gebhart/patrepeval huggingface dataset:
Methods in and applications of the sequencing of short non-coding RNAs (2013)

Short non-coding RNAs are important for all domains of life. With the advent of modern molecular biology their applicability to medicine has become apparent in settings ranging from diagonistic biomarkers to therapeutics and fields ranging from oncology to neurology. In addition, a critical, recent technological development is high-throughput sequencing of nucleic acids. The convergence of modern biotechnology with developments in RNA biology presents opportunities in both basic research and medical settings. Here I present two novel methods for leveraging high-throughput sequencing in the study of short non-coding RNAs, as well as a study in which they are applied to Alzheimer's Disease (AD). The computational methods presented here include High-throughput Annotation of Modified Ribonucleotides (HAMR), which enables researchers to detect post-transcriptional covalent modifications to RNAs in a high-throughput manner. In addition, I describe Classification of RNAs by Analysis of Length (CoRAL), a computational method that allows researchers to characterize the pathways responsible for short non-coding RNA biogenesis. Lastly, I present an application of the study of non-coding RNAs to Alzheimer's disease. When applied to the study of AD, it is apparent that several classes of non-coding RNAs, particularly tRNAs and tRNA fragments, show striking changes in the dorsolateral prefrontal cortex of affected human brains. Interestingly, the nature of these changes differs between mitochondrial and nuclear tRNAs, implicating an association between Alzheimer's disease and perturbation of mitochondrial function. In addition, by combining known genetic factors of AD with genes that are differentially expressed and targets of regulatory RNAs that are differentially expressed, I construct a network of genes that are potentially relevant to the pathogenesis of the disease. By combining genetics data with novel results from the study of non-coding RNAs, we can further elucidate the molecular mechanisms that underly Alzheimer's disease pathogenesis.
Incorporating Tantalum Oxide Nanoparticles into Implantable Polymeric Biomedical Devices for Radiological Monitoring (2023)

Longitudinal radiological monitoring of biomedical devices is increasingly important, driven by the risk of device failure following implantation. Polymeric devices are poorly visualized with clinical imaging, hampering efforts to use diagnostic imaging to predict failure and enable intervention. Introducing nanoparticle contrast agents into polymers is a potential method for creating radiopaque materials that can be monitored via computed tomography. However, the properties of composites may be altered with nanoparticle addition, jeopardizing device functionality. Thus, the material and biomechanical responses of model nanoparticle-doped biomedical devices (phantoms), created from 0-40 wt% tantalum oxide (TaO<sub>x</sub> ) nanoparticles in polycaprolactone and poly(lactide-co-glycolide) 85:15 and 50:50, representing non, slow, and fast degrading systems, respectively, are investigated. Phantoms degrade over 20 weeks in vitro in simulated physiological environments: healthy tissue (pH 7.4), inflammation (pH 6.5), and lysosomal conditions (pH 5.5), while radiopacity, structural stability, mechanical strength, and mass loss are monitored. The polymer matrix determines overall degradation kinetics, which increases with lower pH and higher TaO<sub>x</sub> content. Importantly, all radiopaque phantoms could be monitored for a full 20 weeks. Phantoms implanted in vivo and serially imaged demonstrate similar results. An optimal range of 5-20 wt% TaO<sub>x</sub> nanoparticles balances radiopacity requirements with implant properties, facilitating next-generation biomedical devices.
Adrenomedullin Binding Protein in the Plasma of Multiple Species: Characterization by Radioligand Blotting (1999)

Frequently, peptide hormones circulate in plasma associated with specific binding proteins that modify the clearance and biochemical activities of the peptide. Our experimental approach was to use 125I-ligand blotting procedures to probe for the presence of specific adrenomedullin (AM) binding proteins (AMBPs). Plasma proteins from chick, calf, dog, goat, guinea pig, human, mouse, pig, rabbit and sheep blood were separated electrophoretically in 10% nonreducing SDS-polyacrylamide gels and transferred to nitrocellulose. Nonspecific binding of tracer was blocked on the nitrocellulose with a hydrolyzed casein matrix. Blots were probed with synthetic human 125I-AM. Autoradiogram scanning of blots revealed a mixture of 140- and/or 120- kD protein complexes that bound 125I-AM in all species tested. Binding of the ligand was specific as judged by a linear competitive displacement of the tracer binding from human, bovine and pig plasma AMBP bands with increasing concentrations of nonlabelled AM in the binding buffer. A series of peptide fragments of AM representing amino- and carboxyterminal regions of the hormone, or amylin, calcitonin gene-related peptide (CGRP), or insulin failed to displace intact 125I-AM from ligand blot bands. Bovine plasma proteins from healthy and parasitized calves with an infection-related stunting syndrome were separated electrophoretically, transferred to nitrocellulose and probed with 125I-AM; phosphoimage densitometry analysis revealed a 67% decrease in AMBP band intensity in the 120 and 140 kD proteins from infected calves. We conclude that a specific binding protein(s) for AM exists in mammalian and avian blood that might impact on the bioactivity and function of AM in health and disease.
Energy-Aware Sensor Networks via Sensor Selection and Power Allocation (2017)

Finite energy reserves and the irreplaceable nature of nodes in battery-driven wireless sensor networks (WSNs) motivate energy-aware network operation. This paper considers energy-efficiency in a WSN by investigating the problem of minimizing the power consumption consisting of both radiated and circuit power of sensor nodes, so as to determine an optimal set of active sensors and corresponding transmit powers. To solve such a mixed discrete and continuous problem, the paper proposes various sensor selection and power allocation algorithms of low complexity. Simulation results show an appreciable improvement in their performance over a system in which no selection strategy is applied, with a slight gap from derived lower bounds. The results further yield insights into the relationship between the number of activated sensors and its effect on total power in different regimes of operation, based on which recommendations are made for which strategies to use in the different regimes.
Regression of human kidney cancer following allogeneic stem cell transplantation is associated with recognition of an HERV-E antigen by T cells (2008)

During the preparation of the manuscript, the definition of the error bars was inadvertently omitted. In all figures, error bars indicate SEM.
Baculoviral IAP Repeat-Containing-4 Protects Optic Nerve Axons in a Rat Glaucoma Model (2002)

Gene therapy represents an attractive approach for the treatment of eye diseases such as glaucoma. Ocular administration of viral vectors produces localized retinal gene expression with reduced risks of side effects reported with systemic administration of viral vectors. Recombinant adeno-associated viral (AAV) vectors have proven effective in producing long-term retinal gene expression, due to stable integration of DNA into the genome and lack of host immune response to the virus. Recently developed AAV constructs using the chicken beta-actin (CBA) promoter drive highly efficient transgene expression in retinal ganglion cells (RGCs), photoreceptors, and pigment epithelium. Rats were given unilateral intravitreal injections of AAV-CBA vector coding for human baculoviral IAP repeat-containing protein-4 (BIRC4), a potent caspase inhibitor. Ocular hypertension was induced in the same eye by sclerosis of aqueous humor outflow channels. After chronic exposure to elevated intraocular pressure, we performed optic nerve axon counts to determine the neuroprotective effects of retinal BIRC4 expression, and compared axon survival with vector and balanced salt solution control groups. Gene therapy delivering BIRC4 significantly promoted optic nerve axon survival in a chronic ocular hypertensive model of rat glaucoma. Blocking RGC apoptosis with caspase inhibitors represents a promising approach for treatment of human glaucoma.
Migratory birds in southern Brazil are a source of multiple avian influenza virus subtypes (2017)

Lagoa do Peixe National Park is a source of multiple AIV subtypes, with the levels of influenza virus in birds being highest at the end of their wintering period in this region. H6N1 viruses were the predominant subtype identified. These viruses were more similar to viruses of South American lineage than to those of North American lineage.
Tolerable CD variation analyzer using perturbed nominal models demonstrated on altPSM (2005)

At the 65 nm node and beyond, printing the dense and isolated pitches as well as the 2D patterns within tight tolerance across the full range of known process conditions becomes a major challenge, and even more critical in the context of double exposure masks. Post-OPC simulation at nominal conditions is not sufficient to accurately assess and disposition severe errors and monitor residual proximity effects and their implications such as channel length variation. In this paper, we explore a methodology that adopts multiple simulations to model the variability in the lithography process. This approach is predicting the process behavior by the modulation of the related lithography parameters, such as: dose, focus, and overlay. The goal is to identify the unacceptable deviation of the printed image from the designed target due to process variations. The method also provides a better statistical evaluation of the quality and robustness of the implemented Resolution Enhancement Techniques (RET) & Design for Manufacturability (DfM) solution.
Design and Analysis of a Slope Voltage Control for a DFIG Wind Power Plant (2011)

This paper addresses a detailed design of a wind power plant and turbine slope voltage control in the presence of communication delays for a wide short-circuit ratio range operation. The implemented voltage control scheme is based upon the secondary voltage control concept, which offers fast response to grid disturbances, despite the communication delays, i.e., this concept is based on a primary voltage control, located in the wind turbine, which follows an external voltage reference sent by a central controller, called secondary voltage control, which is controlling the voltage at the point of connection with the grid. The performance has been tested using PSCAD/EMTDC program. The plant layout used in the simulations is based on an installed wind power plant, composed of 23 doubly fed generator wind turbines. The resulting performance is evaluated using a compilation of grid code voltage control requirements. The results show that fast response to grid disturbances can be achieved using the secondary voltage control scheme, and the fulfillment of the design requirements can be extended for a wide range of short-circuit ratios.
Development and characterization of advanced process technologies for the fabrication of crystalline-Si solar cells (2010)

Photovoltaic devices were fabricated at IBM TJ Watson Research Center using a research line designed to run different substrate types concurrently. The process knowledge gained from CMOS IC fabrication is applied to solar cell fabrication to create cells with plated Cu front metallization, Al back contacts, and PECVD SiN ARC. The interaction between substrate type and process conditions for saw damage etch, PECVD SiN deposition and emitter formation (thermal budget exposure) is presented in this paper. Electroplating process characterization results are discussed. The effects on the electrical characteristics of the photovoltaic device due to the process parameters chosen, and due to extrinsic defects, are discussed.
Toward standard process models for OPC (2007)

We present description of the Compact Model 1 (CM1) resist model designed for use in OPC and OPC verification. We discuss model formulation and compare model predictions to the resist measurements. We propose to use CM1 model as a standard pattern transfer model during chip-scale process simulations.
Multimodal Unrolled Robust PCA for Background Foreground Separation (2022)

Background foreground separation (BFS) is a popular computer vision problem where dynamic foreground objects are separated from the static background of a scene. Typically, this is performed using consumer cameras because of their low cost, human interpretability, and high resolution. Yet, cameras and the BFS algorithms that process their data have common failure modes due to lighting changes, highly reflective surfaces, and occlusion. One solution is to incorporate an additional sensor modality that provides robustness to such failure modes. In this paper, we explore the ability of a cost-effective radar system to augment the popular Robust PCA technique for BFS. We apply the emerging technique of algorithm unrolling to yield real-time computation, feedforward inference, and strong generalization in comparison with traditional deep learning methods. We benchmark on the RaDICaL dataset to demonstrate both quantitative improvements of incorporating radar data and qualitative improvements that confirm robustness to common failure modes of image-based methods.
A study of Instance Manager for programmable IoT nodes (2014)

Spreading Internet of Thing devices, we need an effective method for managing the devices. For that reason, we proposed Instance Manager that can provide intelligent services to end users with effective way. The proposed system has virtual objects as representing devices released by many companies for integrating the services provided by each device. In this paper, we will explain how to devise Instance Manager and a Virtual Object from real IoT device.
Large-Scale Multipair Two-Way Relay Networks with Distributed AF Beamforming (2013)

We consider a multipair two-way relay network where multiple communication pairs simultaneously exchange information with the help of multiple relay nodes. All nodes are equipped with a single antenna and channel state information is available at the relay nodes. Each relay uses very simple signal processing in a distributed manner, called distributed amplify-and-forward (AF) relaying. A closed-form expression for the achievable rate is derived. We show that the distributed AF scheme outperforms conventional orthogonal relaying. When the number of relays is large, the distributed AF relaying scheme can achieve the capacity scaling given by the cut-set upper bound. Furthermore, when the number of relays grows large, the transmit powers of each terminal and of the relay can be made inversely proportional to the number of relays while maintaining a given quality-of-service. If the transmit power of each terminal is kept fixed, the transmit power of each relay can be scaled down inversely proportional to the square of the number of relays.
Experimental and mathematical analysis of cAMP nanodomains (2017)

In their role as second messengers, cyclic nucleotides such as cAMP have a variety of intracellular effects. These complex tasks demand a highly organized orchestration of spatially and temporally confined cAMP action which should be best achieved by compartmentalization of the latter. A great body of evidence suggests that cAMP compartments may be established and maintained by cAMP degrading enzymes, e.g. phosphodiesterases (PDEs). However, the molecular and biophysical details of how PDEs can orchestrate cAMP gradients are entirely unclear. In this paper, using fusion proteins of cAMP FRET-sensors and PDEs in living cells, we provide direct experimental evidence that the cAMP concentration in the vicinity of an individual PDE molecule is below the detection limit of our FRET sensors (<100nM). This cAMP gradient persists in crude cytosol preparations. We developed mathematical models based on diffusion-reaction equations which describe the creation of nanocompartments around a single PDE molecule and more complex spatial PDE arrangements. The analytically solvable equations derived here explicitly determine how the capability of a single PDE, or PDE complexes, to create a nanocompartment depend on the cAMP degradation rate, the diffusive mobility of cAMP, and geometrical and topological parameters. We apply these generic models to our experimental data and determine the diffusive mobility and degradation rate of cAMP. The results obtained for these parameters differ by far from data in literature for free soluble cAMP interacting with PDE. Hence, restricted cAMP diffusion in the vincinity of PDE is necessary to create cAMP nanocompartments in cells.
The Evolving Clinical Landscape for Dendritic Cell Vaccines and Cancer Immunotherapy (2019)

The last 5 years has seen a renaissance in clinical trials for DC vaccination, with a number of increasingly sophisticated approaches being reported in the literature. This Commentary will take an idiosyncratic snapshot of some of the more creative clinical trials.
Static and Dynamic Performance Prediction of Ultrahigh-Voltage Silicon Carbide Insulated-Gate Bipolar Transistors (2020)

The performance of theoretical ultrahigh-voltage power semiconductor devices has been predicted by means of numerical simulations using the Sentaurus technology computer-aided design tool. A general silicon carbide punch-through insulated-gate bipolar transistor (IGBT) structure has been implemented with suitable physics-based models and parameters to reflect the device characteristics in a wide range of device blocking voltages from 20 to 50 kV. The models for 20 kV class IGBTs have been implicitly validated by means of published experimental results. Mixed-mode simulations were performed that predicted total switching energy loss densities of 335, 629, 906, and 999 mJ/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for 20, 30, 40, and 50 kV class devices, respectively, at 25 °C, JC = 20 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , and an ambipolar carrier lifetime of 20 μs. While the IGBT on-state forward voltage drop reduces, the switching losses increase with higher charge-carrier lifetime for a given current density (e.g., 20 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ). The large span of simulation results will be used as an input support to the design of future high-power converters.
Corrosion properties in friction stir welded 304 austenitic stainless steel (2006)

A 304 austenitic stainless steel was friction stir welded using polycrystalline cubic boron nitride (PCBN) tool. Relationship between corrosion properties and microstructure was examined in the weld using several corrosion tests and microstructural observation techniques. The stir zone (SZ) had better corrosion properties than the base material (BM). The corrosion tests showed that the intergranular corrosion was developed in the heat-affected zone (HAZ) compared to the BM and SZ although the grain boundaries were not severely corroded. TEM/EDS analysis revealed that Cr depletion zone near grain boundary in the HAZ was shallow and narrow. Friction stir welding (FSW) suppressed sensitisation in the HAZ, which could be explained by short duration at sensitisation temperatures during welding. On the other hand, many grain boundaries were deeply corroded in the AS, where the corrosion resistance was significantly degraded. The microstructural observation revealed that sigma phase was formed in the AS during FSW. Sigma formation produced the wide and deep Cr depletion zone with the minimum Cr content less than 12 wt % in the vicinity of the grain boundary in the AS, which severely deteriorated the corrosion resistance in the AS.
Periodic Porous 3D Electrodes Mitigate Gas Bubble Traffic during Alkaline Water Electrolysis at High Current Densities (2020)

Abstract Alkaline water electrolysis at high current densities is plagued by gas bubble generation and trapping in stochastic porous electrodes (e.g., Ni foams), which causes a significant reduction in the number of electrolyte accessible catalyst active sites. Here, 3D printed Ni (3DPNi) electrodes with highly controlled, periodic structures are reported that suppress gas bubble coalescence, jamming, and trapping and, hence, result in rapid bubble release. The 3DPNi electrodes decorated with carbon‐doped NiO achieve a high current density of 1000 mA cm −2 in 1.0 m KOH electrolyte at hydrogen evolution reaction and oxygen evolution reaction overpotentials of 245 and 425 mV, respectively. This work demonstrates a new approach to the deterministic design of 3D electrodes to facilitate rapid bubble transport and release to enhance the total electrode catalytic activity at commercially relevant current densities.
Synthesis of well‐defined photoresist materials by SET‐LRP (2010)

Abstract Single electron transfer‐living radical polymerization (SET‐LRP) provides an excellent tool for the straightforward synthesis of well‐defined macromolecules. Heterogeneous Cu(0)‐ catalysis is employed to synthesize a novel photoresist material with high control over the molecular architecture. Poly(γ‐butyrolactone methacrylate)‐ co ‐(methyladamantly methacrylate) was synthesized. Kinetic experiments were conducted demonstrating that both monomers, γ‐butyrolactone methacrylate (GBLMA) and methyl adamantly methacrylate (MAMA), are successfully homopolymerized. In both cases polymerization kinetic is of first order and the molecular weights increase linearly with conversion. The choice of a proper solvent was decisive for the SET‐LRP process and organic solvent mixtures were found to be most suitable. Also, the kinetic of the copolymerization of GBLMA and MAMA was investigated. Following first order kinetics in overall monomer consumption and exhibiting a linear relationship between molecular weights and conversion a “living” process was established. This allowed for the straightforward synthesis of well‐defined photoresist polymers. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 2251–2255, 2010
Electron Transfer Reactivity of Type Zero Pseudomonas aeruginosa Azurin (2011)

Type zero copper is a hard-ligand analogue of the classical type 1 or blue site in copper proteins that function as electron transfer (ET) agents in photosynthesis and other biological processes. The EPR spectroscopic features of type zero Cu(II) are very similar to those of blue copper, although lacking the deep blue color, due to the absence of thiolate ligation. We have measured the rates of intramolecular ET from the pulse radiolytically generated C3-C26 disulfide radical anion to the Cu(II) in both type zero C112D/M121L and type 2 C112D Pseudomonas aeruginosa azurins in pH 7.0 aqueous solutions between 8 and 45 °C. We also have obtained rate/temperature (10-30 °C) profiles for ET reactions between these mutants and the wild-type azurin. Analysis of the rates and activation parameters for both intramolecular and intermolecular ET reactions indicates that the type zero copper reorganization energy falls in a range (0.9-1.1 eV) slightly above that for type 1 (0.7-0.8 eV), but substantially smaller than that for type 2 (>2 eV), consistent with XAS and EXAFS data that reveal minimal type zero site reorientation during redox cycling.
Squaraine dyes for organic photovoltaic cells (2015)

In this review, we present the recent advances in squaraine dye materials and their applications to organic photovoltaic cells.
Supplementary Figure S1 - S8 from Preclinical Activity of the Novel Anti-Prolactin Receptor (PRLR) Antibody–Drug Conjugate REGN2878-DM1 in PRLR-Positive Breast Cancers (2023)

&lt;p&gt;Supplementary Figures S1 - S8 as referenced in the main article&lt;/p&gt;