gebhart/patrepeval huggingface dataset:
Fundamental frequency estimation of musical signals using a two-way mismatch procedure (1994)

Fundamental frequency (F0) estimation for quasiharmonic signals is an important task in music signal processing. Many previously developed techniques have suffered from unsatisfactory performance due to ambiguous spectra, noise perturbations, wide frequency range, vibrato, and other common artifacts encountered in musical signals. In this paper a new two-way mismatch (TWM) procedure for estimating F0 is described which may lead to improved results in this area. This computer-based method uses the quasiharmonic assumption to guide a search for F0 based on the short-time spectra of an input signal. The estimated F0 is chosen to minimize discrepancies between measured partial frequencies and harmonic frequencies generated by trial values of F0. For each trial F0, mismatches between the harmonics generated and the measured partial frequencies are averaged over a fixed subset of the available partials. A weighting scheme is used to reduce the susceptibility of the procedure to the presence of noise or absence of certain partials in the spectral data. Graphs of F0 estimate versus time for several representative recorded solo musical instrument and voice passages are presented. Some special strategies for extending the TWM procedure for F0 estimations of two simultaneous voices in duet recordings are also discussed.
Stochastic Linear Bandits with Protected Subspace (2020)

We study a variant of the stochastic linear bandit problem wherein we optimize a linear objective function but rewards are accrued only orthogonal to an unknown subspace (which we interpret as a \textit{protected space}) given only zero-order stochastic oracle access to both the objective itself and protected subspace. In particular, at each round, the learner must choose whether to query the objective or the protected subspace alongside choosing an action. Our algorithm, derived from the OFUL principle, uses some of the queries to get an estimate of the protected space, and (in almost all rounds) plays optimistically with respect to a confidence set for this space. We provide a $\tilde{O}(sd\sqrt{T})$ regret upper bound in the case where the action space is the complete unit ball in $\mathbb{R}^d$, $s &lt; d$ is the dimension of the protected subspace, and $T$ is the time horizon. Moreover, we demonstrate that a discrete action space can lead to linear regret with an optimistic algorithm, reinforcing the sub-optimality of optimism in certain settings. We also show that protection constraints imply that for certain settings, no consistent algorithm can have a regret smaller than $Ω(T^{3/4}).$ We finally empirically validate our results with synthetic and real datasets.
Supply and Demand of Chemists in the United States (2015)

A Presidential Task Force on Supply and Demand of Chemists in the U.S. was appointed by ACS President Marinda Li Wu in 2013. The purpose was to gather data to inform and guide ACS National Committees as they provide programs, products and services to the ACS membership. This is the final report of this Presidential Task Force. The initial Presidential Task Force report with its three recommendations was first shared with Dr. Wu in August 2014. Pertinent recommendations were then shared with six stakeholder committees of the ACS to gather more feedback for refinement of the recommendations. The final Presidential Task Force report was issued in September 2014 and disseminated within the ACS.
Engagement of interleukin-7 receptor stimulates tyrosine phosphorylation, phosphoinositide turnover, and clonal proliferation of human T-lineage acute lymphoblastic leukemia cells (1991)

The purposes of this study were to examine the biologic effects of the engagement of the interleukin-7 receptor (IL-7R) with recombinant human interleukin-7 (rhIL-7) in immunophenotypically distinct T-lineage acute lymphoblastic leukemia (ALL) blasts and to elucidate the biochemical nature of the IL-7R-linked transmembrane signal in rhIL-7-responsive T-lineage ALL blast populations. In the absence of costimulants, rhIL-7 stimulated the in vitro proliferation and colony formation of freshly isolated leukemic blasts from six to eight T-lineage ALL patients with a mean plating efficiency of 196 +/- 53 (background subtracted) colonies/10(5) blasts plated. Stimulation of T-lineage ALL blasts with rhIL-7 resulted in markedly enhanced tyrosine phosphorylation of six distinct phosphoproteins with molecular weights of 57, 72, 98, 123, 150, and 190 Kd, and induced a rapid increase in the production of inositol-1,4,5-trisphosphate (Ins-1,4,5-P3), which was inhibitable by the tyrosine-specific protein kinase inhibitor genistein, but not by the serine/threonine-specific protein kinase C inhibitor H7. Similarly, rhIL-7 stimulated Ins-1,4,5-P3 production in CEM-1.3 T-lineage ALL cells and this stimulation was inhibitable by the tyrosine-specific protein kinase inhibitors genistein and herbimycin A, but not by H-7. Thus, the transmembrane signal triggered by engagement of the IL-7R is intimately linked to a functional tyrosine-specific protein kinase pathway and stimulates the phosphoinositide (PI) turnover and proliferation of T-lineage ALL blasts. The presented data confirm and extend previous studies on the expression of functional IL-7R on T-lineage ALL blasts and support the hypothesis that IL-7 may play an important regulatory role in the biology of T-lineage ALL.
Investigation the Effect of Particle Size Distribution on Processing Parameters Optimisation in Selective Laser Melting Process (2011)

Selective Laser Melting is an efficient process for producing metal parts with minimal subtractive post-processing required. Analysis of the parameters controlling the part quality has been performed focusing on the energy intensity during processing and the effect of the particle size distribution on factors such as ultimate tensile strength and surface finish. It is shown that the controlling the energy intensity is key to quality and can be affected by varying, for example, laser beam diameter or the scanning rate.
Chronic lithium treatment affects rat brain and serum dehydroepiandrosterone (DHEA) and DHEA-sulphate (DHEA-S) levels (2004)

Lithium (Li) is an established effective treatment for bipolar disorder. However, the molecular mechanism of its action is still unknown. Dehydroepiandrosterone (DHEA) and its sulphate ester (DHEA-S) are adrenal hormones also synthesized de novo in the brain as neurosteroids. Recent studies have suggested that DHEA has mood-elevating properties and may demonstrate antidepressant effects. 3(2)-Phosphoadenosine 5-phosphate (PAP) phosphatase is a novel Li-inhibitable enzyme involved in sulphation processes. In the present study we examined the impact of 10 d Li treatment on serum and brain DHEA and DHEA-S levels in rats. Our results show that Li administration lowered frontal cortex and hippocampus DHEA and DHEA-S levels, in line with our hypothesis assuming that Lis inhibition of PAP phosphatase leads to elevated PAP levels resulting in inhibition of sulphation and reduction in brain DHEA-S levels. Future studies should address the involvement of neurosteroids in the mechanism of Lis mood stabilization.
Chemical generation of checkpoint inhibitory T cell engagers (CiTEs) for the treatment of cancer (2023)

Bispecific antibodies (bsAbs) provide enticing therapeutic opportunities in the area of immunotherapy, especially in the field of immuno-oncology. These constructs can bind two separate antigenic epitopes and thus provide access to unique mechanisms of action (MoAs). A key MoA is unlocked by bispecific T cell engagers (BiTEs), which cause T cells to be cross-linked with a targeted cancer cell, ultimately leading to death of the targeted cell. It has been shown that the combination of a BiTE with checkpoint inhibition, such as blockade of the PD-1/PD-L1 pathway, can lead to a synergistic effect and greater efficacy. Constructs built from a BiTE core (anti-CD3/anti-cancer antigen) with an immunomodulatory protein added, have been dubbed checkpoint-inhibitory T cell-engagers (CiTEs). Both bsAbs and CiTEs have traditionally been generated via protein engineering. However, recently, improved chemical methods for the construction of bsAbs have been reported. This includes a strategy developed by the Chudasama and Baker groups to synthesize homogenous fragment-based bsAbs from antibodies’ fragments antigen binding (Fabs), utilising click-enabled pyridazinediones (PDs) for functional disulfide re-bridging, followed by strain-promoted inverse electron-demand Diels-Alder cycloaddition (SPIEDAC) click chemistry to attach the two Fabs to each other. In this paper, we describe a first-in-class chemical method to generate biotin-functionalized three-protein conjugates, building significantly on the previously described PD-method. The three-protein constructs generated here include two such CiTE molecules, one containing an anti-PD-1 Fab, the other containing an immunomodulatory enzyme Salmonella typhimurium sialidase; FabCD3-FabHER2-FabPD-1-Biotin and FabHER2-FabCD3-Sia-Biotin. These constructs (along with suitable controls) were tested for their biological activity, and each of their protein components were shown to retain their function. Their efficacy was also compared to a simpler BiTE scaffold and was shown to be superior, with the sialidase-containing CiTE especially showing significantly enhanced potency in vitro. The chemical method described here has the potential to enable the rapid generation of a plethora of multi-protein constructs, which we envisage would be especially useful in hit-identification screening but could also potentially be scaled up for drug-development after further optimization.
Resonant tank motor model for voltage reflection simulations with PWM drives (2003)

Reflected wave transient voltages that are impressed on drive output cables and low voltage AC induction motors are normally simulated with steep fronted dv/dt pulse waveforms from PWM voltage source inverters. System simulation arises from a need to correlate reflected wave peak voltage and risetime with the dielectric insulation capability of both the motor and cable. To obtain reasonable results, accurate models of each component must be employed. This investigation concentrates on parameter identification for a high frequency resonant tank motor model from fractional to several hundred horsepower.
AQP9 and UT‐A facilitate hepatocyte basolateral membrane urea permeability in mouse (2012)

In mammals, nitrogen from protein degradation is disposed as urea. Several studies have investigated expression of urea transporters in hepatocytes, where urea is produced. Nevertheless, the role of protein facilitated urea transport in liver remains unknown. In the presented study we determine urea permeability in isolated basolateral hepatocyte membranes by stopped flow light scattering measurements. The urea channel inhibitors phloretin and dimethylurea reduced the urea permeability by 70% and 40%, respectively. In basolateral membranes isolated from AQP9 (AQP9−/−) and UT‐A (UT‐A−/−) single knockout, and AQP9−/−:UTA−/− double knockout mice, urea permeability (Purea) was decreased by 30%, 40%, and 76%, respectively, compared to wild type mice. In addition, we investigated the physiological role of AQP9 in mouse hepatocyte function following exposure to high oral glutamine doses or high protein diet. These conditions did not affect the concentrations of urea or ammonia in AQP9−/− mouse tissues and plasma, respectively. Similarly, hepatocyte urea synthesis of UT‐A−/− mice appeared normal. We currently conclude that both, AQP9 and a UT‐A gene product, constitute primary but redundant urea channels in hepatocytes. This study was supported by the Lundbeck Foundation.
A controlled study of progabide in partial seizures (1987)

The results of a multicenter, double-blind, placebo-controlled clinical trial of the efficacy and safety of progabide (PGB) in the treatment of partial seizures are presented. This study was performed with a number of rigorous controls not usually present in clinical trials. These included uniform co-medication in which all patients received only phenytoin and carbamazepine; concentrations of these two drugs were maintained within narrow, predefined concentration ranges. There was no statistically significant difference between PGB and placebo in seizure frequency and seizure duration for most of the analyses performed. One patient was withdrawn from the study because of hepatotoxicity. PGB was associated with a significant inhibition of phenytoin but not carbamazepine clearance. The results of this study indicate that PGB was not a potent antiepileptic drug in this population of persons with intractable epilepsy.
Replication Data for: Quantifying oxygen induced surface enrichment of a dilute PdAu alloy catalyst (2022)

The data underlying this published work have been made publicly available in this repository as part of the IMASC Data Management Plan. This work was supported as part of the Integrated Mesoscale Architectures for Sustainable Catalysis (IMASC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012573.
Expression pattern analysis of transcribed HERV sequences is complicated by ex vivorecombination (2007)

As RT-PCR probably will be instrumental for isolating an infectious HERV-K(HML-2) variant, generation of "new" HERV-K(HML-2) sequences by ex vivo recombination seems inevitable. Further complicated by an unknown amount of allelic sequence variation in HERV-K(HML-2) proviruses, newly identified HERV-K(HML-2) variants should be interpreted very cautiously.
Characterization and Reaction to Fire of Polymer Nanocomposites with and without Conventional Flame Retardants (2008)

In this work, the reaction to fire of polymer nanocomposites (thermoplastic polyurethane, polylactide and polyamide-6) containing different nanofillers (organoclay, polyhedral silsesquioxanes or POSS and carbon nanotube) is investigated. When high level of nanodispersion is achieved (shown by transmission electron microscopy (TEM)), they exhibit good flame retardancy in specific scenarii (high heat flux), but fail to flammability tests (LOI, UL-94). The mechanism of protection is the formation of mineral layer associated to char promotion but the protective coating is not efficient enough to provide the highest standard of protection. It is shown that this technology gives the best results combined with conventional flame retardants and leads to synergistic effects. The aspects of nanodispersion of the filler with the flame retardant are also fully commented in the paper using TEM and electron microprobe.
Impact of Imperfections on the Performance of M-phase Filters (2013)

Although a high-Q M-phase filter has a simple structure, there are numerous implementation-related imperfections that must be scrutinized carefully and evaluated for their impact on the filter. The phase noise of the LO clocks, the second-order nonlinearity of the switches, the phase error between the LOs, and the harmonic downconversion and thermal noise of switches are examples of some of these imperfections. We will examine the impact of these imperfections in this chapter. For the sake of simplicity, we will discuss the effects of these imperfections in the four-phase bandpass filter but will apply our findings to the M-phase high-Q bandpass filters.
Single-layer graphene oxide sheet: a novel substrate for dip-pen nanolithography (2011)

Graphene oxide (GO) sheet is used as a novel substrate for dip-pen nanolithography (DPN). After GO is transferred onto SiO(2) using the Langmuir-Blodgett technique, CoCl(2) is patterned on both GO and exposed SiO(2) substrates simultaneously by DPN, which is used for growth of different structured carbon nanotubes.
Operator quantum error correction (2006)

This paper is an expanded and more detailed version of the work \cite{KLP04} in which the Operator Quantum Error Correction formalism was introduced. This is a new scheme for the error correction of quantum operations that incorporates the known techniques --- i.e. the standard error correction model, the method of decoherence-free subspaces, and the noiseless subsystem method --- as special cases, and relies on a generalized mathematical framework for noiseless subsystems that applies to arbitrary quantum operations. We also discuss a number of examples and introduce the notion of "unitarily noiseless subsystems''.
Adjustable-Cost Overlays for Runtime Compilation (2015)

Previous work has shown that virtual architectures, or overlays, can greatly reduce lengthy FPGA compile times by providing application-specialized resources along with a flexible interconnect to support application changes. However, retaining full configurability of interconnect has also required significant area overhead. In this paper, we introduce a family of overlay architectures called super nets and an associated design methodology that uses data path merging to provide minimal-overhead support for multiple source net lists, and optionally provides an adjustable amount of source flexibility through a secondary interconnect network. We demonstrate that super nets can enable runtime compilation up to 13,000× faster than direct register-transfer logic (RTL) implementation, with up to 70% lower area than selectively enabled RTL data paths. Finally, we explore the design space of this family of overlays and show that it affords significant freedom to trade additional area for increased flexibility to support deviations from the source set, as introduced during development or by optimizations performed at runtime.
Mesenchymal Stromal Cells From AML Bone Marrow Are Abnormal by Gene Expression Profiling. (2010)

Abstract Abstract 1055 Cytogenetic and other evidence suggests that the mesenchymal stromal cell (MSC) is abnormal in bone marrow (BM) affected by acute myelogenous leukemia (AML). To gain further insight into molecular and physiologic abnormalities, we used Affymetrix HG-U133 Plus 2 microarrays to compare gene expression between BM-MSCs from 12 AML patients and BM-MSCs from 4 normal donors (ND). BM-MSCs were purified by in vitro culture as adherent cells with a purity of over 95%. Comparison at the single-gene level between AML and ND samples found only one differentially-expressed probe by t tests at a false-discovery rate (FDR) of 0.1. Comparison by the gene set enrichment analysis (GSEA) method of Subramanian et al., which is a more powerful way to find small differences that are significantly enriched within sets of biologically-related genes, first found that many enriched gene sets were predominantly the result of data from one AML sample. After excluding this sample, GSEA at an FDR of 0.25 found 115 downregulated gene sets for AML BM-MSCs from the Gene Ontology-based “C5” category of the mSigDB collection of gene sets. 19 of the 20 most significantly enriched downregulated gene sets were related to cell cycle progression, indicating that BM-MSCs are less proliferative in AML than in normal BM. An upregulated enriched gene set in AML BM-MSCs, from the “C2” category of curated gene sets, was composed of extracellular matrix genes for keratins, collagen, and laminin; while surprising, this is consistent with reports of BM-derived MSCs differentiating into epithelial cells after autografting, and suggest that BM-MSCs in AML may remodel the extracellular matrix. Overall, these results indicate that BM-MSCs in AML patients are substantially different from normal BM-MSCs. These and other differences could have substantial effects on the BM microenvironment and therapy response in AML, and should be studied further. Disclosures: No relevant conflicts of interest to declare.
Structural Topology Optimization of Turbomachinery Components Using New Manufacturing Techniques and Innovative Materials (2017)

Structural topology optimization is an innovative approach in turbomachinery to satisfy the increasing demand for higher rotational speeds, light components and optimized natural frequencies, with a remarkable economic impact. Although this approach has never been extensively applied before to rotating machines, it is very promising for the mechanical optimization of rotor and stator components. This approach enables the creation of complex three-dimensional geometries, which are usually difficult or impossible to be built using traditional manufacturing methods. Thanks to innovative technologies and to the use of innovative materials, it is now possible to effectively exploit topology optimization. It allows to change the topology of the structures, significantly improving material distribution within a given design space for a given set of boundary conditions and loads. In this work, the authors have deeply investigated the applicability of topology optimization to the fields of turbomachinery and rotordynamics.
Supplemental Figure Legend from Dendritic Cells in Irradiated Mice Trigger the Functional Plasticity and Antitumor Activity of Adoptively Transferred Tc17 Cells via IL12 Signaling (2023)

&lt;p&gt;Supplemental Figure Legend&lt;/p&gt;
P2‐298: The novel strategy for generation of effective and safe Alzheimer's disease vaccine based on conventional influenza virus vaccine modified to express Aβ1–11 (2008)

The antibodies to the beta-amyloid (Aβ) peptide endows therapeutic effects in Alzheimer's disease both in pre-clinical and clinical settings. This approach is currently hampered by elicitation of pathological autoreactivity. In order to overcome this problem,we have developed several strategies to limit generation of autoreactive Th cells. For example, we first reported generation of an epitope vaccine composed of small immunodominant self B cell epitope of Aβ42 fused with a foreign promiscous CD4+Th cell epitope, PADRE, which induced high titers of anti-Aβ antibodies without generation of potentially harmful autoreactive T cells. Importantly, these antibodies were therapeutically active, as we showed in two different mouse models of AD, APP/Tg 2576 and 3xTg-AD. After having demonstrated feasibility of antibody response to Aβ in the absence of autoreactive Th cells, we suggested that in humans anti-Aβ antibody could be safer if they will be generated in pre-symptomatic people. More specifically, we hypothesized that in these people who did not develop yet significant deposits of toxic species of Aβ in the brains anti-Aβ antibodies may not induce microhemorrhages. In order to test this hypothesis, we decided to use the influenza virus platform for delivery of immunodominant B cell epitopes of Aβ42 (Aβ1–10) into the host. We demonstrated that such dual vaccine activates only anti-viral Th cells and induces robust anti-Aβ and anti-influenza antibodies in wild-type and APP/Tg mice. Currently, we are testing the ability of APP/Tg mice previously vaccinated with influenza vaccine, as opposed to non-influenza-vaccinated animals, promote more rapid and potent anti-Aβ antibody production when boosted once with dual vaccine. In other words, we are investigating the role of pre-existing anti-viral memory Th cells in rapid and efficient generation of anti-Aβ antibody responses in APP/Tg mice. As we suggested, these experiments could simulate the situation in people with early pre-clinical stage AD repeatedly vaccinated/infected with flu virus. Importantly, if successful, dual-vaccine can be used in people with AD at a very early stage that can be diagnosed by measuring tau/Aβ and ptau/Aβ ratio in CSF and/or by screening for accumulation of Aβ in the brains using PIB-PET scan.
Isosteric Ring Exchange as a Useful Scaffold Hopping Tool in Agrochemistry (2023)

Replacing one ring in a molecule by a different carba- or heterocycle is an important scaffold hopping manipulation, because biologically active compounds and their analogues, which underwent such a transformation, are often similar in size, shape, and physicochemical properties and, therefore, likely in their potency as well. This review will demonstrate, how isosteric ring exchange led to the discovery of highly active agrochemicals and which ring interchanges have proven to be most successful.