gebhart/patrepeval huggingface dataset:
Data-driven missing data imputation in cluster monitoring system based on deep neural network (2019)

Abstract Due to cluster instability, not in the cluster monitoring system. This paper focuses on the missing data imputation processing for the cluster monitoring application and proposes a new hybrid multiple imputation framework. This new imputation approach is different from the conventional multiple imputation technologies in the fact that it attempts to impute the missing data for an arbitrary missing pattern with a model-based and data-driven combination architecture. Essentially, the deep neural network, as the data model, extracts deep features from the data and deep features are further calculated then by a regression or data-driven strategies and used to create the estimation of missing data with the arbitrary missing pattern. This paper gives evidence that if we can train a deep neural network to construct the deep features of the data, imputation based on deep features is better than that directly on the original data. In the experiments, we compare the proposed method with other conventional multiple imputation approaches for varying missing data patterns, missing ratios, and different datasets including real cluster data. The result illustrates that when data encounters larger missing ratio and various missing patterns, the proposed algorithm has the ability to achieve more accurate and stable imputation performance.
Smart Indoor Parking System Based on Dijkstra’s Algorithm (2019)

Smart Indoor Parking System is a parking system that assigns the car to the nearest parking to the entrance by using Dijkstra’s Algorithm and assigns according to the size of the car. There are many types of parking system have been proposed such as smart parking system by using Wireless Sensor Network (WSN) but all these methods have their own advantage and limitation. Besides that, there are also several problems with the current parking system such as lack of parking management system efficiency. Therefore, this Smart Indoor Parking System is proposed to increase the efficiency of current parking management system. The aim of this Smart Indoor Parking System is to provide the customer with the nearest parking to the entrance. The parking is assigned according to the size of the car to utilize the parking space. Then, the parking place is displayed on the monitor besides the boom gate before allowing the driver to enter the parking lot. The parking number will help the driver to be able to find a parking lot in a short period of time without the need to search the parking by themselves. The priority is given to the driver who presses the button first. The input signal from the IR sensor located at the entrance and the parking lot is processing to assign the nearest parking lot based on Dijkstra’s Algorithm. In this project, the simulation is carried out by using Proteus. This simulation includes all the circuits for determining the direction of the nearest parking lot. Programming in the Arduino is implemented to calculate the nearest parking lot based on Dijkstra’s Algorithm. In conclusion, the Smart Indoor Parking System can be used in the real-time application.
Deriving Life Multipliers for Electrolytic Capacitors (2004)

Aluminum electrolytic capacitors are routinely used as input bus capacitors in the power supply sections of electronic equipment such as motor drives, UPS systems, and welders. Most of these capacitors fail eventually from wearout. This article offers a brief explanation of how capacitor manufacturers quantify the effects of applied voltage, ripple current, frequency, ambient temperature, and airflow on capacitor life. The general capacitor life equation is
Versatile Redox-Responsive Polyplexes for the Delivery of Plasmid DNA, Messenger RNA, and CRISPR-Cas9 Genome-Editing Machinery (2018)

Gene therapy holds great promise for the treatment of many diseases, but clinical translation of gene therapies has been slowed down by the lack of safe and efficient gene delivery systems. Here, we report two versatile redox-responsive polyplexes (i.e., cross-linked and non-crosslinked) capable of efficiently delivering a variety of negatively charged payloads including plasmid DNA (DNA), messenger RNA, Cas9/sgRNA ribonucleoprotein (RNP), and RNP-donor DNA complexes (S1mplex) without any detectable cytotoxicity. The key component of both types of polyplexes is a cationic poly( N, N'-bis(acryloyl)cystamine- co-triethylenetetramine) polymer [a type of poly( N, N'-bis(acryloyl)cystamine-poly(aminoalkyl)) (PBAP) polymer] containing disulfide bonds in the backbone and bearing imidazole groups. This composition enables efficient encapsulation, cellular uptake, controlled endo/lysosomal escape, and cytosolic unpacking of negatively charged payloads. To further enhance the stability of non-crosslinked PBAP polyplexes, adamantane (AD) and β-cyclodextrin (β-CD) were conjugated to the PBAP-based polymers. The cross-linked PBAP polyplexes formed by host-guest interaction between β-CD and AD were more stable than non-crosslinked PBAP polyplexes in the presence of polyanionic polymers such as serum albumin, suggesting enhanced stability in physiological conditions. Both cross-linked and non-crosslinked polyplexes demonstrated either similar or better transfection and genome-editing efficiencies, and significantly better biocompatibility than Lipofectamine 2000, a commercially available state-of-the-art transfection agent that exhibits cytotoxicity.
Pixel Design Optimization of Fringe-Field Switching Mode for Applying Negative Liquid Crystals in High-Resolution Mobile Displays (2014)

We demonstrate an optimized fringe-field switching pixel structure to apply negative liquid crystals (nLCs) for high-resolution mobile displays. Pixel transmittance can be improved by applying nLCs, but the driving voltage increases because Δε of the nLC is lower than that of the positive LC (pLC). In spite of applying an nLC, a similar driving voltage can be achieved by changing the pixel structure. It is easy to obtain a low driving voltage in a strong electric field by applying a thinner passivation layer using photo acryl (PAC). In addition, while the edge electrodes of the conventional Vcom-on-top (VOT) structure are operated with in-plane switching, all electrodes of the pixel-on-top (POT) structure are operated with fringe-field switching. Therefore, the driving voltage can be reduced by applying a POT structure with PAC. Furthermore, crosstalk can be improved because the capacitance (Cdp) between data lines and pixel electrodes is reduced by applying a POT structure. As a result, applying the proposed structure with nLC has two advantages. First, transmittance increases by more than 20% based on 4.5-in-high definition pixels. Second, crosstalk in the POT structure is more stable than that in the VOT structure, despite variations in low gate voltage (VGL). Consequently, because of higher transmittance and stable crosstalk, the proposed POT structure with nLC can be used for mobile displays.
Hydrogen bond strength and β‐sheet propensities: The role of a side chain blocking effect (1994)

Amino acid side chains can enhance peptide group hydrogen bond strength in protein structures by obstructing the competing hydrogen bond to solvent in the unfolded state. Available data indicate that the steric blocking effect contributes an average of 0.5 kJ per residue to protein hydrogen bond strength and accounts for the intrinsic beta-sheet propensities of the amino acids. In available data for helical models, the contribution to alpha-helix propensities is obscured especially by large context-dependent effects. These issues are all related by a common side chain-dependent steric clash which disfavors peptide to water H-bond formation, peptide to catalyst complexation in hydrogen exchange reactions (Bai et al., Proteins 17:75-86, 1993), and peptide to peptide H-bonding in the helical main chain conformation (Creamer and Rose, Proc. Natl. Acad. Sci. U.S.A. 89:5937-5941, 1992) but not in beta-strands.
A 0.044-mm<sup>2</sup> 0.5-to-7-GHz Resistor-Plus-Source-Follower-Feedback Noise-Cancelling LNA Achieving a Flat NF of 3.3±0.45 dB (2018)

A wideband noise-cancelling low-noise amplifier (LNA) combining resistor feedback and source-follower feedback (SFF) is proposed. The SFF facilitates upsizing of the feedback resistor to improve the gain and noise figure (NF), without compromising the input-impedance matching. Another benefit is that the noise contributions of both the feedback resistor and noise-cancelling transistors are significantly reduced. Fabricated in 65-nm CMOS, the LNA exhibits a voltage gain of 16.8 dB, and a flat NF of 3.3 ± 0.45 dB over a -3-dB bandwidth of 0.5 to 7 GHz. The power consumption is 11.3 mW at 1.2 V, and the die area is 0.044 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Competition between TRAF2 and TRAF6 Regulates NF-κB Activation in Human B Lymphocytes (2010)

These results indicate that TRAF2 can signal in human B cells, but it is not essential for CD40-mediated NF-kappaB activation. Moreover, TRAF2 can compete with TRAF6 for CD40 binding, and thereby limit the capacity of CD40 engagement to induce NF-kappaB activation.
SLAMF7 Is a Critical Negative Regulator of IFN-α–Mediated CXCL10 Production in Chronic HIV Infection (2018)

Current advances in combined antiretroviral therapy have rendered HIV infection a chronic, manageable disease; however, the problem of persistent immune activation still remains despite treatment. The immune cell receptor SLAMF7 has been shown to be upregulated in diseases characterized by chronic immune activation. In this study, we studied the function of the SLAMF7 receptor in immune cells of HIV patients and the impacts of SLAMF7 signaling on peripheral immune activation. We observed increased frequencies of SLAMF7<sup>+</sup> PBMCs in HIV<sup>+</sup> individuals in a clinical phenotype-dependent manner, with discordant and long-term nonprogressor patients showing elevated SLAMF7 levels, and elite controllers showing levels comparable to healthy controls. We also noted that SLAMF7 was sensitive to IFN-⍺ stimulation, a factor elevated during HIV infection. Further studies revealed SLAMF7 to be a potent inhibitor of the monocyte-derived proinflammatory chemokine CXCL10 (IP-10) and other CXCR3 ligands, except in a subset of HIV<sup>+</sup> patients termed SLAMF7 silent (SF7S). Studies utilizing small molecule inhibitors revealed that the mechanism of CXCL10 inhibition is independent of known SLAMF7 binding partners. Furthermore, we determined that SLAMF7 activation on monocytes is able to decrease their susceptibility to HIV-1 infection in vitro via downregulation of CCR5 and upregulation of the CCL3L1 chemokine. Finally, we discovered that neutrophils do not express SLAMF7, are CXCL10<sup>+</sup> at baseline, are able to secrete CXCL10 in response to IFN-⍺ and LPS, and are nonresponsive to SLAMF7 signaling. These findings implicate the SLAMF7 receptor as an important regulator of IFN-⍺-driven innate immune responses during HIV infection.
MicroRNAs Enable mRNA Therapeutics to Selectively Program Cancer Cells to Self-Destruct (2018)

The advent of therapeutic mRNAs significantly increases the possibilities of protein-based biologics beyond those that can be synthesized by recombinant technologies (eg, monoclonal antibodies, extracellular enzymes, and cytokines). In addition to their application in the areas of vaccine development, immune-oncology, and protein replacement therapies, one exciting possibility is to use therapeutic mRNAs to program undesired, diseased cells to synthesize a toxic intracellular protein, causing cells to self-destruct. For this approach to work, however, methods are needed to limit toxic protein expression to the intended cell type. Here, we show that inclusion of microRNA target sites in therapeutic mRNAs encoding apoptotic proteins, Caspase or PUMA, can prevent their expression in healthy hepatocytes while triggering apoptosis in hepatocellular carcinoma cells.
Accountability in Child Welfare Services: Developing a Statewide Outcome Evaluation Program. (2005)

Questions are often raised regarding the effectiveness and value of treatment programs for children and families. Recently, programs have been increasingly held accountable for services offered. In response, the member agencies of IARCCA have developed a comprehensive outcome measurement program. This article describes the project, focusing on the conditions that led to its inception and how the measurement plan was developed. In addition, the article includes information on the selection of personnel, measurement instruments, and methods and on the process of data collection. Summary results are provided, including how these results are utilized to improve services. Finally, the continued expansion and future directions of the Outcome Project are discussed.
A Network Management Tool For Inter-domain Policy Routing (2005)

In recent years, the number of organizations connected to thie Internet has grown, resulting in an increasingly diverse set of connected users. As a result, network managers have growing concerns about the security and control of network resources. This concern has led protocol engineers to design routing protocols, such as Inter-Domain Policy Routing (IDPR), that include policy restrictions. The introduction of these protocols present a number of new problems to network administrators as they may not be able to easily understand how the policies of different networks interact. A network manager would like to create policies that prevent unauthorized traffic, without impeding legitimate traffic: flows. In the presence of charging mechanisms, a manager may wish to use policy terms to assist in minimizing costs by avoiding the use of commercial networks whenever possible. In this paper we describe a route synthesis simulation tool (IISST) which we have implemented to examine some of these network management issues. We show how it is used to explore some hypothetical situations that a network administrator would face in managing policy routing. Mr. Meyer's work was supported by a CERFnet Graduate Research Fellowship and by the National Science Foundation. * Dr. Estrin's work was supported by the National Science Foundation. 5.3.1 NOMS '92 CH3134-419210000-0133 $3.00
Controllable Uniform Green Light Emitters Enabled by Circular HEMT-LED Devices (2018)

This paper reports a monolithic integration of GaN high-electron-mobility transistor (HEMT) and green light-emitting diode (LED), where the circular HEMT is surrounded by a ring-shaped LED and two devices are seamlessly interconnected by the LED's n-GaN layer and the HEMT's two-dimensional electron gas (2DEG) channel. By adopting such a novel circular layout design, the green HEMT-LED shows a controllable and uniform green light emission at 507 nm by simply tuning its gate voltage. This enables a uniform, controllable green LED light source, serving as an essential element in the red–green–blue (RGB) LED solution for a wide range of applications, such as tunable-spectrum white LED illumination, multichannel visible light communication with wavelength division multiplexing, RGB-based full-color LED displays, and optogenetics.
PIPER: An FFT‐based protein docking program with pairwise potentials (2006)

The Fast Fourier Transform (FFT) correlation approach to protein-protein docking can evaluate the energies of billions of docked conformations on a grid if the energy is described in the form of a correlation function. Here, this restriction is removed, and the approach is efficiently used with pairwise interaction potentials that substantially improve the docking results. The basic idea is approximating the interaction matrix by its eigenvectors corresponding to the few dominant eigenvalues, resulting in an energy expression written as the sum of a few correlation functions, and solving the problem by repeated FFT calculations. In addition to describing how the method is implemented, we present a novel class of structure-based pairwise intermolecular potentials. The DARS (Decoys As the Reference State) potentials are extracted from structures of protein-protein complexes and use large sets of docked conformations as decoys to derive atom pair distributions in the reference state. The current version of the DARS potential works well for enzyme-inhibitor complexes. With the new FFT-based program, DARS provides much better docking results than the earlier approaches, in many cases generating 50% more near-native docked conformations. Although the potential is far from optimal for antibody-antigen pairs, the results are still slightly better than those given by an earlier FFT method. The docking program PIPER is freely available for noncommercial applications.
Salt‐resistant short antimicrobial peptides (2016)

Antimicrobial peptides (AMPs) are promising leads for the development of antibiotics against drug resistant bacterial pathogens. However, in vivo applications of AMPs remain obscure due to salt and serum mediated inactivation. The high cost of chemical synthesis of AMPs also impedes potential clinical application. Consequently, short AMPs resistant toward salt and serum inactivation are desirable for the development of peptide antibiotics. In this work, we designed a 12-residue amphipathic helical peptide RR12 (R-R-L-I-R-L-I-L-R-L-L-R-amide) and two Trp containing analogs of RR12 namely RR12Wpolar (R-R-L-I-W-L-I-L-R-L-L-R-amide), and RR12Whydro (R-R-L-I-R-L-W-L-R-L-L-R-amide). Designed peptides demonstrated potent antibacterial activity; MIC ranging from 2 to 8 μM, in the presence of sodium chloride (150 mM and 300 mM). Antibacterial activity of these peptides was also detected in the presence of human serum. Designed peptides, in particular RR12 and RR12Whydro, were only poorly hemolytic. As a mode of action; these peptides demonstrated efficient permeabilization of bacterial cell membrane and lysis of cell structure. We further investigated interactions of the designed peptides with lipopolysaccharide (LPS), the major component of the outer membrane permeability barrier of Gram-negative bacteria. Designed peptides adopted helical conformations in complex with LPS. Binding of peptides with LPS has yielded dissociation the aggregated structures of LPS. Collectively, these designed peptides hold ability to be developed for salt-resistant antimicrobial compounds. Most importantly, current work provides insights for designing salt-resistant antimicrobial peptides. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 345-356, 2016.
Biologic course of cervical human papillomavirus infection (1987)

To determine the natural course of cervical human papillomavirus infection, we prospectively studied all new patients referred to the colposcopy clinic at the Naval Hospital Bethesda, from April 1981 to August 1983, whose screening cervical cytology demonstrated features consistent with human papillomavirus infection as the only abnormality. Histologic confirmation of human papillomavirus infection was required for entry into the study. All patients were evaluated by repeat cytology, colposcopy, endocervical curettage, and colposcopically directed biopsy as indicated at intervals of three to six months. Patients who developed classic features of cervical intraepithelial neoplasia were treated by standard modalities, whereas patients with evidence of human papillomavirus infection without associated cervical intraepithelial neoplasia were not treated. Confirmation of the resolution of human papillomavirus infection required negative cytology and colposcopy on two consecutive evaluations. Of the 45 patients for whom complete follow-up data are available, five (11.1%) had cervical intraepithelial neoplasia at the time of their initial evaluation, 15 (33.3%) progressed to cervical intraepithelial neoplasia over an average of 10.9 months, 18 (40%) resolved over an average of 13.7 months, and seven (15.6%) persisted with neither progression nor resolution for an average of 21 months. These data suggest that about one-third of patients who have histologically confirmed human papillomavirus cervical infection can be expected to develop cervical intraepithelial neoplasia within a year.
Catalytic Properties of Hairpin Ribozymes Derived from Chicory Yellow Mottle Virus and Arabis Mosaic Virus Satellite RNAs (1995)

Regions of the negative strands of the satellite RNAs of chicory yellow mottle virus (sCYMV1) and arabis mosaic virus (sArMV) have similarity in sequence and predicted secondary structure compared to the tobacco ringspot virus satellite RNA (sTRSV) hairpin ribozyme, suggesting that they may also be catalytic RNAs of a similar type. Our experiments show that the hairpin ribozyme-like sequences derived from sCYMV1 and sArMV have high phosphodiesterase activity. The Kcat values determined are similar to that of the highly active native sTRSV hairpin ribozyme under the same conditions, although the Km values are much higher. The Km of the sArMV ribozyme was reduced 3-fold, with no change in kcat, by extending substrate hybridization in helix 2. Additionally, the three hairpin ribozymes prefer different GUX sequences on the immediate 3'-side of the cleavage site. The sTRSV hairpin ribozyme cleaves GUX substrates with catalytic efficiencies in the relative order GUC >> GUU > GUG = GUA. The sCYMV1 ribozyme cleaves GUA > GUC, GUG, GUU. The sArMV ribozyme prefers GUA > GUG > GUU > GUC. The functional domain, regulating substrate selection at this position, must reside in the nucleotides that vary between the ribozyme--substrate complexes. The sTRSV ribozyme is most efficient at cleaving GUC complexes, while the sCYMV1 and sArMV ribozymes are most efficient for cleaving GUA-containing sequences.