution x-ray lithography (1978)

An axisymmetric distribution of electrons incident on a carbon target causes heating of the target. The thermal conductivity of the various carbon polymorphs varies rapidly with temperature. We have solved the nonlinear steady-state heat-flow problem. We show that type IIb diamond would be an ideal source for carbon K radiation and that such a static target will sustain a power input of 6.5 kW on an area whose diameter is 1 mm and might, with proper design, operate at an even higher power input on the same area. We show that a power input of 6.5 kW at 6.0 kV on the above area would produce carbon K radiation of sufficient intensity so that the exposure time for PMMA (polymethylmethacrylate, an x-ray resist of extremely high resolution but relatively low sensitivity) is only 1 min for a source-to-substrate distance of 2.54 cm.
Development of Creep-Resistant, Alumina-Forming Ferrous Alloys for High-Temperature Structural Use (2018)

This paper overviews recent advances in developing novel alloy design concepts of creep-resistant, alumina-forming Fe-base alloys, including both ferritic and austenitic steels, for high-temperature structural applications in fossil-fired power generation systems. Protective, external alumina-scales offer improved oxidation resistance compared to chromia-scales in steam-containing environments at elevated temperatures. Alloy design utilizes computational thermodynamic tools with compositional guidelines based on experimental results accumulated in the last decade, along with design and control of the second-phase precipitates to maximize high-temperature strengths. The alloys developed to date, including ferritic (Fe-Cr-Al-Nb-W base) and austenitic (Fe-Cr-Ni-Al-Nb base) alloys, successfully incorporated the balanced properties of steam/water vapor-oxidation and/or ash-corrosion resistance and improved creep strength. Development of cast alumina-forming austenitic (AFA) stainless steel alloys is also in progress with successful improvement of higher temperature capability targeting up to ∼1100°C. Current alloy design approach and developmental efforts with guidance of computational tools were found to be beneficial for further development of the new heat resistant steel alloys for various extreme environments.
Association of <i>IL4R</i> Haplotypes With Type 1 Diabetes (2002)

We have investigated, in 282 multiplex Caucasian families (the Human Biological Data Interchange Repository), the association of type 1 diabetes with polymorphisms in the IL4R gene. IL4R encodes a subunit of the interleukin-4 receptor, a molecule critical to T-helper cell development. By genotyping eight different IL4R single-nucleotide polymorphisms (SNPs) and identifying haplotypes (complex alleles) in the multiplex type 1 diabetic families who were stratified for HLA genotype, we have observed significant evidence of linkage and association of the IL4R gene to type 1 diabetes. In particular, we have identified a specific haplotype that appears to be protective and observed that this protective effect is strongest among individuals not carrying the HLA DR3/DR4 genotype (which confers the strongest genetic risk for type 1 diabetes). These findings suggest an important role for the IL4R gene in immune-related disease susceptibility and illustrate the value of using multi-SNP haplotype information in association studies.
Overcoming HIV pathways for escape using rationally-designed anti-HIV antibodies (2013)

A completely protective vaccine against HIV has not been found, thus possible prevention/treatment options involving delivery of broadly neutralizing antibodies (bNAbs) identified in a minority of HIV-infected individuals are being considered. bNAbs that target conserved epitopes on the HIV envelope spike can prevent infection in animal models, delay rebound of HIV after cessation of anti-retroviral drugs, and treat an ongoing infection9. Enhancing the efficacy of bNAbs; in particular, designing bNAbs that retain potency against escape mutants selected during exposure to bNAbs, would facilitate their use as therapeutics. We previously used structure-based design to create NIH45-46G54W, a CD4-binding site (CD4bs) antibody with superior potency and/or breadth compared with other bNAbs. Here we report even more effective variants of NIH45-46G54W designed using analyses of the NIH45-46/gp120 complex structure and sequences of antibody-resistant HIV clones. One mutant, 45-46m2, neutralizes 96% of HIV strains in a cross-clade panel and viruses isolated from an HIV-infected individual that are resistant to all other known bNAbs, making it the single most broad and potent anti-HIV antibody to date. A detailed description of its mechanism is presented based on a 45-46m2/gp120 crystal structure. A second mutant, 45-46m7, designed to thwart resistance from NIH45-46G54W due to mutations in a V5/loop D gp120 consensus sequence, restores neutralization of HIV consensus sequence mutants, thus effectively targeting a common route of HIV escape. In combination, almost all HIV isolates are effectively neutralized, reducing the possible routes for the evolution of fit viral escape mutants.
Record Linkage Based on Entities' Behavior (2008)

Record linkage is the problem of identifying similar records across different data sources. Traditional record linkage techniques focus on using simple database attributes in a textual similarity comparison to decide on matched and non-matched records. Recently, record linkage techniques have considered useful extracted knowledge and domain information to help enhancing the matching accuracy. In this paper, we present a new technique for record linkage that is based on entity’s behavior, which can be extracted from a transaction log. In the matching process, we measure the improvement of identifying a behavior when comparing two entities by merging their transaction log. To do so, we use two matching phases; first, a candidate generation phase, which is fast and provide almost no false negatives, while producing low precision. Second, an accurate matching phase, which enhances the precision of the matching at high run time cost. In the candidates phase generation, behavior is represented by points in the complex plan, where we perform approximate evaluations. In the accurate matching phase, we use a heuristic called compressibility, where identified behaviors are more compressible. Our experiments show that the proposed technique can be used to enhance the record linkage quality while being practical for large logs. We also perform extensive sensitivity analysis for the technique’s accuracy and performance.
PWE-022 Patient Acceptability Of A Novel, Non-invasive Method Of Colonic Sampling For Biomarker Analysis (2014)

Introduction Biomarker analysis is commonly used for the diagnosis of those presenting with colorectal symptoms and monitoring of inflammatory bowel disease (IBD), but the acceptability of stool sampling is poor. It is proposed that material rich in the colonic mucocellular layer is deposited on the anal surface post-defaecation and can be sampled for biomarker analysis. Our aim was to develop a novel, non-invasive method of material collection post-defaecation and assess patient acceptability. Methods Patients with IBD (active cases and those in remission), irritable bowel syndrome (IBS) and a group of healthy volunteers were recruited. Participants were instructed to collect material from the surface of the anus immediately post-defaecation using a specially designed swab covered with flocked nylon (designed by DiagNodus Ltd). The collection process and preparation of samples was performed by patients at home using a specially designed kit. Samples were mailed back, ready for cytological and immunochemical analysis. Patients were provided with kits and asked to collect and return samples at predefined time-points. Patients completed a simple questionnaire to evaluate: (a) procedure convenience/acceptability, (b) ease of sample collection, (c) adequacy of time required for sampling and (d) overall impression each using a 5-point rating scale (1=poor to 5=good). Results 112 patients were recruited comprising of 60 patients with active IBD, 14 patients with IBD in remission, 31 patients with IBS and 7 healthy volunteers. Collected samples were returned by 97 (86.6%) study participants (88.3% of patients with active IBD, 78.6% of patients with IBD in remission, 87.1% of patients with IBS and 100% of healthy volunteers). Completed questionnaires were returned by 92 trial participants (94.8% of those providing samples). The mean and standard deviation (SD) of participant responses is provided in the table below. Abstract PWE-022 Table 1 Mean SD Convenience/Acceptability 4.57 0.497 Sampling ease 4.54 0.595 Adequacy of time required for sampling 4.53 0.575 Overall impression 4.57 0.553 Sampling was not associated with discomfort or harm. The material obtained proved suitable for both cytological assessment and protein biomarker estimation. Conclusion Material from the colonic mucocellular layer deposited in the anal area following defaecation is readily collectable using our specially designed kit and can provide material for both cytological assessment and biomarker quantification. This simple, reliable process is well tolerated and convenient as patients can provide samples from the comfort of their own home. This new technique warrants further study in different patient groups. Disclosure of Interest V. Chhaya: None Declared, A. Poullis: None Declared, T. Bandaletova Shareholder of: DiagNodus Ltd, Conflict with: Founder of DiagNodus Ltd, A. Loktionov Shareholder of: DiagNodus Ltd, Conflict with: Founder of DiagNodus Ltd.
Accurate Evaluation of Multiple-Access Performance in TH-PPM and TH-BPSK UWB Systems (2004)

A characteristic function method is proposed for precisely calculating the bit-error probability of time-hopping (TH) ultra-wideband (UWB) systems with multiple-access interference in an additive white Gaussian noise environment. The analytical expressions are validated by simulation and used to assess the accuracy of the Gaussian approximation. The Gaussian approximation is shown to be inaccurate for predicting bit-error rates (BERs) for medium and large signal-to-noise ratio (SNR) values. The performances of TH pulse position modulation (PPM) and binary phase-shift keying (BPSK) modulation schemes are accurately compared in terms of the BER. It is shown that the BPSK system outperforms the binary PPM system for all values of SNR. The sensitivity of the performance of the modulation schemes to the system parameters is also addressed through numerical examples.
Extending the range of wireless power transmission for bio-implants and wearables (2018)

This paper reports the latest achievements on an electrodynamic wireless power transmission (EWPT) system employing low-frequency (∼17 Hz), low-amplitude (< 1 mT) magnetic fields. Compared to inductively or resonantly coupled coils, the EWPT approach facilitates power transmission to multiple receivers in a cluttered environment with little restriction on their orientation. Using a 5.5 cm3 receiver, a maximum of 22 mW power transfer (4 mW/cm3 power density), and a maximum transmission distance of 60 cm are independently demonstrated. These capabilities are achieved using one of two transmitter technologies: a coil-based transmitter, and a rotating-magnet transmitter. Through-body transmission and multi-receiver transmission are also demonstrated, opening the way for applications targeting bio-implants and wearables.