gebhart/patrepeval huggingface dataset:
Impact of single-microphone dereverberation on DNN-based meeting transcription systems (2014)

Over the past few decades, a range of front-end techniques have been proposed to improve the robustness of automatic speech recognition systems against environmental distortion. While these techniques are effective for small tasks consisting of carefully designed data sets, especially when used with a classical acoustic model, there has been limited evidence that they are useful for a state-of-the-art system with large scale realistic data. This paper focuses on reverberation as a type of distortion and investigates the degree to which dereverberation processing can improve the performance of various forms of acoustic models based on deep neural networks (DNNs) in a challenging meeting transcription task using a single distant microphone. Experimental results show that dereverberation improves the recognition performance regardless of the acoustic model structure and the type of the feature vectors input into the neural networks, providing additional relative improvements of 4.7% and 4.1% to our best configured speaker-independent and speaker-adaptive DNN-based systems, respectively.
A concurrent canonical and modified miRNAome pan-cancer study on TCGA and TARGET cohorts leads to an enhanced resolution in cancer (2022)

The repository provides the raw read counts expression data (miRNA-Seq and RNA-Seq) and the source code developed for each analysis performed in this study.
Low Energy Electron Beam Activated IGZO-based Thin Film Transistor (2020)

The effect of electron beam irradiation (EBI) on Indium-Gallium-Zinc-oxide (IGZO)-based thin film transistor (TFT) is investigated. The TFT is formed to bottom gate structure on highly doped Si wafer for evaluating EBI effect. Before EBI treatment on IGZO based TFT, the electron density of EBI is measured by cut off probe. At an RF power of 150 W, the electron density varies from 4.04 × 108 to 1.59 × 109 cm−3 with EBI DC voltage from 50 to 1500 V. The TFT is treated by various kinds of EBI DC voltages with induced time from 0 to 180 s in a gas ambient (Ar/O2 = 10/0.3 sccm) at 100 °C. The maximum field-effect mobility (μEF)isabout 18 cm2/V-sec which is obtained as the sample annealed after EBI treatment. In addition, EBI treatment creates amorphous states into the IGZO channel which is interactively found by high resolution transmission-electron-microscopy characteristics. EBI treatment is applied to the bottom gate of IGZO based TFT on poly-imide (PI) film. After channel activation, the μEF is increased from 3.9 to 27.2 cm2/V-sec. From this study, it is anticipated that EBI will be a promising annealing method for fabricating flexible IGZO-based TFT.
Adenosine A1 and Prostaglandin E Receptor 3 Receptors Mediate Global Airway Contraction after Local Epithelial Injury (2012)

Epithelial injury and airway hyperresponsiveness are prominent features of asthma. We have previously demonstrated that laser ablation of single epithelial cells immediately induces global airway constriction through Ca(2+)-dependent smooth muscle shortening. The response is mediated by soluble mediators released from wounded single epithelial cells; however, the soluble mediators and signaling mechanisms have not been identified. In this study, we investigated the nature of the epithelial-derived soluble mediators and the associated signaling pathways that lead to the L-type voltage-dependent Ca(2+) channel (VGCC)-mediated Ca(2+) influx. We found that inhibition of adenosine A1 receptors (or removal of adenosine with adenosine deaminase), cyclooxygenase (COX)-2 or prostaglandin E receptor 3 (EP3) receptors, epidermal growth factor receptor (EGFR), or platelet-derived growth factor receptor (PDGFR) all significantly blocked Ca(2+) oscillations in smooth muscle cells and airway contraction induced by local epithelial injury. Using selective agonists to activate the receptors in the presence and absence of selective receptor antagonists, we found that adenosine activated the signaling pathway A1R→EGFR/PDGFR→COX-2→EP3→VGCCs→calcium-induced calcium release, leading to intracellular Ca(2+) oscillations in airway smooth muscle cells and airway constriction.
Synthesis and base-pairing properties of C-nucleotides having 1-substituted (2009)

Oligonucleotides including C-nucleotides having 1-substitued 1H-1,2,3-triazoles as artificial nucleobases were conveniently synthesized by the post-elongation modification method using the copper(I)-cata- lyzed alkyne-azide 1,3-dipolar cycloaddition (CuAAC) reaction. The base-pairing properties of the tria- zole nucleobase analogs in forming duplexes with oligonucleotides were investigated by the Tm experiments.
Chemoselective oxidation of [(arylthioalkyl pyrrolidino)carbenechromium(0) pentacarbonyl complexes: synthesis of (arylsulfinyl and arylsulfonylalkyl pyrrolidino)carbene complexes (1995)

The chemoselective oxidation of pentacarbonyl-[amino(arylthioalkyl)carbene]chromium(O) complexes by using N-sulfonyloxaziridine or dimethyldioxirane affords the corresponding sulfoxide or sulfone derivatives in good to high chemical yields
Targeted Maximum Likelihood Estimation of Effect Modification Parameters in Survival Analysis (2011)

The Cox proportional hazards model or its discrete time analogue, the logistic failure time model, posit highly restrictive parametric models and attempt to estimate parameters which are specific to the model proposed. These methods are typically implemented when assessing effect modification in survival analyses despite their flaws. The targeted maximum likelihood estimation (TMLE) methodology is more robust than the methods typically implemented and allows practitioners to estimate parameters that directly answer the question of interest. TMLE will be used in this paper to estimate two newly proposed parameters of interest that quantify effect modification in the time to event setting. These methods are then applied to the Tshepo study to assess if either gender or baseline CD4 level modify the effect of two cART therapies of interest, efavirenz (EFV) and nevirapine (NVP), on the progression of HIV. The results show that women tend to have more favorable outcomes using EFV while males tend to have more favorable outcomes with NVP. Furthermore, EFV tends to be favorable compared to NVP for individuals at high CD4 levels.
Lysine-Tryptophan-Crosslinked Peptides Produced by Radical SAM Enzymes in Pathogenic Streptococci (2017)

Macrocycles represent a common structural framework in many naturally occurring peptides. Several strategies exist for macrocyclization, and the enzymes that incorporate them are of great interest, as they enhance our repertoire for creating complex molecules. We recently discovered a new peptide cyclization reaction involving a crosslink between the side chains of lysine and tryptophan that is installed by a radical SAM enzyme. Herein, we characterize relatives of this metalloenzyme from the pathogens Streptococcus agalactiae and Streptococcus suis. Our results show that the corresponding enzymes, which we call AgaB and SuiB, contain multiple [4Fe-4S] clusters and catalyze Lys-Trp crosslink formation in their respective substrates. Subsequent high-resolution-MS and 2D-NMR analyses located the site of macrocyclization. Moreover, we report that AgaB can accept modified substrates containing natural or unnatural amino acids. Aside from providing insights into the mechanism of this unusual modification, the substrate promiscuity of AgaB may be exploited to create diverse macrocyclic peptides.
Abstract CT085: Pharmacodynamic correlates in a phase I study of INCMGA00012, a PD-1 antagonistic monoclonal antibody (2019)

Background: The role of the PD-1 / PD-L1 axis in limiting T cell activity has been well established. Effective blockade of this pathway has been demonstrated to lead to an increase in T cell activity and to yield clinical activity in cancer patients. INCMGA00012 is a humanized IgG4 monoclonal antibody that binds to human PD-1 and blocks its interaction with PD-L1/PD-L2. This therapeutic antibody has demonstrated acceptable tolerability with evidence of clinical activity in a phase 1 study in patients with solid tumors (NCT03059823). Pharmacodynamic markers demonstrating biological activity of INCMGA0012 were assessed in samples collected during the study.Methods: Blood samples were collected at baseline and at various time points following treatment from patients receiving doses of either 3mg/Kg (Q2W) in the tumor-specific expansion cohort or a flat-dose of 500 or 750mg (Q4W) in the tumor-agnostic expansion cohort. Receptor occupancy was measured on circulating T cells by flow cytometry and serum cytokine levels were measured using either a proximity extension assay or immunoassays. In addition, circulating immune cell phenotyping was analyzed using flow cytometry and PBMC functionality evaluated using ex-vivo re-stimulation.Results: All tested doses of INCMGA0012 evaluated demonstrated a full saturation of the PD-1 receptor at trough on circulating CD4 and CD8 T cells. In all tested cohorts, an increase in serum CXCL9 and CXCL10 was observed following infusion with INCMGA0012. Moreover, an increase in the proliferation of circulating T cells was observed on treatment compared to baseline. Concurrently, following ex vivo re-stimulation, T cells isolated from peripheral blood mononuclear cells demonstrated an increased capacity to secrete cytokines.Conclusion: These results provide evidence that INCMGA0012 is biologically active and leads to an increase in IFNγ-related protein levels (i.e. CXCL9 and CXCL10) and in T cell proliferation. The clinical activity of INCMGA0012 is undergoing further evaluation in several indications, including endometrial cancer, Merkel cell carcinoma and squamous carcinoma of the anal canal. Several combination studies have also been initiated.Citation Format: Thomas Condamine, Sherry Owens, Patricia Feldman, Ross La Motte-Mohs, John Muth, Bradley Sumrow, Paul Moore, Robert Newton. Pharmacodynamic correlates in a phase I study of INCMGA00012, a PD-1 antagonistic monoclonal antibody [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT085.
Patient reported outcomes among treatment modalities for prostate cancer. (2016)

IPSS and SHIM score patterns differed among treatment modalities. These data can be used to predict changes in urinary and sexual function over time based on modality and baseline score.
Free-form Fresnel RXI-RR Köhler design for high-concentration photovoltaics with spectrum-splitting (2011)

Development of a novel HCPV nonimaging concentrator with high concentration (&gt;500x) and built-in spectrum splitting concept is presented. It uses the combination of a commercial concentration GaInP/GaInAs/Ge 3J cell and a concentration Back-Point-Contact (BPC) silicon cell for efficient spectral utilization, and external confinement techniques for recovering the 3J cell's reflection. The primary optical element (POE) is a flat Fresnel lens and the secondary optical element (SOE) is a free-form RXI-type concentrator with a band-pass filter embedded in it - Both the POE and SOE performing K&#246;hler integration to produce light homogenization on the receiver. The band-pass filter transmits the IR photons in the 900-1200 nm band to the silicon cell. A design target of an "equivalent" cell efficiency ~46% is predicted using commercial 39% 3J and 26% Si cells. A projected CPV module efficiency of greater than 38% is achievable at a concentration level larger than 500X with a wide acceptance angle of &plusmn;1&deg;. A first proof-of concept receiver prototype has been manufactured using a simpler optical architecture (with a lower concentration, ~100x and lower simulated added efficiency), and experimental measurements have shown up to 39.8% 4J receiver efficiency using a 3J cell with a peak efficiency of 36.9%.
GaInAsSb Detectors And Lasers For Mid-Infrared Optical Communications (1987)

Room-temperature Ga0.82 InO.18As0.17Sb0.83/GaSb photodiodes have been fabricated for use at wavelengths to 2.3&mu;pm. Back-illuminated heterojunction p-n photodiodes show high external quantum efficiency (65%) for wavelengths between 1.8 and 2.3 &mu;m. Front-illuminated pin homojunction photodiodes have an impulse response of 110 ps and respond to pseudorandom modulation at rates as high as 4 Gbit/s. Double heterostructure Ga0.841n0.16As0.15Sb0.85/A10.34Ga0.66As0.04Sb0.96 lasers have pulsed threshold current densities as low as 3.5 kA/cm2 at room temperature and operate cw at temperatures of up to 235K.
Longitudinal assessment of segmental motion of the cervical spine following total disc arthroplasty: a comparative analysis of devices (2022)

Analysis by TDA device brand demonstrated that motion preservation differs depending on disc design. Certain devices, including M6-C and Mobi-C, improve ROM on flexion/extension from preoperatively to postoperatively and continue to increase slightly at final follow-up. On the other hand, devices such as PCM and ProDisc-C contributed to greater segmental stiffness, with a gradual decline in ROM seen with ProDisc-C. Further studies are needed to understand how much segmental ROM is ideal after TDA for preservation of physiological cervical kinematics.
Plato Dialogue System: A Flexible Conversational AI Research Platform (2020)

As the field of Spoken Dialogue Systems and Conversational AI grows, so does the need for tools and environments that abstract away implementation details in order to expedite the development process, lower the barrier of entry to the field, and offer a common test-bed for new ideas. In this paper, we present Plato, a flexible Conversational AI platform written in Python that supports any kind of conversational agent architecture, from standard architectures to architectures with jointly-trained components, single- or multi-party interactions, and offline or online training of any conversational agent component. Plato has been designed to be easy to understand and debug and is agnostic to the underlying learning frameworks that train each component.
Photonic crystal cavities and waveguides (2002)

Recently, it has also become possible to microfabricate high reflectivity mirrors by creating two- and three-dimensional periodic structures. These periodic "photonic crystals" can be designed to open up frequency bands within which the propagation of electromagnetic waves is forbidden irrespective of the propagation direction in space and define photonic bandgaps. When combined with high index contrast slabs in which light can be efficiently guided, microfabricated two-dimensional photonic bandgap mirrors provide us with the geometries needed to confine and concentrate light into extremely small volumes and to obtain very high field intensities. Here we show the use of these "artificially" microfabricated crystals in functional nonlinear optical devices, such as lasers, modulators, and waveguides.
Continuous-wave coherent Raman spectroscopy via plasmonic enhancement for picomolar detection (Conference Presentation) (2020)

We report a successful combination of stimulated Raman spectroscopy (SRS) and surface-enhanced Raman scattering (SERS) using cw laser sources and gold/silica nanoparticles with embedded reporter molecules. We describe the preparation method for our gold/silica nanoparticles as well as the effect of probe wavelength, pump and probe power, polarization and sample concentration on the cwSESRS signal. Altogether, a stable 10-12 orders of magnitude enhancement in the stimulated Raman signal is achieved because of the amplification of both pump and probe beams, leading us to detect pico-molar nanoparticle concentrations. The coherent Raman spectra matches the incoherent conventional Raman spectra of the reporter molecules. Unlike conventional incoherent SERS, this approach offers several advantages including improved trace analyte detection, the low cost accessibility of cw sources, and a coherent stimulated signal of microwatt intensities for applications such as Molecular Holography.
Strong Suppression of Thermal Conductivity in the Presence of Long Terminal Alkyl Chains in Low‐Disorder Molecular Semiconductors (2021)

While the charge transport properties of organic semiconductors have been extensively studied over the recent years, the field of organics-based thermoelectrics is still limited by a lack of experimental data on thermal transport and of understanding of the associated structure-property relationships. To fill this gap, a comprehensive experimental and theoretical investigation of the lattice thermal conductivity in polycrystalline thin films of dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]thiophene (Cn-DNTT-Cn with n = 0, 8) semiconductors is reported. Strikingly, thermal conductivity appears to be much more isotropic than charge transport, which is confined to the 2D molecular layers. A direct comparison between experimental measurements (3ω-Völklein method) and theoretical estimations (approach-to-equilibrium molecular dynamics (AEMD) method) indicates that the in-plane thermal conductivity is strongly reduced in the presence of the long terminal alkyl chains. This evolution can be rationalized by the strong localization of the intermolecular vibrational modes in C8-DNTT-C8 in comparison to unsubstituted DNTT cores, as evidenced by a vibrational mode analysis. Combined with the enhanced charge transport properties of alkylated DNTT systems, this opens the possibility to decouple electron and phonon transport in these materials, which provides great potential for enhancing the thermoelectric figure of merit ZT.
Mechanism of sperm-zona pellucida penetration during mammalian fertilization: 26S proteasome as a candidate egg coat lysin. (2007)

Despite years of research work, biologists remain divided over the issue of zona pellucida function during fertilization and the mode of sperm-ZP penetration. The present review examines the emerging evidence for the participation of ubiquitin-proteasome pathway in the process of sperm-ZP penetration generated in the last five years in species of mammals, ascidians and invertebrates. The 26S proteasome, a multi-subunit protease, selectively recognizes, and degrades, egg coat substrate proteins tagged by a covalent ligation of a small, multimeric protein, ubiquitin. Our in vitro work with pig gametes indicates that the sperm-borne 26S proteasomes selectively degrade an ubiquitinated ZP (glyco)protein during fertilization. We suggest that one or more of the ZP proteins are ubiquitinated, and proteasomes associated with the inner acrosomal membrane, are exposed as a result of acrosomal exocytosis. Sperm-ZP penetration may involve the ZP-deubiquitination, with several proteasomal subunits becoming phosphorylated. Polyubiquitin chain recognition activities associated with the sperm acrosomal proteasome could also contribute to anti-polyspermy control after sperm-egg fusion. Here, we bring together the relevant recent data on the mechanism of sperm-ZP penetration in mammals. Such observations could possibly lead to the development of novel non-hormonal contraceptives, improvement of infertility diagnostics and optimization of assisted reproduction.
Investigating Pattern Transfer in the Small-Gap Regime Using Electron-Beam Stabilized Nanoparticle Array Etch Masks (2010)

Extreme small-gap lithography is necessary for future bit-patterned media, but is under-explored due to lack of etch masks with small enough gaps. Self-assembled nanoparticle arrays featuring 2 nm gaps are promising candidates, but exhibit lateral instability during etching. We present a novel one-step method for stabilizing their order by exposing to intense electron beam doses, and show pattern transfer into an underlying Si wafer. Electron beam-induced cross-linking of the surfactant is hypothesized to explain the improved stability. We suggest that this process could be used to pattern hard masks for subsequent pattern transfer into underlying magnetic films, with the gap and feature size required for bit patterned media to achieve densities in excess of 2 terabits per square inch.
Unsupervised Italian word sense disambiguation using WordNets and unlabeled corpora (2002)

This paper presents a novel method for unsupervised word sense disambiguation, which combines multiple information sources, including semantic relations, large unlabeled corpora, and cross-lingual distributional statistics. This method extends and builds on the JHU system that participated in the SENSEVAL2 exercise. Experiments performed on the SENSEVAL2 Italian lexical-sample data show significant improvements over previously published results on this data set.
MicroRNAs play a central role in molecular dysfunctions linking inflammation with cancer (2013)

It is now largely admitted that a pro-inflammatory environment may curtail anti-tumor immunity and favor cancer initiation and progression. The discovery that small non-coding regulatory RNAs, namely microRNAs (miRNAs), regulate all aspects of cell proliferation, differentiation, and function has shed a new light on regulatory mechanisms linking inflammation and cancer. Thus, miRNAs such as miR-21, miR-125b, miR-155, miR-196, and miR-210 that are critical for the immune response or hypoxia are often overexpressed in cancers and leukemias. Given the high number of their target transcripts, their deregulation may have a number of deleterious consequences, depending on the cellular context. In this review, we focus on how the factors encoded by transcripts targeted by these five miRNAs, be they transcription factors, tumor-suppressors, or regulators of different signaling pathways, can deregulate the immune response and favor pro-tumor immunity. Furthermore, we expose how the misdirected action of the main regulators of these miRNAs, such as nuclear factor κB (NF-κB), activator protein-1 (AP-1), and signal transduction and activators of transcription (STAT) transcription factors, or AKT and transforming growth factor β (TGFβ) signaling pathways, can contribute to decrease anti-tumor immunity and enhance cell proliferation and oncogenesis. We conclude by briefly discussing about how these discoveries may possibly lead to the development of new miRNA-based cancer therapies.
Neutropenia alters lung cytokine production in mice and reduces their susceptibility to pulmonary cryptococcosis (2003)

Neutrophils are generally considered to contribute to host defense through their potent microbicidal activity. However, there is accumulating evidence that neutrophils also have an important regulatory role in establishing the balance of Th1 and Th2 responses. This study investigated the role of neutrophils in defense against pulmonary Cryptococcus neoformans infection using neutrophil-depleted BALB/c mice generated by administering mAb RB6-8C5. Neutropenic mice with pulmonary infection survived significantly longer than control mice, but there was no difference between groups infected intravenously. On day 1 of infection, neutropenic mice had significantly smaller fungal burdens than control mice. On day 7, neutropenic mice had significantly higher lung concentrations of IL-10, TNF-alpha, IL-4, and IL-12 than control mice, but there was no difference in IFN-gamma and MCP-1 levels. Neutrophils influenced the outcome of cryptococcal infection in mice through mechanisms that did not involve a reduction in early fungal burden. The absence of neutrophils in lung tissue during the initial stages of infection appeared to alter the inflammatory response in a manner that was subsequently beneficial to the host. Higher levels of Th1- and Th2-associated cytokines in neutropenic mice could have simultaneously promoted a strong cellular response while reducing inflammatory damage to the lung. Our results support the emerging concept that neutrophils play an important function in modulating the development of the immune response.