gebhart/patrepeval huggingface dataset:
Morpholino Monolayers: Preparation and Label-free DNA Analysis by Surface Hybridization (2009)

Surface hybridization, a reaction in which nucleic acid molecules in solution react with nucleic acid partners immobilized on a surface, is widely practiced in life science research. In these applications the immobilized partner, or "probe", is typically single-stranded DNA. Because DNA is strongly charged, high salt conditions are required to enable binding between analyte nucleic acids ("targets") in solution and the DNA probes. High salt, however, compromises prospects for label-free monitoring or control of the hybridization reaction through surface electric fields; it also stabilizes secondary structure in target species that can interfere with probe-target recognition. In this work, initial steps toward addressing these challenges are taken by introducing morpholinos, a class of uncharged DNA analogues, for surface-hybridization applications. Monolayers of morpholino probes on gold supports can be fabricated with methods similar to those employed with DNA and are shown to hybridize efficiently and sequence-specifically with target strands. Hybridization-induced changes in the interfacial charge organization are analyzed with electrochemical methods and compared for morpholino and DNA probe monolayers. Molecular mechanisms connecting surface hybridization state to the interfacial capacitance are identified and interpreted through comparison to numerical Poisson-Boltzmann calculations. Interestingly, positive as well as negative capacitive responses (contrast inversion) to hybridization are possible, depending on surface populations of mobile ions as controlled by the applied potential. Quantitative comparison of surface capacitance with target coverage (targets/area) reveals a nearly linear relationship and demonstrates sensitivities (limits of quantification) in the picogram per square millimeter range.
Design, fabrication and implementation of a novel multi-parameter control microfluidic platform for three-dimensional cell culture and real-time imaging (2008)

New and more biologically relevant in vitro models are needed for use in drug development, regenerative medicine, and fundamental scientific investigation. While the importance of the extracellular microenvironment is clear, the ability to investigate the effects of physiologically relevant biophysical and biochemical factors is restricted in traditional cell culture platforms. Moreover, the versatility for multi-parameter manipulation, on a single platform, with the optical resolution to monitor the dynamics of individual cells or small population is lacking. Here we introduce a microfluidic platform for 3D cell culture in biologically derived or synthetic hydrogels with the capability to monitor cellular dynamics in response to changes in their microenvironment. Direct scaffold microinjection, was employed to incorporate 3D matrices into microfluidic devices. Our system geometry permits a unique window for studying directional migration, e.g. sprouting angiogenesis, since sprouts grow predominantly in the microscopic viewing plane. In this study, we demonstrate the ability to generate gradients (non-reactive solute), surface shear, interstitial flow, and image cells in situ. Three different capillary morphogenesis assays are demonstrated. Human adult dermal microvascular endothelial cells (HMVEC-ad) were maintained in culture for up to 7 days during which they formed open lumen-like structures which was confirmed with confocal microscopy and by perfusion with fluorescent microspheres. In the sprouting assay, time-lapse movies revealed cellular mechanisms and dynamics (filopodial projection/retraction, directional migration, cell division and lumen formation) during tip-cell invasion of underlying 3D matrix and subsequent lumen formation.
Apolipoprotein Mimetic Peptides: Potential New Therapies for Cardiovascular Diseases (2021)

Since the seminal breakthrough of treating diabetic patients with insulin in the 1920s, there has been great interest in developing other proteins and their peptide mimetics as therapies for a wide variety of other medical disorders. Currently, there are at least 60 different peptides that have been approved for human use and over 150 peptides that are in various stages of clinical development. Peptides mimetic of the major proteins on lipoproteins, namely apolipoproteins, have also been developed first as tools for understanding apolipoprotein structure and more recently as potential therapeutics. In this review, we discuss the biochemistry, peptide mimetics design and clinical trials for peptides based on apoA-I, apoE and apoC-II. We primarily focus on applications of peptide mimetics related to cardiovascular diseases. We conclude with a discussion on the limitations of peptides as therapeutic agents and the challenges that need to be overcome before apolipoprotein mimetic peptides can be developed into new drugs.
Carbon Nanotubes for Microelectronics? (2005)

Despite all prophecies of its end, silicon-based microelectronics still follows Moore's Law and continues to develop rapidly. However, the inherent physical limits will eventually be reached. Carbon nanotubes offer the potential for further miniaturization as long as it is possible to selectively deposit them with defined properties.
Detection and Characterization of Cracks Using Lamb Wave Propagation (2015)

The goal of a structural health monitoring system is to implement processes to detect and characterize damages in engineering structures. These systems may use many different physical phenomena to detect and characterize damages. One of these phenomena is elastic wave propagation in thin plate like structures, known as Lamb wave propagation. To develop a SHM (structural health monitoring) system based on Lamb wave propagation we first need to understand how Lamb waves interact with different damage types. The aim of this study is to develop an understanding of how Lamb waves interact with different types of damages using analytical modeling and FEM. The goal is to identify and characterize a surface breaking crack by understanding its effect on Lamb waves scattered from it. doi: 10.12783/SHM2015/75
A luminescent lanthanide approach towards direct visualization of primary cilia in living cells (2017)

We report a direct imaging tool, HGEu001, for primary cilia in living cells, which is specific, and based on the UV light or near infrared laser (via two-photon excitation) induced long-lived europium luminescence.
Fundamental Study for the Solution of Thermoacoustic Phenomenon Using Numerical Calculation: Relationship between the Stack Installation Position and Heat Flow (2012)

Thermoacoustic systems have several advantages owing to their simple structure driven by heat energy such as waste heat and solar heat. However, because their energy conversion efficiency is low, they have not been developed for practical use. Therefore, to improve energy conversion efficiency, a method of system design development is examined in this report using numerical calculations. First, calculation results obtained using the transfer-matrix methods are compared with experimentally obtained results, which confirms their good agreement. Secondly, calculated results of each heat flow element in the stack show that heat flow proportional to the temperature gradient QD, which decreases the performance of the system, is dominant. Finally, the installation position of the stack is changed to reduce the ratio that QD occupies in the heat flow. Results show a decrease in the ratio obtained by moving the stack installation position closer to the center of the tube. Energy conversion efficiency was increased eight times.
High-Temperature Operation of Diamond Junction Field-Effect Transistors With Lateral p-n Junctions (2013)

High-temperature performance of diamond junction field-effect transistors (JFETs) with lateral p-n junctions is demonstrated. Diamond JFETs fabricated by n-type selective growth can be operated at 723 K, and show very low leakage currents of ~ 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-13</sup> A and high ON/OFF ratios . Specific on-resistance decreases from 52.2 mΩ·cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at 300 K to 1.4 mΩ·cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at 723 K. At high temperatures, the device shows steep subthreshold swings very close to the theoretical limit. The low leakage currents are maintained even at a high drain voltage of -100 V. These excellent properties at high temperatures and high voltage show that diamond JFETs can work in harsh environments.
Novel medium noise model of perpendicular magnetic recording medium (1999)

Perpendicular magnetic recording has a possibility of solving the thermal stability of a recording medium[ll. But noise of perpendicular recording medium must be much more reduced to attain over 20 Hb.in2 recording density.
Optical Low-Pass Filter for a Single-Vidicon Color Television Camera (1972)

An optical low-pass filter is indispensable for a single-vidicon color TV camera, in which a color-encoding dichroic filter is used, in order to eliminate the interference between luminance and chrominance signals. Properties of a rectangular-phase grating are described from the viewpoint of application of the color TV camera. The grating placed in the optical system acts as a one-dimensional optical low-pass filter, its optical transfer function (OTF) decreasing linearly as the frequency increases up to the cutoff frequency. The cutoff frequency and the dc level of the OTF are expressed as functions of grating parameters. The cutoff frequency is unaffected by varying the aperture stop of the optical system. It is shown that the trapezoidal-wave phase grating is also useful for the optical low-pass filter.
Quantitative corrosion monitoring and detection using ultrasonic Lamb waves (2005)

Corrosion is a major problem for airframe operators. For the aircraft industry in general, the direct costs of corrosion are estimated at $2.2 billion. As part of their strategy to control corrosion, airframe operators constantly seek to improve their ability to anticipate, manage and identify corrosion activity. Motivated by the need for an on-line real-time corrosion-monitoring tool for industry and aircraft a prototype system and analysis approach is presented. The tool employs ultrasonic Lamb waves along with a dispersion compensated synthetic aperture focusing technique (SAFT) to detect emerging pitting damage. In order to develop an automated detection approach the noise sources of the SAFT processed defect maps were examined and modeled. The random noise was found to be neither stationary nor normally distributed. Locally varying Weibull distribution parameters are used to characterize the image noise. An algorithm is developed to quantify the uncertainty in the corrosion detection and to allow assignment of a constant false alarm probability to any region of the monitored area.
Inside Back Cover: SrB<sub>5</sub>O<sub>7</sub>F<sub>3</sub> Functionalized with [B<sub>5</sub>O<sub>9</sub>F<sub>3</sub>]<sup>6−</sup> Chromophores: Accelerating the Rational Design of Deep‐Ultraviolet Nonlinear Optical Materials (Angew. Chem. Int. Ed. 21/2018) (2018)

For the next generation of deep-ultraviolet nonlinear optical materials, fluorooxoborates have been considered to be highly promising. In their Communication on page 6095 ff. S. Pan and co-workers prepare the first asymmetric alkaline-earth-metal fluorooxoborate, SrB5O7F3, with the unprecedented [B5O9F3]6− fundamental building block, which was rationally designed and synthesized as a potential deep-ultraviolet nonlinear optical material.
Low-Frequency Underwater Flex-Beam Transducer (1992)

No host preference of P. latus was observed among white and colored cotton cultivar. Abamectin and spirodiclofen presented relevant sublethal effects that should be considered for the integrated management of this pest.
The KaGE RLS algorithm (2003)

A new fast recursive least squares (RLS) algorithm, the Kalman gain estimator (KaGE), is introduced. By making use of RLS interpolation as well as prediction, the algorithm generates the transversal filter weights without suffering the poor numerical attributes of the fast transversal filter (FTF) algorithm. The Kalman gain vector is generated at each time step in terms of interpolation residuals. The interpolation residuals are calculated in an order recursive manner. For an N/sup th/-order problem, the procedure requires O(Nlog/sub 2/N) operations per iteration. This is achieved via a divide-and-conquer approach. Computer simulations suggest that the new algorithm is numerically robust, running successfully for many millions of iterations.
Adaptive self-healing electronic epineurium for chronic bidirectional neural interfaces (2020)

Realizing a clinical-grade electronic medicine for peripheral nerve disorders is challenging owing to the lack of rational material design that mimics the dynamic mechanical nature of peripheral nerves. Electronic medicine should be soft and stretchable, to feasibly allow autonomous mechanical nerve adaptation. Herein, we report a new type of neural interface platform, an adaptive self-healing electronic epineurium (A-SEE), which can form compressive stress-free and strain-insensitive electronics-nerve interfaces and enable facile biofluid-resistant self-locking owing to dynamic stress relaxation and water-proof self-bonding properties of intrinsically stretchable and self-healable insulating/conducting materials, respectively. Specifically, the A-SEE does not need to be sutured or glued when implanted, thereby significantly reducing complexity and the operation time of microneurosurgery. In addition, the autonomous mechanical adaptability of the A-SEE to peripheral nerves can significantly reduce the mechanical mismatch at electronics-nerve interfaces, which minimizes nerve compression-induced immune responses and device failure. Though a small amount of Ag leaked from the A-SEE is observed in vivo (17.03 ppm after 32 weeks of implantation), we successfully achieved a bidirectional neural signal recording and stimulation in a rat sciatic nerve model for 14 weeks. In view of our materials strategy and in vivo feasibility, the mechanically adaptive self-healing neural interface would be considered a new implantable platform for a wide range application of electronic medicine for neurological disorders in the human nervous system.
Characterization of Nanodiamond-based anti-HIV drug Delivery to the Brain (2018)

Human Immunodeficiency Virus Type 1 (HIV-1) remains one of the leading causes of death worldwide. Present combination antiretroviral therapy has substantially improved HIV-1 related pathology. However, delivery of therapeutic agents to the HIV reservoir organ like Central nervous system (CNS) remains a major challenge primarily due to the ineffective transmigration of drugs through Blood Brain Barrier (BBB). The recent advent of nanomedicine-based drug delivery has stimulated the development of innovative systems for drug delivery. In this regard, particular focus has been given to nanodiamond due to its natural biocompatibility and non-toxic nature-making it a more efficient drug carrier than other carbon-based materials. Considering its potential and importance, we have characterized unmodified and surface-modified (-COOH and -NH<sub>2</sub>) nanodiamond for its capacity to load the anti-HIV-1 drug efavirenz and cytotoxicity, in vitro. Overall, our study has established that unmodified nanodiamond conjugated drug formulation has significantly higher drug loading capacity than surface-modified nanodiamond with minimum toxicity. Further, this nanodrug formulation was characterized by its drug dissolution profile, transmigration through the BBB, and its therapeutic efficacy. The present biological characterizations provide a foundation for further study of in-vivo pharmacokinetics and pharmacodynamics of nanodiamond-based anti-HIV drugs.
Amorphous Germanium as an Electron or Hole Blocking Contact on High-Purity Germanium Detectors (1977)

Experiments were performed in an attempt to make thin n+ contacts on high-purity germanium by the solid phase1 epitaxial regrowth of arsenic doped amorphous germanium. After cleaning the crystal surface with argon sputtering and trying many combinations of layers, it was not found possible to induce recrystallization below 673K. However, it was found that simple thermally evaporated amorphous Ge made fairly good electron or hole blocking contacts. Excellent spectrometers have been made with amorphous Ge replacing the n+ contact. As presently produced, the amorphous Ge contact diodes show a large variation in high-voltage leakage current.
Inhibition of endothelial cell migration by vascular endothelial growth factor receptor-1 peptides. (2005)

The soluble vascular endothelial growth factor receptor-1 (sVEGFR-1) is a polypeptide secreted by endothelial cells that contains six out of the seven extracellular Ig-like domains of the transmembrane VEGFR-1 and a unique sequence of 30 amino acids. The biological role of sVEGFR-1 has not been clarified yet, even though it is considered a negative modulator of VEGF and PlGF activity, blocking the interaction of these growth factors with their membrane receptors. We have recently demonstrated that endothelial cells adhere on sVEGFR-1 and migrate in response to the polypeptide through a mechanism that involves the integrin alpha5beta1. Moreover, endothelial cells deposit the sVEGFR-1 into the extracellular matrix. These data suggest a role for sVEGFR-1 in processes of primary importance during angiogenesis, such as migration and interaction of endothelial cells with the extracellular matrix.\n To test this hypothesis, we designed a series of VEGFR-1 peptides, potentially able to block the sVEGFR-1/alpha5beta1 integrin interaction. Based on the structural analysis of VEGFR-1 second Ig-like domain, a set of eight peptides was synthesised. Peptides were tested for the ability to inhibit endothelial cell adhesion on sVEGFR-1 or fibronectin. Peptide A4 reduced cell adhesion on sVEGFR-1 and fibronectin by 50% and 30%, respectively. We next evaluated the effects of peptide A4 on endothelial cell migration induced by fibronectin, sVEGFR-1, VEGF or PlGF. Treatment with peptide A4 resulted in 30% inhibition of basal migration (without stimulus) and abrogation of the response to either sVEGFR-1 or PlGF, whereas it did not affect migration induced by fibronectin or VEGF. A control peptide, containing the amino acids of peptide A4 in a scrambled sequence, did not have any effect on endothelial cell migration. To further define the region of peptide A4 responsible of its inhibitory activity, a second set of peptides corresponding to a part of peptide A4 sequence was tested. Peptide B3 resulted to be the most efficient in inhibiting endothelial cell migration.\n In conclusion, peptide B3 behaves as a selective inhibitor of endothelial cell migration induced by sVEGFR-1 or PlGF. As cell migration is a fundamental step in the process of angiogenesis, peptide B3 could represent a leading molecule for the design of new drugs to be used in the treatment of cancer or other angiogenesis-related diseases.\n\nSupported by the Italian Ministry of Health and Compagnia di San Paolo.
Improving lesion detectability in PET imaging with a penalized likelihood reconstruction algorithm (2015)

Ordered Subset Expectation Maximization (OSEM) is currently the most widely used image reconstruction algorithm for clinical PET. However, OSEM does not necessarily provide optimal image quality, and a number of alternative algorithms have been explored. We have recently shown that a penalized likelihood image reconstruction algorithm using the relative difference penalty, block sequential regularized expectation maximization (BSREM), achieves more accurate lesion quantitation than OSEM, and importantly, maintains acceptable visual image quality in clinical wholebody PET. The goal of this work was to evaluate lesion detectability with BSREM versus OSEM. We performed a twoalternative forced choice study using 81 patient datasets with lesions of varying contrast inserted into the liver and lung. At matched imaging noise, BSREM and OSEM showed equivalent detectability in the lungs, and BSREM outperformed OSEM in the liver. These results suggest that BSREM provides not only improved quantitation and clinically acceptable visual image quality as previously shown but also improved lesion detectability compared to OSEM. We then modeled this detectability study, applying both nonprewhitening (NPW) and channelized Hotelling (CHO) model observers to the reconstructed images. The CHO model observer showed good agreement with the human observers, suggesting that we can apply this model to future studies with varying simulation and reconstruction parameters.
RRH and small cells — The implications for spectrum sharing (2015)

This paper considers the implications of different infrastructure options on a spectrum sharing scenario in cellular networks, featuring a mixture of macro cells and low-power nodes (LPNs). Our aim is to provide a systematic approach to spectrum sharing. This requires dealing not only with various aspects of the spectrum but also understanding the infrastructure requirements. Considering the general trends towards deployments of dense and ultra-dense networks of LPNs, of particular interest are two types of nodes - remote radio heads (RRHs) and small cells. They pose different requirements on the transport network - RRHs have strict requirements on throughput, latency, and jitter while small cells allow the use of different transport network technologies. The spectrum sharing model considered here is based on the well-known Carrier Aggregation of LTE-Advanced, designed to support topologies with RRHs, and Dual Connectivity, introduced to support deployments with small cells. In addition, the model also incorporates spectral resources from two distinct shared spectrum classes that are heterogeneous in a number of aspects. They include spectrum access rights, together with the cost of accessing the spectrum, as well as the quality of spectrum in terms of its availability and protection from inter-system interference. The analysis in this paper is focused on the downlink throughput for a typical user, where a cellular operator determines the required spectrum resources from a particular spectrum class. The objective is to meet a particular Quality of Service (QoS) requirement, defined as the minimum average throughput. In that, the paper analyses interaction between the options supporting RRHs that is small cells, and the sharing model, taking into account certain implementation aspects of LTE-Advanced. It provides a comprehensive evaluation and sensitivity analysis of a number of parameters of interest to the cellular operator, such as network load, the density of LPNs, inter-system interference, power levels, and QoS targets.
A New Sandwich ELISA Test Simultaneously Detecting E7 Proteins of HPV-16, 18 and 45 in Cervical Smears (2016)

Persistent infections by high-risk papilloma viruses (HPV) are the main etiological factor for cervical cancer, and E7 oncoproteins were suggested as new markers for tumor progression. The objective of this study was to generate a new Enzyme-Linked Immunosorbent Assay (ELISA)-based detection system to monitor expression of the E7 proteins of the high-risk HPV (hrHPV) types HPV-16, HPV-18, and HPV-45 in cervical smears. Using a combination of rabbit monoclonal antibodies raised against E7 proteins of HPV-16 and HPV-18/HPV-45, respectively, a trivalent E7-ELISA was developed and validated, using recombinant E7 proteins of various HPV types and lysates from E7positive cervical carcinoma cells. The amount of 0.5 picogram of E7 protein per well was determined as detection limit.