gebhart/patrepeval huggingface dataset:
Efficient Generalized Boundary Detection Using a Sliding Information Distance (2020)

We present a general machine learning algorithm for boundary detection within general signals based on an efficient, accurate, and robust approximation of the universal normalized information distance. Our approach uses an adaptive sliding information distance (SLID) combined with a wavelet-based approach for peak identification to locate the boundaries. Special emphasis is placed on developing an adaptive formulation of SLID to handle general signals with multiple unknown and/or drifting section lengths. Although specialized algorithms may outperform SLID when domain knowledge is available, these algorithms are limited to specific applications and do not generalize. SLID excels in these cases. We demonstrate the versatility and efficacy of SLID on a variety of signal types, including synthetically generated sequences of tokens, binary executables for reverse engineering applications, and time series of seismic events.
Treatment of Men with Erectile Dysfunction with Transurethral Alprostadil (1997)

In men with erectile dysfunction, transurethral alprostadil therapy resulted in erections in the clinic and in intercourse at home.
EDFA-free all-optical 2R regeneration using a compact self-seeded Fabry-Pe/spl acute/rot laser diode (2006)

This study presents an erbium-doped fiber amplifier (EDFA)-free all-optical 2R (reamplification and reshaping) regeneration scheme based on a compact self-seeded Fabry-Pe/spl acute/rot laser diode. The proposed 2R regenerator achieves a straight line transmission at 10 Gb/s over 76 km without either the EDFA or the external probe laser, both of which are traditionally required. Additionally, device characteristics such as data-rate transparency, input dynamic range, amplified gain, and 2R regeneration performance are investigated experimentally.
Development of a conditionally immortalized human pancreatic β cell line (2014)

Diabetic patients exhibit a reduction in β cells, which secrete insulin to help regulate glucose homeostasis; however, little is known about the factors that regulate proliferation of these cells in human pancreas. Access to primary human β cells is limited and a challenge for both functional studies and drug discovery progress. We previously reported the generation of a human β cell line (EndoC-βH1) that was generated from human fetal pancreas by targeted oncogenesis followed by in vivo cell differentiation in mice. EndoC-βH1 cells display many functional properties of adult β cells, including expression of β cell markers and insulin secretion following glucose stimulation; however, unlike primary β cells, EndoC-βH1 cells continuously proliferate. Here, we devised a strategy to generate conditionally immortalized human β cell lines based on Cre-mediated excision of the immortalizing transgenes. The resulting cell line (EndoC-βH2) could be massively amplified in vitro. After expansion, transgenes were efficiently excised upon Cre expression, leading to an arrest of cell proliferation and pronounced enhancement of β cell-specific features such as insulin expression, content, and secretion. Our data indicate that excised EndoC-βH2 cells are highly representative of human β cells and should be a valuable tool for further analysis of human β cells.
Biocompatible Infinite‐Coordination‐Polymer Nanoparticle–Nucleic‐Acid Conjugates for Antisense Gene Regulation (2014)

Abstract Herein, we report the synthesis of DNA‐functionalized infinite‐coordination‐polymer (ICP) nanoparticles as biocompatible gene‐regulation agents. ICP nanoparticles were synthesized from ferric nitrate and a ditopic 3‐hydroxy‐4‐pyridinone (HOPO) ligand bearing a pendant azide. Addition of Fe III to a solution of the ligand produced nanoparticles, which were colloidally unstable in the presence of salts. Conjugation of DNA to the Fe III –HOPO ICP particles by copper‐free click chemistry afforded colloidally stable nucleic‐acid nanoconstructs. The DNA–ICP particles, when cross‐linked through sequence‐specific hybridization, exhibited narrow, highly cooperative melting transitions consistent with dense DNA surface loading. The ability of the DNA–ICP particles to enter cells and alter protein expression was also evaluated. Our results indicate that these novel particles carry nucleic acids into mammalian cells without the need for transfection agents and are capable of efficient gene knockdown.
A macromolecular approach to eradicate multidrug resistant bacterial infections while mitigating drug resistance onset (2018)

Polymyxins remain the last line treatment for multidrug-resistant (MDR) infections. As polymyxins resistance emerges, there is an urgent need to develop effective antimicrobial agents capable of mitigating MDR. Here, we report biodegradable guanidinium-functionalized polycarbonates with a distinctive mechanism that does not induce drug resistance. Unlike conventional antibiotics, repeated use of the polymers does not lead to drug resistance. Transcriptomic analysis of bacteria further supports development of resistance to antibiotics but not to the macromolecules after 30 treatments. Importantly, high in vivo treatment efficacy of the macromolecules is achieved in MDR A. baumannii-, E. coli-, K. pneumoniae-, methicillin-resistant S. aureus-, cecal ligation and puncture-induced polymicrobial peritonitis, and P. aeruginosa lung infection mouse models while remaining non-toxic (e.g., therapeutic index-ED<sub>50</sub>/LD<sub>50</sub>: 1473 for A. baumannii infection). These biodegradable synthetic macromolecules have been demonstrated to have broad spectrum in vivo antimicrobial activity, and have excellent potential as systemic antimicrobials against MDR infections.
Finding distractors in images (2015)

We propose a new computer vision task we call “distractor prediction.” Distractors are the regions of an image that draw attention away from the main subjects and reduce the overall image quality. Removing distractors-for example, using in-painting - can improve the composition of an image. In this work we created two datasets of images with user annotations to identify the characteristics of distractors. We use these datasets to train an algorithm to predict distractor maps. Finally, we use our predictor to automatically enhance images.
A new insect cell line from Trichoplusia ni (BTI-Tn-5B1-4) susceptible to Trichoplusia ni single enveloped nuclear polyhedrosis virus (1994)

The replication of Trichoplusia ni SNPV (TnSNPV) in a new Lepidopteran cell line, BTI-Tn-5B1-4 (Tn-5B1-4), is presented. This cell line was highly susceptible to TnSNPV with infection rates exceeding 90% by 48 hr postinfection (p1). Budded virus (BV) was present in the culture medium 14 hr pi and reached a maximum titer of 3.2 × 106TCID50/ml 48 hr pi. Cell-associated virus was produced 12 hr pi and reached a maximum titer of 2.4 × 106TCID50/ml 36 hr pi. Serial passage of TnSNPV was initiated in Tn-5B1-4 cells with infectious hemolymph obtained from T. ni larvae infected with TnSNPV occlusion bodies (OBs). TnSNPV was subsequently grown in this cell line for 60 serial passages. Levels of BV infectivity were maintained at approximately 3.2 × 105TCID50/ml through passage 60. Early passage virus (i.e., 1–7 passages) resulted in approximately 500 to 700 OB/cell, whereas later passages (i.e., 7–60) showed an average decrease from 450 to 100 OB/cell. Bioassay results showed high infectivity (approximately 95%) with early passage virus; however, infectivity dropped off rapidly in later passages with no larval infectivity seen after passage 20. In addition, the effects of cryopreservation on virulence and yield of TnSNPV-BV, produced in the Tn-5B1-4 parental cell line, BTI-Tn-5B1, at 4 and -100°C, were investigated. By 6 weeks, BV titers for samples stored at both temperatures had decreased by as much as one order of magnitude. Although gradual decreases in titer were observed under both storage conditions, −100°C appeared to be more suitable for long term cryopreservation.
Inhibition of NF-κB Activation by Peptides Targeting NF-κB Essential Modulator (NEMO) Oligomerization (2004)

NF-kappa B essential modulator/IKK-gamma (NEMO/IKK-gamma) plays a key role in the activation of the NF-kappa B pathway in response to proinflammatory stimuli. Previous studies suggested that the signal-dependent activation of the IKK complex involves the trimerization of NEMO. The minimal oligomerization domain of this protein consists of two coiled-coil subdomains named Coiled-coil 2 (CC2) and leucine zipper (LZ) (Agou, F., Traincard, F., Vinolo, E., Courtois, G., Yamaoka, S., Israel, A., and Veron, M. (2004) J. Biol. Chem. 279, 27861-27869). To search for drugs inhibiting NF-kappa B activation, we have rationally designed cell-permeable peptides corresponding to the CC2 and LZ subdomains that mimic the contact areas between NEMO subunits. The peptides were tagged with the Antennapedia/Penetratin motif and delivered to cells prior to stimulation with lipopolysaccharide. Peptide transduction was monitored by fluorescence-activated cell sorter, and their effect on lipopolysaccharide-induced NF-kappa B activation was quantified using an NF-kappa B-dependent beta-galactosidase assay in stably transfected pre-B 70Z/3 lymphocytes. We show that the peptides corresponding to the LZ and CC2 subdomains inhibit NF-kappa B activation with an IC(50) in the mum range. Control peptides, including mutated CC2 and LZ peptides and a heterologous coiled-coil peptide, had no inhibitory effect. The designed peptides are able to induce cell death in human retinoblastoma Y79 cells exhibiting constitutive NF-kappa B activity. Our results provide the "proof of concept" for a new and promising strategy for the inhibition of NF-kappa B pathway activation through targeting the oligomerization state of the NEMO protein.
Formation of air-stable copper–silver core–shell nanoparticles for inkjet printing (2009)

Copper nanoparticles can be utilized as a low-cost replacement for silver and gold nanoparticles which are currently used in inkjet printing of conductive patterns. However, the main obstacle for using copper nanoparticles is their spontaneous oxidation at ambient conditions. Here we describe the synthesis of nonoxidizable copper nanoparticles by coating them with a silver shell, and inkjet printing of these particles. The formation of these core–shell nanoparticles is driven by a transmetalation reaction on the surface of copper nanoparticles, where the copper atoms present on the particles' surface are used as the reducing agent for the silver. This process results in formation of solely copper–silver core–shell nanoparticles, with no individual silver particles. It was found that coating 40 nm copper nanoparticles with a 2 nm layer of silver prevents oxidation of the copper core and preserves its metallic characteristic. Characterization of these nanoparticles by HR-TEM, SEM, EDS, XRD, spectrophotometry and XPS confirm the core–shell structure and their stability to oxidation. Inkjet printing of concentrated aqueous dispersions of these copper–silver nanoparticles was done on various substrates, and it was found that conductive and decorative patterns with metallic appearance, stable to oxidation (up to 150 °C) are formed.
Development of a simple user-friendly commercial digital holographic microscope (2008)

We report the development of a simple commercial digital holographic microscope. The hologram is recorded using a CCD sensor and numerically reconstructed to provide quantitative analysis of the object. The laser source is coupled via fibre optics and the opto-mechanical setup is flexible and customizable for either the reflection or transmission mode. The user-friendly software allows live reconstruction, simultaneously providing both the amplitude and phase images. System performance is improved with phase unwrapping and interferometric comparison. Additional features include various image enhancements, cross-sectional and line profiling, measurement and data analysis tools for quantitative 3D imaging and surface topography measurement. The performance of the product is tested on different micro devices, glass and silicon surfaces.
20 GHz High Performance Planar Si/InGaAs P-i-n Photodetector (1997)

Planar Si/InGaAs wafer fused p-i-n photodetectors were fabricated. They show high internal quantum efficiency, high speed, record low dark current, and no evidence of charge trapping, recombination centers or a bandgap discontinuity at the heterointerface.
3D photography on your desk (2002)

A simple and inexpensive approach for extracting the three-dimensional shape of objects is presented. It is based on 'weak structured lighting'; it differs from other conventional structured lighting approaches in that it requires very little hardware besides the camera: a desk-lamp, a pencil and a checker-board. The camera faces the object, which is illuminated by the desk-lamp. The user moves a pencil in front of the light source casting a moving shadow on the object. The 3D shape of the object is extracted from the spatial and temporal location of the observed shadow. Experimental results are presented on three different scenes demonstrating that the error in reconstructing the surface is less than 1%.
An adaptive digital filter using a system of orthogonal functions (1988)

Abstract The FIR adaptive digital filter has been applied widely to the echo canceller, automatic equalizer, and the noise canceller. For the viewpoint of the realizable transfer function, the FIR filter can be regarded as an adaptive digital filter which adjusts the zeros of the transfer function under the strong constraint that the poles of the transfer function can exist only at the origin of z ‐plane. This paper proposes an adaptive digital filter, which can adjust independently all adaptive parameters specifying the zeros, with the poles of the transfer function being placed at arbitrary positions within the unit circle of z ‐plane. First, a system of orthogonal functions is described which can realize the poles of the transfer function at arbitrary positions within the unit circle of z ‐plane. The adaptive digital filter utilizing this system of orthogonal functions is discussed. Finally, the effectiveness in convergence is demonstrated by computer simulation.
Fuzzy logic guided inverse treatment planning (2003)

A fuzzy logic technique was applied to optimize the weighting factors in the objective function of an inverse treatment planning system for intensity-modulated radiation therapy (IMRT). Based on this technique, the optimization of weighting factors is guided by the fuzzy rules while the intensity spectrum is optimized by a fast-monotonic-descent method. The resultant fuzzy logic guided inverse planning system is capable of finding the optimal combination of weighting factors for different anatomical structures involved in treatment planning. This system was tested using one simulated (but clinically relevant) case and one clinical case. The results indicate that the optimal balance between the target dose and the critical organ dose is achieved by a refined combination of weighting factors. With the help of fuzzy inference, the efficiency and effectiveness of inverse planning for IMRT are substantially improved.
Novel balance rehabilitation and training apparatus to improve functional balance (2014)

A new balance rehabilitation and training apparatus has been developed to allow a balance-impaired person to cope with his or her fear of falling while safely and independently performing exercises necessary to improve functional balance. The apparatus consists of a stable platform where the user stands and a vertical structure that supports free-floating handles that the user holds with both hands while performing various exercises. The purpose of study 1 was to determine whether this new apparatus significantly alters the biological postural control system, and the purpose of study 2 was to document the benefits of balance training using the apparatus. Study 1 was a randomized repeated-measures design with six healthy adult subjects (mean age = 35.5 yr), and study 2 was a 4 wk intervention case study with a generally healthy 63-yr-old individual. The results suggest that postural sway characteristics and the cortical and proprioceptive feedback were not limited when using the apparatus. We also observed improvements in balance control and postural stability with 4 wk of training with the apparatus. These results support that the apparatus could be an effective tool to help individuals safely and independently perform balance exercises while potentially preventing falls and minimizing fear of falling.
Selective Harmonic Compensation (SHC) PWM for grid-interfacing high-power converters (2011)

Compensating the pre-existing (background) harmonics from the power system in a grid-interfacing high-power converter system through the Active-Front-End (AFE) converter is a very attractive approach to improve the system harmonic performance. However, this is challenging due to the low switching frequency requirement of the high-power applications, and therefore traditional methods for active power filters cannot be applied. This paper proposes a new PWM technique, Selective Harmonic Compensation (SHC), which actively compensates the pre-existing harmonics from the power system, but still operates at very low switching frequencies. Details of the proposed SHC are presented and an SHC application example with a high-power Current Source Rectifier (CSR) is provided in this paper. The simulations and experiments are carried out on a 1 MVA CSR model in Matlab and a 10 kVA CSR prototype controlled by dSPACE-CPLD system. Results show that the proposed SHC scheme can improve the line current harmonic performance significantly.
A Neu Differentiation Factor (NDF) Domain Essential for Proliferation and Alterations in Morphology of Colonic Epithelial CellsIn Vitro (1998)

The Neu Differentiation Factors (NDFs, also termed "heregulins") are a family of proteins that were first isolated as ligands for the HER2 (ergB2, or p185neu) receptor protein tyrosine kinase. Here we show that NDF acts to stimulate the proliferation and alter the cellular morphology of colonic epithelial cells in culture. Dramatic NDF-induced changes in cellular morphology were noted in the colonic epithelial cell line, LIM 1215. In addition, the expression of specific cell proteins, such as carcinoembryonic antigen and integrin beta 4, was induced in LIM 1215 cells by NDF. These effects were more pronounced with the beta isoform than with the alpha isoform of NDF. The EGF-homology domain of NDF beta was sufficient to stimulate the proliferation and alteration in cell morphology. The use of chemically synthesized chimeric NDF alpha and NDF beta proteins enabled use to identify a region of seven amino acids in the EGF-homology domain of NDF beta that is required for both activities. These in vitro experiments suggest that NDF may act as a regulator of growth and differentiation of colonic epithelial cells in vivo.
Molecular Determinants for Protein Stabilization by Insertional Fusion to a Thermophilic Host Protein (2015)

A universal method that improves protein stability and evolution has thus far eluded discovery. Recently, however, studies have shown that insertional fusion to a protein chaperone stabilized various target proteins with minimal negative effects. The improved stability was derived from insertion into a hyperthermophilic protein, Pyrococcus furiosus maltodextrin-binding protein (PfMBP), rather than from changes to the target protein sequence. In this report, by evaluating the thermodynamic and kinetic stability of various inserted β-lactamase (BLA) homologues, we were able to examine the molecular determinants of stability realized by insertional fusion to PfMBP. Results indicated that enhanced stability and suppressed aggregation of BLA stemmed from enthalpic and entropic mechanisms. This report also suggests that insertional fusion to a stable protein scaffold has the potential to be a useful method for improving protein stability, as well as functional protein evolution.
High Speed Circuit Measurements Using Photoemission Sampling (1986)

We report the development of a new technique for measurement of high speed signals in electronic devices. The method is based on the energy analysis of electrons emitted from the surface of a metallization line on the device by multiphoton photoelectric effect in vacuum using a low powered, cw mode-locked laser source. Changes in the potential of the surface give rise to shifts in the photoemitted electron energies, which can be measured using a simple, retarding field electron energy analyzer. Since the method involves the direct measurement of voltage on a metal line, it can be used on any type of electronic device, regardless of the electronic material being used to fabricate the device. Furthermore, the opacity of the metal eliminates the possibility of perturbation of device performance by absorption of the laser radiation in the semiconductor.
Calcium Spirulan, an Inhibitor of Enveloped Virus Replication, from a Blue-Green Alga <i>Spirulina platensis</i> (1996)

Bioactivity-directed fractionation of a hot H2O extract from a blue-green alga Spirulina platensis led to the isolation of a novel sulfated polysaccharide named calcium spirulan (Ca-SP) as an antiviral principle. This polysaccharide was composed of rhamnose, ribose, mannose, fructose, galactose, xylose, glucose, glucuronic acid, galacturonic acid, sulfate, and calcium. Ca-SP was found to inhibit the replication of several enveloped viruses, including Herpes simplex virus type 1, human cytomegalovirus, measles virus, mumps virus, influenza A virus, and HIV-1. It was revealed that Ca-SP selectively inhibited the penetration of virus into host cells. Retention of molecular conformation by chelation of calcium ion with sulfate groups was suggested to be indispensable to its antiviral effect.
Transcriptional Regulation of the Mouse Presenilin-1 Gene (1997)

The presenilin-1 (PS-1) gene encodes at least three separate mRNA transcripts from its 12 exons, which are spread over 50 kilobase pairs of mouse DNA. The first transcript begins with exon 1A, whereas the other transcripts begin with exon 1B. Different portions of exon 1B are spliced to give long and short mRNAs. The expression of all of these transcripts depends on a single promoter located just upstream of exon 1A. Although this region lacks a TATA box and a number of common initiator sequences, it does contain a CAAT box, a heat-shock responsive element, a polyomavirus enhancer activator-3 site, an Ets 1-3 site, and multiple-Sp1 and multiple-Ap2 binding sites, which are typically found in eukaryotic promoters. We have combined a reporter gene with various portions of this putative PS-1 promoter and measured firefly luciferase activity relative to an internal renilla luciferase standard. We identified a 25-base pair fragment spanning the 5'-transcription start site of exon 1A as containing the core of the promoter activity. The sequences downstream of this region had undetectable promoter activity, suggesting that this core element is the gene's only promoter, and it controls expression of all three transcripts. Although human PS-1 mRNA expression is clearly different from the mouse PS-1 mRNA pattern, the human and mouse core promoters do share limited homology.