gebhart/patrepeval huggingface dataset:
Music-listening regulates human microRNA expression (2020)

Music-listening and performance have been shown to affect human gene expression. In order to further elucidate the biological basis of the effects of music on the human body, we studied the effects of music-listening on gene regulation by sequencing microRNAs of the listeners (Music Group) and their controls (Control Group) without music exposure. We identified upregulation of six microRNAs (hsa-miR-132-3p, hsa-miR-361-5p, hsa-miR-421, hsa-miR-23a-3p, hsa-miR-23b-3p, hsa-miR-25-3p) and downregulation of two microRNAs (hsa-miR-378a-3p, hsa-miR-16-2-3p) in Music Group with high musical aptitude. Some upregulated microRNAs were reported to be responsive to neuronal activity (miR-132, miR-23a, miR-23b) and modulators of neuronal plasticity, CNS myelination, and cognitive functions like long-term potentiation and memory. miR-132 plays a critical role in regulating TAU protein levels and is important for preventing tau protein aggregation that causes Alzheimer's disease. miR-132 and <i>DICER</i>, upregulated after music-listening, protect dopaminergic neurons and are important for retaining striatal dopamine levels. Some of the transcriptional regulators (<i>FOS, CREB1, JUN, EGR1,</i> and <i>BDNF</i>) of the upregulated microRNAs were immediate early genes and top candidates associated with musical traits. <i>BDNF</i> and SNCA, co-expressed and upregulated in music-listening and music-performance, are both are activated by GATA2, which is associated with musical aptitude. Several miRNAs were associated with song-learning, singing, and seasonal plasticity networks in songbirds. We did not detect any significant changes in microRNA expressions associated with music education or low musical aptitude. Our data thereby show the importance of inherent musical aptitude for music appreciation and for eliciting the human microRNA response to music-listening.
Searching for a Single Community in a Graph (2018)

In standard graph clustering/community detection, one is interested in partitioning the graph into more densely connected subsets of nodes. In contrast, the search problem of this article aims to only find the nodes in a single such community, the target, out of the many communities that may exist. To do so, we are given suitable side information about the target; for example, a very small number of nodes from the target are labeled as such. We consider a general yet simple notion of side information: all nodes are assumed to have random weights, with nodes in the target having higher weights on average. Given these weights and the graph, we develop a variant of the method of moments that identifies nodes in the target more reliably, and with lower computation, than generic community detection methods that do not use side information and partition the entire graph. Our empirical results show significant gains in runtime, and also gains in accuracy over other graph clustering algorithms.
Structure and Properties of Hexa- and Undecablock Terpolymers with Hierarchical Molecular Architectures (2009)

We report the synthesis, phase behavior, and viscoelastic and mechanical properties of a new type of multiblock copolymer composed of glassy poly(cyclohexylethylene) (C), semicrystalline poly(ethylene) (E), and elastomeric poly(ethylene-alt-propylene) (P). Five nearly monodisperse CECEC−P hexablock terpolymers and one (CECEC)2−P undecablock copolymer were synthesized by sequential anionic polymerization followed by catalytic hydrogenation. These multiblock copolymers, which contain equal volume fractions of P and compositionally symmetric CECEC, microphase separate by two different processes: segregation induced by crystallization of the E blocks and through chemical incompatibility between C, E, and P. These materials contain two different complex morphologies each with two length scales determined by the local (C−E) and overall (C−E−P) order−disorder transition temperatures relative to the glass and crystallization temperatures of the C and E blocks, respectively. Structure was determined by SAXS, TEM, and mechanical spectroscopy. Tensile tests reveal that the hexablock copolymers are tough (ca. ≥750% strain at break) and exhibit high elastic recovery despite the presence of P domains comprised of loose elastomeric end blocks. The (CECEC)2−P undecablock, which orders from the homogeneous melt as a consequence of crystallization of the E blocks, exhibits roughly three times the stress at failure without the loss of other physical properties. These results offer new insights into the development of enhanced mechanical response based on hierarchical molecular design.
System for capturing CO2 from a fuel cell (2023)

A carbon dioxide capture system for capturing carbon dioxide from an exhaust stream. The system may include a fuel cell configured to output a first exhaust stream comprising carbon dioxide and water. The system may further include an electrolyzer cell configured to receive a first portion of the first exhaust stream and output a second exhaust stream comprising oxygen and carbon dioxide. The fuel cell may be a solid oxide fuel cell. The electrolyzer cell may be a molten carbonate electrolysis cell.
Design and Adaptation of Multi-Interference Steering (2019)

With the rapid development in wireless communication technologies, interference has become a main impediment to network performance, making interference management (IM) a critical issue. Interference steering (IS) is emerging as a novel way of IM, which can steer the spatial feature of interference to a target subspace by exploiting the interactions of multiple signals over the air to avoid the disturbance to the interfered receiver. In reality, there always exists multiple interferences from single or multiple sources. We propose three ways to realize IS. The first two of them are categorized as individual interference steering (IIS), in which multiple interfering signals are separately adjusted to either an identical direction (a single-target IS, STIS) or different directions (multi-target IS, MTIS), incurring single or multiple degrees of freedom (DoFs) overheads, respectively. Furthermore, by recognizing that the goal of IM is to limit the effect of interference-i.e., the effective portion of interference imposed on the intended transmission- we propose aggregated interference steering (AIS) that exploits the constructive or destructive effects of multiple interfering signals. By considering the overall effect of multiple interferences, the DoF cost of AIS is reduced to one regardless of the number of interference to be managed. Finally, the proposed three IS realizations are adapted to minimize the power cost of steering interference. Our theoretical analysis and in-depth simulation results have shown that the proposed IS schemes can effectively manage multiple interference via better utilizing the DoF and transmit power. The AIS is shown to be advantageous in both power cost and DoF consumption.
A Small Molecule for Controlled Generation of Peroxynitrite (2016)

2-Methyl-3-[1-(N,N-dimethylamino)diazen-1-ium-1,2-diol-2-ato-methyl]-naphthalene-1,4-dione 1 (HyPR-1), a small molecule containing a superoxide generator strategically linked to a diazeniumdiolate-based nitric oxide donor, is reported. Evidence for HyPR-1's ability to generate peroxynitrite in the presence of an enzyme as well as enhance peroxynitrite within cells is provided. The utility of this tool in generating peroxynitrite for cellular studies is demonstrated.
Adaptive Fuzzy Filtering for Artifact Reduction in Compressed Images and Videos (2009)

A fuzzy filter adaptive to both sample's activity and the relative position between samples is proposed to reduce the artifacts in compressed multidimensional signals. For JPEG images, the fuzzy spatial filter is based on the directional characteristics of ringing artifacts along the strong edges. For compressed video sequences, the motion compensated spatiotemporal filter (MCSTF) is applied to intraframe and interframe pixels to deal with both spatial and temporal artifacts. A new metric which considers the tracking characteristic of human eyes is proposed to evaluate the flickering artifacts. Simulations on compressed images and videos show improvement in artifact reduction of the proposed adaptive fuzzy filter over other conventional spatial or temporal filtering approaches.
High efficiency vortex trapping of circulating tumor cells (2015)

Circulating tumor cells (CTCs) are important biomarkers for monitoring tumor dynamics and efficacy of cancer therapy. Several technologies have been demonstrated to isolate CTCs with high efficiency but achieve a low purity from a large background of blood cells. We have previously shown the ability to enrich CTCs with high purity from large volumes of blood through selective capture in microvortices using the Vortex Chip. The device consists of a narrow channel followed by a series of expansion regions called reservoirs. Fast flow in the narrow entry channel gives rise to inertial forces, which direct larger cells into trapping vortices in the reservoirs where they remain circulating in orbits. By studying the entry and stability of particles following entry into reservoirs, we discover that channel cross sectional area plays an important role in controlling the size of trapped particles, not just the orbital trajectories. Using these design modifications, we demonstrate a new device that is able to capture a wider size range of CTCs from clinical samples, uncovering further heterogeneity. This simple biophysical method opens doors for a range of downstream interventions, including genetic analysis, cell culture, and ultimately personalized cancer therapy.
Response to Radioimmunotherapy Correlates with TumorpO2Measured by EPR Oximetry in Human Tumor Xenografts (2001)

The efficacy of radiation treatment depends upon local oxygen concentration. We postulated that the variability in responsiveness of tumor xenografts to a fixed dose of radioimmunotherapy might be related to the tumor pO2 at the time that radioimmunotherapy was administered. We evaluated the growth of xenografts of CALU-3 tumors, a non-small cell lung carcinoma, in response to an 8.9-MBq dose of 131I-RS-7-anti-EGP-1 and correlated tumor growth rate with initial tumor pO2 measured by EPR oximetry. The greatest growth delay in response to radioimmunotherapy had the highest initial pO2, and the fastest-growing tumors had the lowest initial pO2. We then determined the dynamic effect of radioimmunotherapy on tumor pO2 by serial measurements of pO2 for 35 days after radioimmunotherapy. This information could be important for ascertaining the likelihood that a tumor will respond to additional doses as part of a multiple dose scheme. Serial tumor pO2 measurements may help identify a window of opportunity when the surviving tumor regions will be responsive to a second round of radioimmunotherapy or a second therapeutic modality such as chemotherapy or an anti-vascular agent. After radioimmunotherapy, there was an increase in tumor pO2 followed by a decrease below initial levels in most mice. Thus defined times may exist when a tumor is more or less radiosensitive after radioimmunotherapy.
Modeling intracranial electrodes (2021)

Abstract Background Intracranial electrodes are implanted in patients with drug-resistant epilepsy as part of their pre-surgical evaluation. This allows investigation of normal and pathological brain functions with excellent spatial and temporal resolution. The spatial resolution relies on methods that precisely localize the implanted electrodes in the cerebral cortex, which is critical for drawing valid anatomical inferences about brain function. Multiple methods have been developed to localize implanted electrodes, mainly relying on pre-implantation MRI and post-implantation CT images. However, there is no standard approach to quantify the performance of these methods systematically. The purpose of our work is to model intracranial electrodes to simulate realistic implantation scenarios, thereby providing methods to optimize localization algorithm performance. Results We implemented novel methods to model the coordinates of implanted grids, strips, and depth electrodes, as well as the CT artifacts produced by these. We successfully modeled a large number of realistic implantation “scenarios” , including different sizes, inter-electrode distances, and brain areas. In total, more than 3300 grids and strips were fitted over the brain surface, and more than 850 depth electrode arrays penetrating the cortical tissue were modeled. More than 37000 simulations of electrode array CT artifacts were performed in these “scenarios” , mimicking the intensity profile and orientation of real artifactual voxels. Realistic artifacts were simulated by introducing different noise levels, as well as overlapping electrodes. Conclusions We successfully developed the first platform to model implanted intracranial grids, strips, and depth electrodes and realistically simulate CT artifacts and noise. These methods set the basis for developing more complex models, while simulations allow the performance evaluation of electrode localization techniques systematically. The methods described in this article, and the results obtained from the simulations, are freely available via open repositories. A graphical user interface implementation is also accessible via the open-source iElectrodes toolbox.
Calibration Method for High-Density-Plasma Chemical Vapor Deposition Simulation (2002)

We present a consistent calibration method for high-density-plasma chemical vapor deposition (HDP-CVD) topography simulation using the gap-filling process of the inter-metal dielectric (IMD). For the HDP-CVD model, four phenomena, thermal deposition, ion-enhanced deposition, sputter-etching by Ar+ ion, and redeposition, were considered. The contribution of each phenomenon to surface evolution was determined on the basis of six parameters. All six parameters were calibrated by methods including deposition/etching rate measurement, an experiment using the test structure and plasma simulation. The simulation calibrated by these methods has high predictive accuracy in terms of the gap-fill capability in trenches.
Importance, Applications and Features of Assays Measuring SARS-CoV-2 Neutralizing Antibodies (2023)

More than three years ago, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused the unforeseen COVID-19 pandemic with millions of deaths. In the meantime, SARS-CoV-2 has become endemic and is now part of the repertoire of viruses causing seasonal severe respiratory infections. Due to several factors, among them the development of SARS-CoV-2 immunity through natural infection, vaccination and the current dominance of seemingly less pathogenic strains belonging to the omicron lineage, the COVID-19 situation has stabilized. However, several challenges remain and the possible new occurrence of highly pathogenic variants remains a threat. Here we review the development, features and importance of assays measuring SARS-CoV-2 neutralizing antibodies (NAbs). In particular we focus on in vitro infection assays and molecular interaction assays studying the binding of the receptor binding domain (RBD) with its cognate cellular receptor ACE2. These assays, but not the measurement of SARS-CoV-2-specific antibodies per se, can inform us of whether antibodies produced by convalescent or vaccinated subjects may protect against the infection and thus have the potential to predict the risk of becoming newly infected. This information is extremely important given the fact that a considerable number of subjects, in particular vulnerable persons, respond poorly to the vaccination with the production of neutralizing antibodies. Furthermore, these assays allow to determine and evaluate the virus-neutralizing capacity of antibodies induced by vaccines and administration of plasma-, immunoglobulin preparations, monoclonal antibodies, ACE2 variants or synthetic compounds to be used for therapy of COVID-19 and assist in the preclinical evaluation of vaccines. Both types of assays can be relatively quickly adapted to newly emerging virus variants to inform us about the magnitude of cross-neutralization, which may even allow us to estimate the risk of becoming infected by newly appearing virus variants. Given the paramount importance of the infection and interaction assays we discuss their specific features, possible advantages and disadvantages, technical aspects and not yet fully resolved issues, such as cut-off levels predicting the degree of in vivo protection.
Characterization of a light-responding trans-activator responsible for differentially controlling reaction center and light-harvesting-I gene expression in Rhodobacter capsulatus (1994)

The purple nonsulfur photosynthetic bacterium Rhodobacter capsulatus regulates synthesis of its photosystem in response to two environmental stimuli, oxygen tension and light intensity. Here we describe the identification and characterization of the trans-acting regulatory gene hvrA, which we show is involved in differentially controlling reaction center and light-harvesting gene expression in response to alterations in light intensity. An hvrA mutant strain is shown to lack the capability to trans-activate light-harvesting-I and reaction center gene expression but retain normal light-harvesting-II and photopigment regulation, in response to a reduction in light intensity. As a consequence of altered expression, hvrA mutant strains exhibit reduced photosynthetic growth capabilities under dim-light conditions. The results of this study and additional studies indicate that regulated synthesis of the photosystem involves complex sets of overlapping regulatory circuits that differentially control photosystem gene expression in response to environmental stimuli such as oxygen tension and light intensity.
553: Comprehensive Prospective Comparative Analysis of Outcomes between Open and Laparoscopic Radical Prostatectomy (2007)

THE JOURNAL OF UROLOGy giving a cumulative 5-yr BCR-free rate of 75% (n=1001). The mean follow-up was 22.3 mo (95%CI, 20,24.6). In multivariable Cox regression analysis, higher serum PSA (p < 0.001 ). palpable nodule (p = 0.009), presence of extracapsular extension (ECE; p = 0.038), seminal vesicle invasion (SVI; p < 0.001 ), pathologic Gleason 4 + 3 (p < 0.001 ), and pathologic Gleason 8-10 (p < 0.001) when compared to pathologic Gleason < 6 were significantly associated with shorter time to BCR. The concordance index for the model was 0.86. The overall PSM rate was 13%; 9% for capsule-confined disease (pT2) and 24% for extracapsular extension (pT3).
Design study on microphone arrays (2015)

This paper presents a design of microphone array system that is intended for conference room applications. Different microphone array configurations have been considered in this work to demonstrate the importance of array layout. The filter-and-sum broadband beamformer is designed by using weighted least square (WLS) optimization method. As existing near-field broadband beamformers are sensitive to changes in microphone characteristics and position, robust designs need to be considered that include microphone characteristics mismatch (gain and phase) in the design. Furthermore, it is shown that the aperture size is important for the designed beamformer performance. Golden section search technique is used to find optimal aperture size and weights. The important roles that microphone array layout, robust design and aperture size play in the design of the broadband beamformer are demonstrated.
Join query optimization in parallel database systems (2002)

The authors present a new framework for studying query optimization. They first note that scheduling and optimization must go together in a parallel environment. They introduce the concept of response time envelopes which integrates scheduling and optimization. It is shown that it can be used effectively to develop parallel query optimization algorithms which have same order of complexity as the traditional sequential query optimization algorithms and produce provably optimal or near optimal join plans.
Group IV mid-infrared photonics [Invited] (2018)

&lt;p&gt;In this paper we review our recent results on group IV mid-infrared photonic devices. In particular, passive structures suitable for long wavelength operation, such as suspended Si, Ge-on-Si and suspended Ge, are analyzed. In addition, Ge-on-insulator waveguides have been characterized at 3.8 μm. Several active devices have been also realized: optical modulators in silicon and germanium, and silicon and graphene detectors operating at shorter mid-IR wavelengths.&lt;/p&gt;
Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C (2013)

We have, for the first time, identified epigenetic alterations in patient samples carrying a mutation in a gene involved in the regulation of histone modifications. These data support the concept that DNA methylation and H3 lysine 4 methylation are functionally interdependent. The data provide new insights into the molecular pathogenesis of intellectual disability. Further, our data suggest that some DNA methylation marks identified in blood can serve as biomarkers of epigenetic status in the brain.
Process monitor of 3D-device features by using FIB and CD-SEM (2016)

For yield improvement of 3D-device manufacturing, metrology for the variability of individual device-features is on hot issue. Transmission Electron Microscope (TEM) can be used for monitoring the individual cross-section. However, efficiency of process monitoring is limited by the speed of measurement including preparation of lamella sample. In this work we demonstrate speedy 3D-profile measurement of individual line-features without the lamella sampling. For instance, we make a-few-micrometer-wide and 45-degree-descending slope in dense line-features by using Focused Ion Beam (FIB) tool capable of 300mm-wafer. On the descending slope, obliquely cut cross-section of the line features appears. Then, we transfer the wafer to Critical-Dimension Secondary Electron Microscope (CDSEM) to measure the oblique cross-section in normal top-down view. As the descending angle is 45 degrees, the oblique cross-section looks like a cross-section normal to the wafer surface. For every single line-features the 3D dimensions are measured. To the reference metrology of the Scanning TEM (STEM), nanometric linearity and precision are confirmed for the height and the width under the hard mask of the line features. Without cleaving wafer the 60 cells on the wafer can be measured in 3 hours, which allows us of near-line process monitor of in-wafer uniformity.
Atomic Layer Deposition of Strontium Titanate Films Using Sr([sup t]Bu[sub 3]Cp)[sub 2] and Ti(OMe)[sub 4] (2009)

Strontium titanate (STO) is a promising candidate as a high- dielectric for dynamic random access memory application. STO thin films are deposited by atomic layer deposition using , , and as precursors. Growth and saturation behavior of STO and binary oxides are evaluated by ellipsometry thickness measurements. The precursor pulse ratio controls the amount of Sr and Ti incorporated in STO films. Stoichiometric is characterized by the lowest crystallization temperature and largest refractive index, density, and dielectric constant. An excess of Ti or Sr results in an increase in the crystallization onset temperature and contraction or expansion of the cubic cell constant of perovskite . Incorporation of more Sr in STO reduces the leakage current density but also increases the capacitance-equivalent thickness.