gebhart/patrepeval huggingface dataset:
Bowed String Sequence Estimation of a Violin Based on Adaptive Audio Signal Classification and Context-Dependent Error Correction (2009)

The sequence of strings played on a bowed string instrument is essential to understanding of the fingering. Thus, its estimation is required for machine understanding of violin playing. Audio-based identification is the only viable way to realize this goal for existing music recordings. A naive implementation using audio classification alone, however, is inaccurate and is not robust against variations in string or instruments. We develop a bowed string sequence estimation method by combining audio-based bowed string classification and context-dependent error correction. The robustness against different setups of instruments improves by normalizing the F0-dependent features using the average feature of a recording. The performance of error correction is evaluated using an electric violin with two different brands of strings and an acoustic violin. By incorporating mean normalization, the recognition error of recognition accuracy due to changing the string alleviates by 8 points, and that due to change of instrument by 12 points. Error correction decreases the error due to change of string by 8 points and that due to different instrument by 9 points.
Engineering optical anisotropy in nonlinear crystals with ultrafast light (2020)

Photonic technology is widely based on anisotropic (and) nonlinear materials, which allow light modulation and parametric light conversion. Because the number of naturally occurring crystals is limited, there is a growing demand for artificial metamaterials with optical properties specifically tailored to a given application. Here, we utilize the top-down method to synthesize sub-wavelength periodic nanostructures inside a uniaxial optically nonlinear crystal (lithium niobate, LiNbO3) by irradiating it with multiple femtosecond laser pulses. By superimposing form-birefringence associated with the light-induced nanostructures onto natural birefringence of the host crystal we create macroscopic domains of a biaxial metamaterial embedded into otherwise uniaxial medium.
El Efecto de Levodopa o Levodopa-Carbidopa (Sinemet) en la Cicatrizacion ??sea (2006)

Costa, Elisabeth R. MS; Weinhold, Paul PhD; Tayrose, Gregory A. BS; Hooker, Jennifer A. MD; Dahners, Laurence E. MD Author Information
Identification of Multiple Structurally Distinct, Nonpeptidic Small Molecule Inhibitors of Protein Arginine Deiminase 3 Using a Substrate-Based Fragment Method (2015)

The protein arginine deiminases (PADs) are a family of enzymes that catalyze the post-translational hydrolytic deimination of arginine residues. Four different enzymologically active PAD subtypes have been characterized and exhibit tissue-specific expression and association with a number of different diseases. In this Article we describe the development of an approach for the reliable discovery of low molecular weight, nonpeptidic fragment substrates of the PADs that then can be optimized and converted to mechanism-based irreversible PAD inhibitors. The approach is demonstrated by the development of potent and selective inhibitors of PAD3, a PAD subtype implicated in the neurodegenerative response to spinal cord injury. Multiple structurally distinct inhibitors were identified with the most potent inhibitors having >10,000 min(-1) M(-1) k(inact)/K(I) values and ≥10-fold selectivity for PAD3 over PADs 1, 2, and 4.
Peroxiredoxin 1 Protects Telomeres from Oxidative Damage and Preserves Telomeric DNA for Extension by Telomerase (2016)

Oxidative damage of telomeres can promote cancer, cardiac failure, and muscular dystrophy. Specific mechanisms protecting telomeres from oxidative damage have not been described. We analyzed telomeric chromatin composition during the cell cycle and show that the antioxidant enzyme peroxiredoxin 1 (PRDX1) is enriched at telomeres during S phase. Deletion of the PRDX1 gene leads to damage of telomeric DNA upon oxidative stress, revealing a protective function of PRDX1 against oxidative damage at telomeres. We also show that the oxidized nucleotide 8-oxo-2'deoxyguanosine-5'-triphosphate (8oxodGTP) causes premature chain termination when incorporated by telomerase and that some DNA substrates terminating in 8oxoG prevent extension by telomerase. Thus, PRDX1 safeguards telomeres from oxygen radicals to counteract telomere damage and preserve telomeric DNA for elongation by telomerase.
Hepatic stellate cells on poly(DL-lactic acid) surfaces control the formation of 3D hepatocyte co-culture aggregates in vitro (2006)

Evidence for the functional superiority of cells cultured as 3D aggregates or on 3D scaffolds over conventional 2D monolayer cultures has created interest in material and cell based methods that influence the formation and structure of multicellular aggregates in vitro. We have created a co-culture of primary rat hepatocytes and hepatic stellate cells on a poly(DL-lactic acid) surface, a poor substrate for rat hepatocyte adhesion, to study the dynamics of multicellular spheroid formation and the resultant cell arrangement. The poly(DL-lactic acid) surface allows dynamic and rapid interaction of hepatocytes and stellate cells to form co-culture spheroids in a complex multistage process (shown by time lapse microscopy). This spheroid morphology supports enhanced cell viability relative to a mono-culture mono-layer system (measured by lactate dehydrogenase leakage). The distribution of the aggregating cell type in the final structure is related to the mechanics of formation i.e. mainly central and peripheral. This study provides a unique and generically applicable insight into the dynamics of multicellular spheroid formation where aggregation is induced by one cell type and imposed on another. This has implications for 3D cell culture models and a wide number of currently used stromal co-culture systems.
Comparative analysis of antibodies to SARS-CoV-2 between asymptomatic and convalescent patients (2021)

The SARS-CoV-2 viral pandemic has induced a global health crisis, which requires more in-depth investigation into immunological responses to develop effective treatments and vaccines. To understand protective immunity against COVID-19, we screened over 60,000 asymptomatic individuals in the Southeastern United States for IgG antibody positivity against the viral Spike protein, and approximately 3% were positive. Of these 3%, individuals with the highest anti-S or anti-RBD IgG level showed a strong correlation with inhibition of ACE2 binding and cross-reactivity against non-SARS-CoV-2 coronavirus S-proteins. We also analyzed samples from 94 SARS-CoV-2 patients and compared them with those of asymptomatic individuals. SARS-CoV-2 symptomatic patients had decreased antibody responses, ACE2 binding inhibition, and antibody cross-reactivity. Our study shows that healthy individuals can mount robust immune responses against SARS-CoV-2 without symptoms. Furthermore, IgG antibody responses against S and RBD may correlate with high inhibition of ACE2 binding in individuals tested for SARS-CoV-2 infection or post vaccination.
Cascaded polarizing beamsplitter cubes in imaging systems (1994)

Linear polarization rotation tilt is a form of polarization aberration present in polarizing beamsplitter cubes when they are used in imaging systems. It is caused by the rotation of the polarizing axis (defined by the plane of incidence at the beamsplitting interface) for off-axis angles of incidence. This aberration is inherent to the geometry of the cube and is unavoidable, causing beam-routing errors and undesirable losses. In systems that use two or more polarizing beamsplitter cubes in succession, the cubes can be oriented to either minimize or maximize the loss, where the maximum loss is five times the minimum loss. This polarization aberration is described and a way to minimize beam-routing errors associated with this aberration in a 4-F optical system is demonstrated.
Enhancing cellular M2M random access with binary countdown contention resolution (2017)

Accommodating Machine-to-Machine applications and their requirements is one of the challenges on the way from LTE towards 5G networks. The envisioned high density of devices, alongside with their sporadic and synchronized transmission patterns, might create signaling storms and overload in the current LTE network. Here, we address the notorious random access (RA) challenge, namely, scalability of the radio link connection establishment protocol in LTE networks. We revisit the binary countdown technique for contention resolution (BCCR), and apply it to the LTE RA procedure. We analytically investigate the performance gains and trade-offs of applying BCCR in LTE. We further simulatively compare BCCR RA with the state-of-the-art RA techniques, and demonstrate its advantages in terms of delay and throughput.
Secretion of Heterologous Proteins, Gram‐Positive Bacteria,Lactococcus lactis (2010)

Abstract Numerous Gram‐positive bacteria are used to produce heterologous proteins allowing easy protein secretion and purification. Among them, lactic acid bacteria (LAB) are interesting hosts since they secrete heterologous protein as both, cell factories and mucosal proteins delivery vectors. For this purpose, Lactococcus lactis , the model LAB, has been widely studied. Here, we review lactococcal expression and secretion systems that have been widely used and developed for heterologous protein production. These systems are based upon improved expression/secretion vectors carrying either inducible or constitutive promoters that allow a tight control of the heterologous protein expression level. These expression systems can include the use of characterized signal sequences as signal‐peptide or synthetic propeptide to drive efficient heterologous protein secretion into the extracellular medium. In parallel, huge knowledge acquired on protein secretion process in model bacteria has allowed us to identify some bottlenecks in processes much as translocation across the membrane, folding and degradation steps. Based on these studies, we describe complementary strategies consisting of host strain modifications to overcome these bottlenecks in L. lactis . Together, these studies are contributed to make L. lactis and other LABs attractive hosts and efficient cell factories for production and delivery of heterologous secreted proteins.
Topological mapping with weak sensory data (2007)

The recent observation of stable quantized conductance in anatase TiO<sub>2</sub> resistive random access memory (ReRAM) devices opens up a new pathway toward the realization of brain-inspired neuromorphic computing devices. Herein, for the first time, ab initio calculations are implemented to understand the resistive switching phenomena in anatase TiO<sub>2</sub>. Oxygen vacancy configurations with different charge states are studied to gain insight into the ON and OFF states of ReRAM devices. Among the trivacancy configurations, the V<sub>o</sub><sup>+</sup> state is observed to induce highly dispersed defect states within the bandgap forming a charge density channel where the carriers behave as free electrons leading to the formation of a conducting filament (CF). On the contrary, the breakdown of the CF is noticed by the removal of an oxygen vacancy from the trivacancy configuration. In this OFF state, the defect state carriers are found to be highly localized. In addition, we have also investigated the effect of charge injection on the crystal field symmetry of the CF. The reduction of symmetry due to the trivacancy configuration lowers the e<sub>g</sub> manifold energy, whereas the divacancy configuration lowers the t<sub>2g</sub> manifold energy.
Development of a Dolby S-type IC using a new master slice method (1991)

A novel IC has been developed to implement the Dolby S-type noise reduction process. The IC was developed using a novel bipolar master slice (M/S) process. This method has several advantages over full custom IC design, including lower cost, fast turn around time, more design flexibility, and quick assessment and correction of design problems. The advantages of the new M/S method were particularly useful in the design of the S-type IC. This is because the system design changed to accommodate integration and performance requirements, and SPICE evaluation was difficult. The resulting IC is a very-high-performance, low-cost, single package which should find good acceptance among manufacturers and consumers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
902 The research on the development of exoskeltonic powered orthosis (2004)

By the progress of the aging, the dependence to the nursing heightens so that the old people who physical fitness declines would be able to smoothly spend the life in every day. As the result, the burden of the nurse increases, and the complaint of feeling of fatigue of the arm, shoulder discomfort, lumbago increases. From this social background, the purpose of this study is to develop the powered orthosis fixed to the arm on the assumption of the nursing action. First, the performance required in the orthosis is verified in this study. Nursing action, which the nurse demonstrates is measured, and the kinematic analysis is done. The orthosis, which satisfied this performance was manufactured and was evaluated. As a result of the evaluation experiment, the EMG value of biceps brachii muscle which was an agonist muscle decreased by using the orthosis. From this result, the effectiveness of the orthosis was confirmed.
Work Of Wetting Associated With The Spreading Of Sessile Drops (2010)

Founded in 1683 in Leiden, the Netherlands, Brill is a leading international academic publisher in the Humanities, Social Sciences, International Law, and Biology. With offices in the Netherlands, Germany, Austria, the USA and Asia, Brill today publishes more than 360 journals and 2,000 new books and reference works each year as well as a large number of databases and primary source research collections.
ChemInform Abstract: First Synthesis of (.+‐.)‐Harzianopyridone by Metalation of Polysubstituted O‐Pyridylcarbamates. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Novel p62dok family members, dok-4 and dok-5, are substrates of the c-Ret receptor tyrosine kinase and mediate neuronal differentiation (2001)

Docking proteins are substrates of tyrosine kinases and function in the recruitment and assembly of specific signal transduction molecules. Here we found that p62dok family members act as substrates for the c-Ret receptor tyrosine kinase. In addition to dok-1, dok-2, and dok-3, we identified two new family members, dok-4 and dok-5, that can directly associate with Y1062 of c-Ret. Dok-4 and dok-5 constitute a subgroup of dok family members that is coexpressed with c-Ret in various neuronal tissues. Activated c-Ret promotes neurite outgrowth of PC12 cells; for this activity, Y1062 in c-Ret is essential. c-Ret/dok fusion proteins, in which Y1062 of c-Ret is deleted and replaced by the sequences of dok-4 or dok-5, induce ligand-dependent axonal outgrowth of PC12 cells, whereas a c-Ret fusion containing dok-2 sequences does not elicit this response. Dok-4 and dok-5 do not associate with rasGAP or Nck, in contrast to p62dok and dok-2. Moreover, dok-4 and dok-5 enhance c-Ret-dependent activation of mitogen-activated protein kinase. Thus, we have identified a subclass of p62dok proteins that are putative links with downstream effectors of c-Ret in neuronal differentiation.
New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies (2016)

Phospho-MurNAc-pentapeptide translocase (MraY) catalyzes the synthesis of Lipid I, a bacterial peptidoglycan precursor. As such, MraY is essential for bacterial survival and therefore is an ideal target for developing novel antibiotics. However, the understanding of its catalytic mechanism, despite the recently determined crystal structure, remains limited. In the present study, the kinetic properties of Bacillus subtilis MraY (BsMraY) were investigated by fluorescence enhancement using dansylated UDP-MurNAc-pentapeptide and heptaprenyl phosphate (C35-P, short-chain homolog of undecaprenyl phosphate, the endogenous substrate of MraY) as second substrate. Varying the concentrations of both of these substrates and fitting the kinetics data to two-substrate models showed that the concomitant binding of both UDP-MurNAc-pentapeptide-DNS and C35-P to the enzyme is required before the release of the two products, Lipid I and UMP. We built a model of BsMraY and performed docking studies with the substrate C35-P to further deepen our understanding of how MraY accommodates this lipid substrate. Based on these modeling studies, a novel catalytic role was put forward for a fully conserved histidine residue in MraY (His-289 in BsMraY), which has been experimentally confirmed to be essential for MraY activity. Using the current model of BsMraY, we propose that a small conformational change is necessary to relocate the His-289 residue, such that the translocase reaction can proceed via a nucleophilic attack of the phosphate moiety of C35-P on bound UDP-MurNAc-pentapeptide.
Experimental identification of kinematic constraints (2002)

This paper proposes techniques for automatically identifying and modeling the kinematic constraints of manipulated objects. The existence of constraints is established by examination of the forces and torques normal and tangential to the object's motion. Constraints are modeled as joints with configuration and history dependent forces. To illustrate these concepts, several experimental examples are presented.
Optimal Signaling and Selection Verification for Single Transmit-Antenna Selection (2007)

In marked contrast with the ideal error-free feedback assumption that is common in the literature, practical systems are likely to have severely bandwidth-limited, error-prone feedback channels. We consider the scenario where feedback from the receiver is used by the transmitter to select the best antenna, out of many available antennas, for data transmission. Feedback errors cause the transmitter to select an antenna different from the one signaled by the receiver. We show that optimizing the signaling assignment, which maps the antenna indices to the feedback codewords, improves performance without introducing any additional redundancy. For a system that uses error-prone feedback to transmit quadrature-phase-shift-keying-modulated data from a single antenna selected from many available spatially correlated antennas, we derive closed-form approximations for the data symbol error probability for an arbitrary number of receive antennas. We use these to systematically find the optimal signaling assignments using a low-complexity algorithm. The optimal signaling is intimately coupled to how the receiver performs selection verification, i.e., how it decodes the data signal when, due to feedback errors, it does not always know which antenna was used for data transmission. We show that ignoring feedback errors at the receiver can lead to an unacceptable performance degradation, and develop optimal and suboptimal, blind and nonblind selection-verification methods. With a small side-information overhead, nonblind verification approaches the ideal perfect selection-verification performance
Beamforming on mobile devices (2011)

In this work, we report the first study of an important realization of directional communication, beamforming, on mobile devices. We first demonstrate that beamforming is already feasible on mobile devices in terms of form factor, device mobility and power efficiency. Surprisingly, we show that by making an increasingly profitable tradeoff between transmit and circuit power, beamforming with state-of-the-art integrated CMOS implementations can be more power-efficient than its single antenna counterpart. We then investigate the optimal way of using beamforming in terms of device power efficiency, by allowing a dynamic number of active antennas. We propose a simple yet effective solution, BeamAdapt, which allows each mobile client in a network to individually identify the optimal number of active antennas with guaranteed convergence and close-to-optimal performance. We finally report a WARP-based prototype of BeamAdapt and experimentally demonstrate its effectiveness in realistic environments, and then complement the prototype-based experiments with Qualnet-based simulation of a large-scale network. Our results show that BeamAdapt with four antennas can reduce the power consumption of mobile clients by more than half compared to a single antenna, while maintaining a required network throughput.
Process Simulation and Cost Analysis for Removing Inorganics from Wood Chips Using Combined Mechanical and Chemical Preprocessing (2016)

Inorganic species (ash) in biomass feedstocks negatively impact thermochemical and biochemical energy conversion processes. In this work, a process simulation model is developed to model the reduction in ash content of loblolly logging residues using a combination of air classification and dilute-acid leaching. Various scenarios are considered, and it is found that costs associated with discarding high-ash material from air classification are substantial. The costs of material loss can be reduced by chemical leaching the high-ash fraction obtained from air classification. The optimal leaching condition is found to be approximately 0.1 wt% sulfuric acid at 24 °C. In example scenarios, total process costs in the range of $6–9﻿/dry tons of product are projected that result in a removal of 14, 62, 39, and 88 % of organics, total ash (inorganics), alkaline earth metals and phosphorus (AAEMS + P), and silicon, respectively. Sensitivity analyses indicate that costs associated with loss of organic material during processing (yield losses), brine disposal, and labor have the greatest potential to impact the total processing cost.
Expression Profiling of Archival Tumors for Long-term Health Studies (2012)

These methods for large-scale QC of FFPE expression profiles enable study of the cancer transcriptome in relation to extensive clinicopathological information, tumor molecular biomarkers, and long-term lifestyle and outcome data.
Multiplexed PCR to screen for a major QTL carrying fusarium head blight resistance in Sumai-3 wheat (2006)

After the initial identification of microsatellites linked to economically important traits of interest, the additional investment to simplify the screening procedure for more routine use is of interest to plant breeders. The objective was to simplify an acrylamide gel based marker-assisted selection (MAS) method to facilitate high-through put screening for Qfhs.ndsu-3BS, a major quantitative trait locus carrying fusarium head blight (FHB) resistance in Sumai-3 wheat (Triticum aestivum L.). Method simplifications included incorporating the use of (1) 96-well DNA extractions, (2) multiplexed PCR reactions using microsatellite primers gwm493 and gwm533, and (3) agarose gels. Our modified FHB-MAS method was verified by screening six resistant (Sumai-3, ND2710, McVey, BacUp, HY644, and Alsen) and 52 susceptible parents and subsequently used to screen 5567 common wheat breeding lines developed from Sumai-3 derivatives. This simple and rapid method allows for the screening of 1000 lines per week, which can be used to skew segregating populations towards more resistant types and thereby advance primarily early and advanced generation lines that carry at least the major FHB QTL. Key words: PCR, Fusarium, microsatellites, gwm493, gwm533, Triticum
Supplemental Figure 4 from Characterization of a Naturally Occurring Breast Cancer Subset Enriched in Epithelial-to-Mesenchymal Transition and Stem Cell Characteristics (2023)

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