gebhart/patrepeval huggingface dataset:
Antimicrobial Polymers and Fibers: Retrospective and Prospective (2001)

Aproaches for imparting antimicrobial activity to polymeric materials have evolved from ancient practices to eclectic, modern strategies. The mechanisms by which microbes attach to polymeric surfaces and acquire resistance to antimicrobial agents are critically reviewed. Representative microorganisms (primarily bacteria, fungi, algae and viruses) are listed that are deleterious from a health or medical perspective and/or cause unwanted damage in materials. A variety of chemical approaches have been effective and include micrencapsulation, polymerization, covalent bond formation and simple insolubilization. Effectiveness of these agents (primarily biocides but also selective antibiotics) against various types of microorganisms and the modes by which they prevent microbial contamination and growth is discussed. Newer synthetic and naturally occurring agents are noted as well as strategies that prevent microbial attachment are discussed. The latter include modification of polymer surfaces, chemicals that disorient biochemical signals to microbes, and other useful concepts and approaches. The interest in this area is relevant to an array of applications where biological activity on fiber and other polymeric surfaces is of concern as biological discoveries reveal that many pathologies are caused by microbial infection.
Moduli space of BPS domain walls (2002)

$\mathcal{N}=2$ supersymmetric QED with several flavors admits multiple, static BPS domain wall solutions. We determine the explicit two-kink metric and examine the dynamics of colliding domain walls. The multikink metric has a toric K\"ahler structure and we reduce the K\"ahler potential to quadrature. In the second part of this paper, we consider semilocal vortices on $\mathbf{R}\ifmmode\times\else\texttimes\fi{}{\mathbf{S}}^{1}.$ We argue that, in the presence of a suitable Wilson line, the vortices separate into domain wall constituents. These play the role of fractional instantons in two-dimensional gauge theories and sigma models.
Controlling Anisotropic Drug Diffusion in Lipid-Fe<sub>3</sub>O<sub>4</sub> Nanoparticle Hybrid Mesophases by Magnetic Alignment (2013)

We present a new strategy to control the anisotropic diffusion of hydrophilic drugs in lyotropic liquid crystals via the dispersion of magnetic nanoparticles in the mesophase, followed by reorientation of the mesophase domains via an external magnetic field. We select a lipid reverse hexagonal phase doped with magnetic iron oxide nanoparticles and glucose and caffeine as model hybrid mesophase and hydrophilic drugs, respectively. Upon cooling through the disorder-order phase transition of the hexagonal phase and under exposure to an external moderate magnetic field (1.1 T), both the nanoparticles and the hexagonal domains align with their columnar axes along the field direction. As a result, the water nanochannels of the inverted hexagonal domains also align parallel to the field direction, leading to a drug diffusion coefficient parallel to the field direction much larger than what was measured perpendicularly: in the case of glucose, for example, this difference in diffusion coefficients approaches 1 order of magnitude. Drug diffusion of the unaligned reverse hexagonal phase, which consists of randomly distributed domains, shows values in between the parallel and transversal diffusion values. This study shows that modifying the overall alignment of anisotropic mesophases via moderate external fields is a valuable means to control the corresponding transport tensor of the mesophase and demonstrates that the orientation of the domains plays an important role in the diffusion process of foreign hydrophilic molecules.
New Rapid Polymerase Chain Reaction‐Immunochromatographic Assay for <i>Porphyromonas gingivalis</i> (2005)

A diagnostic assay based on PCR-ICA was developed for the detection of P. gingivalis, and results were obtained visually in 3 hours. PCR-ICA will be a valuable tool for the rapid detection of target bacteria by chair side.
Silencing Mutations in NOTCH1 Activate Calcium Signaling in B Cells (2014)

Abstract The NOTCH1 pathway is known to be up-regulated in many cancer types including non Hodgkin lymphomas (NHLs), colorectal, breast and pancreatic cancers. The precise downstream effects of NOTCH1 mutations in lymphoma are not known. We applied high throughput sequencing in three different non Hodgkin lymphomas including diffuse large B cell lymphoma (DLBCL, N=94), mantle cell lymphoma (MCL, N=58) and Burkitt lymphoma (BL, N=59). We also sequenced mutations from 208 patients with immune deficiency. In all, we identified 31 mutations in NOTCH1. Five of these mutations were either nonsense or frameshift mutations. Silencing mutations in the PEST domain have been reported in MCLs, and many other silencing mutations were observed in the other lymphoma cohorts as well as immune deficiency cases. The finding of silencing mutations was unexpected, given that in most cancers, NOTCH1 and its pathway are often constitutively active. Calcium signaling is an important mechanism for activating B cells. Given the shared mutations between NHLs and immune deficiencies, we investigated the role of silencing NOTCH1 mutations in altering calcium signaling by engineering lymphoma cells with a deletion of the transmembrane region resulting in silencing of NOTCH1 using the CRISPR system. We designed guide RNAs that spanned a 57 base pair region from exon 28 that encodes the transmembrane domain of the NOTCH1 gene. Each guide RNA was ligated into a pX458 Cas9 GFP expressing plasmid. Namalwa NHL cells were transfected, FACS-sorted for GFP positivity and subcloned. Successful deletion of the target region in Cas9 NOTCH1 cells was confirmed by Sanger sequencing and Western blotting. Cells that were wild type, Cas9 control, or Cas9 NOTCH1 were incubated in a calcium free buffer containing Fluo-4 for detection of intracellular free calcium. Cells were washed and subjected to flow sorting where baseline calcium was recorded. The cells were stimulated with anti-IgM (Fab’)2 and recorded again for response. To test extracellular calcium influx, 4mM CaCl2 was added to the calcium free buffer containing cells and recorded again for response.Upon stimulation with anti-IgM (Fab’)2, we observed a significant increase (p<10-6) of free cytosolic Calcium in the Cas9 NOTCH1 cells compared to both wild type and Cas9 control. Similar results were obtained when measuring extracellular Calcium influx upon addition of CaCl2to the buffered solution of cells. These findings indicate that silencing of NOTCH1 has an activating role in calcium signaling that could contribute to B cell survival and function in NHLs and immune deficiencies. Similar roles have been reported for activating mutations in PIK3CD and STAT3 that contribute to both immune deficiency and cancer. Our study is the first to identify the role of silencing mutations of NOTCH1 in NHLs and immune deficiencies. Disclosures No relevant conflicts of interest to declare.
Current sensing using bismuth rare-earth iron garnet films (1995)

Ferrimagnetic iron garnet films are investigated as current-sensing elements. The Faraday effect within the films permits measurement of the magnetic field or current by a simple polarimetric technique. Polarized diffraction patterns from the films have been observed that arise from the presence of magnetic domains in the films. A physical model for the diffraction is discussed, and results from a mathematical analysis are in good agreement with the experimental observations. A method of current sensing that uses this polarized diffraction is demonstrated.
Design Guideline for Developing Safe Systems that Apply Electricity to the Human Body (2018)

The human body has unique electrical characteristics. These characteristics have been investigated in various studies in human-computer interaction (HCI) and related research fields. Such studies include applications for using the body as a conductive lead for transmission or electric field sensing and activating human muscles or organs. However, electricity is not completely safe for the human body; therefore, to avoid harming users, careful consideration is essential when developing such devices. The knowledge required for such consideration is spread throughout a large number research fields, and it can be difficult for researchers in the HCI field to comprehend all of them. The purpose of this article is to support researchers in developing systems that apply electricity to the human body and to serve as a basis for further research. This article reviews previous research pertaining to HCI in which users come into contact with electricity. In addition, considerations of how and where this type of research can be expanded, along with guidelines grounded in other fields for designing systems safely and addressing ethical concerns, are presented. An understanding of the field and of the related safety issues will enhance the understanding of limitations and potential and can clarify the design space.
A piezoelectric actuator driver circuit for automatic focusing of mobile phone cameras (2008)

The analog front end (AFE) chip is presented to perform precise automatic focus operations with a piezoelectric actuator for mobile phone camera applications. In order to achieve the desired frequency response of a piezoelectric actuator, the frequency of a multi-vibrator oscillator can be swept in various manners such as the frequency step and the number of transitions between frequency changes. A novel method using the resistor ladder circuit is incorporated for a bridge-driving signal generator whose frequency can be linearly swept and controlled according to the input digital code. The AFE chip is implemented in a 0.35-μm 1-poly 4-metal CMOS technology and runs at the single supply voltage of 2.8V.
A Comparison of Purified Poly (ADP‐ribose) Polymerases from Ehrlich Ascites Tumor Cells, Pig Thymus, and HeLa S3 Cells (1981)

Poly(ADP-ribose) polymerases from Ehrlich ascites tumor cells, pig thymus, and HeLa S3 cells were purified by chromatography on DNA-agarose and Blue Sepharose. A molecular mass of 112000 Da was found for all three polymerases. Fragmentation of polyacrylamide-gel-embedded polymerases with cyanogen bromide, and subsequent analysis of the fragments by polyacrylamide gradient gel electrophoresis, showed great similarities with regard to fragment sizes. The amino acid composition of the pig thymus enzyme was very similar to that of the polymerase from Ehrlich ascites tumor cells, and the terminal amino group appeared to be blocked. The HeLa polymerase electrofocused in two peaks at pH 8.8 and 5.5, while the Ehrlich ascites tumor cells and the pig thymus enzyme focused in single peaks at pH 9.4 and 9.6 respectively. Removal of residual DNA by treatment with hydroxyapatite abolished these differences in apparent isoelectric points; all three polymerases focused at pH 9.8. No important differences were found with regard to the effect of a number of substances on the synthesis of poly(ADP-ribose). Apparent Michaelis constants for NAD of 41 microM, 48 microM, and 34 microM were found for polymerase from Ehrlich ascites tumor cells, pig thymus, and HeLa S3 cells, respectively. All these results indicate that the three polymerases, which represented the major poly(ADP-ribose) polymerase activity in the organisms investigated, are closely related proteins.
Phytochemical Constituents, Analgesic and anti-inflammatory Effects of Methanol Extract of Triumfetta rhomboidea Leaves in Animal Models (2009)

Objective: To investigate the analgesic and anti-inflammatory effects of the methanolic extract of the leaves of Triumfetta rhomboidea on mice and rats respectively. And to screen the phytochemical constituent of the extract. Methods: The analgesic effect was determined by acetic acid-induced writhing test in mice. While the anti-inflammatory activity was determined by egg albumin-induced oedema of the rat paw. Phytochemical screening was done by standard procedures. Results: Triumfetta rhomboidea leaf extract (50-400 mg/kg) caused a statistically significant inhibition on the egg albumin-induced eodema or inflammation in Wister albino rats with P＜0.001 (ANOVA). This effect was higher than the observed effect with Piroxicam (0.5 mg/kg) which was used as a standard. The effect was also dose-dependent. Furthermore, Triumfetta rhomboidea extract caused a statistically significant reduction in the number of acetic acid-induced writhing in mice, with P＜0.001 (ANOVA). These effects were also does-dependent and greater than the analgesic effects by paracetamol which was used as a reference drug. Phytochemical screening revealed the presence of flavonoids, steroids, triterpenoids alkaloids, tannins and saponins in Truimfetta rhomboidea leaf extract. Conclusion: Triumfeua rhomboidea can be recommended for acute inflammatory disorders and diseases associated with pains. This also supports its traditional use as an anti-snake bite and anti-cancer or anti-tumor agent. Further study is on the way to find out the mechanism of its action and also to isolate, identify and characterize the active principle responsible for these effects in this plant.
Nanoimprinted distributed feedback lasers comprising TiO<sub>2</sub> thin films: Design guidelines for high performance sensing (2013)

Abstract Design guidelines for optimizing the sensing performance of nanoimprinted second order distributed feedback dye lasers are presented. The guidelines are verified by experiments and simulations. The lasers, fabricated by UV‐nanoimprint lithography into Pyrromethene doped Ormocomp thin films on glass, have their sensor sensitivity enhanced by a factor of up to five via the evaporation of a titanium dioxide (TiO 2 ) waveguiding layer. The influence of the TiO 2 layer thickness on the device sensitivity is analyzed with a simple model that accurately predicts experimentally measured wavelength shifts induced by varied superstrate refractive indices. The superstrate refractive index is additionally shown to determine which of the possible waveguiding modes dominates for lasing, indicating a method to flexibly select the polarization of the laser. The detection limit of the sensor system is further discussed, finding an optimum at 7.5· 10 −6 RIU. Wavelength changes caused by dye bleaching must be taken into account for long‐term measurements.
Bhutan - Environmental analysis of the World Bank Bhutan Third Forestry Project (1992)

It is the principal finding of this Environmental Assessment (EA), conducted as part of the Third Forestry Development Project (Forestry III) pre-appraisal and appraisal missions, that the project activities are of the highest government priority in terms of forest conservation and management, and economic development. Forestry III is an opportunity for the Royal Government of Bhutan (RGOB), The World Bank (WB), and the Swiss Development Corporation (SDC) to cooperate in developing sustainable forestry alternatives for the Eastern Zone of Bhutan. It is particularly important that Forestry III will begin to focus on the sustainable management of the most threatened of Bhutan's forests: broadleaf forests in subtropical, warm temperate and cool temperate climate regions.
EDFA Soft-Failure Detection and Lifetime Prediction based on Spectral Data using 1-D Convolutional Neural Network (2021)

With the emergence of 5G and the immense demand of data in today’s society the reliability of optical networks is even more important. In this context, maintaining the quality-of-service and reliable operation can only be achieved with effective fault management. Precise fault management requires anomaly detection, identification and reaction. While hard failures, i.e. service disruptions, are detected easily, the task of detecting and identifying gradual degradations in the quality of transmission (QoT), so called soft-failures, is challenging. Machine learning (ML) provides powerful tools to accomplish this task. In this work, a novel three-stage soft-failure detection, identification and lifetime prediction framework of EDFAs based on convolutional neural networks (CNN) is proposed. The CNNs are trained on the spectral data extracted from the electrical power spectrum density (PSD) from a coherent receiver. The output of the framework is the remaining useful life (RUL) of the identified failing EDFA in the link. Extensive simulations are performed to validate the proposed framework. Excellent performance is achieved by the framework with the assumption that just one EDFA in the link is failing. The detection stage reaches an accuracy of 99.89% while the identification stage achieves 98.67% on an unseen data set. The RUL prediction stage achieves high regression (R2-) scores of 0.86 for sudden and 0.97 for gradual degradation of the EDFA pump laser.
Design, Synthesis, and Activity of a Novel Series of Factor Xa Inhibitors:  Optimization of Arylamidine Groups (2002)

A novel series of diaryloxypyridines have been designed as selective nanomolar factor Xa (fXa) inhibitors for use as anticoagulants. In this paper, we describe our efforts to identify an additional interaction and a replacement for the distal amidine group that binds in the S3/S4 pocket of fXa. Introduction of a hydroxyl group para to the proximal amidine group increases the potency vs fXa by 1-2 orders of magnitude, which is the result of a hydrogen bond to Ser195 of the catalytic triad. A methyl imidazoline and a dimethylamide are good alternatives for the second amidine. These substitutions have increased the selectivity vs the related serine proteases trypsin and thrombin. The synthesis, in vitro activity, and hypothetical modes of binding to fXa based on trypsin crystallographic data are outlined.
Anisotropic plasma etching of Silicon in gas chopping process by alternating steps of oxidation and etching (2019)

Abstract In the present work a two-stage process for deep anisotropic etching of Silicon based on alternating steps of etching in SF 6 plasma and passivation of Silicon surface by oxidation in O 2 plasma is proposed. This developed Ox-Etch process has advantages of being free from deposited polymers on sidewalls and does not use cryogenic equipment. Etched structures show anisotropic profile with vertical scalloped walls similar to Bosch and STiGer processes. Selectivity of Silicon etch process with respect to SiO 2 mask is up to 120:1. The investigations of etching results depending on process parameters are presented. Main control parameters for Ox-Etch process defining the etch rate and degree of anisotropy are the durations of etch and oxidation steps.
Corneal sensitivity in people with the same and with different iris color. (1976)

Corneal touch thresholds were determined for both eyes of 15 people with different colored irides (a condition known as heterochromia) and of 25 people with similar colored irides. It was found that corneal sensitivity is not significantly different in both eyes of either group. Therefore it is suggested that the fact previously demonstrated that corneal sensitivity is related to iris color is not of corneal origin.
Three-dimensional photolithographic patterning of multiple bioactive ligands in poly(ethylene glycol) hydrogels (2010)

The biomaterials community is faced with the challenge of imitating a vastly complex, physiological tissue environment. While cellular systems towards this end have been traditionally studied in two dimensions (2D), most cells require three-dimensional (3D) cues to produce a physiologically relevant response. Two-photon absorption laser scanning lithography (TPA-LSL) may be applied to photosensitive hydrogel systems to engineer heterogeneous, 3D microenvironments consisting of precisely patterned bioactive signals. In this work, we have developed new operating parameters and system capabilities for TPA-LSL through the patterning of fluorescently labeled monoacrylate PEG-RGDS within PEG-DA hydrogels. Specifically, we have demonstrated a flexible pattern size range, with features ranging from 1 µm to nearly 1 mm. We have also shown patterns of differing concentrations of the cell adhesive ligand RGDS and correlated observed RGDS fluorescence with laser scan speed and intensity. Finally, we have micropatterned multiple, unique bioactive ligands into distinct, 3D forms within a single hydrogel. The results presented here have significantly developed the capabilities of the TPA-LSL micropatterning technique to allow for the fabrication of heterogeneous, 3D cellular microenvironments, which should prove highly useful for future biomimetic applications.
Maximum-Likelihood Sequence Estimation for Optical Phase-Shift Keyed Modulation Formats (2009)

Electronic chromatic dispersion compensation employing maximum-likelihood sequence estimation (MLSE) has recently been the topic of extensive research and a range of commercial products. It is well known that MLSE provides a considerable benefit for amplitude modulated modulation formats such as on-off keying (OOK) and optical duobinary. However, when applied to optical phase modulation formats, such as differential phase-shift keying (DPSK) and differential quadrature phase-shift keying (DQPSK), it has been shown that the benefit is only marginal. This paper investigates joint-decision MLSE (JD-MLSE) detection applied to 10.7-Gb/s DPSK. It demonstrates that a JD-MLSE using the constructive and destructive components preserves the 3-dB optical signal-to-noise ratio (OSNR) advantage of DPSK over OOK in dispersion-limited optical systems. Furthermore, we demonstrate that the use of a shortened MZDI with MLSE for the 10.7-Gb/s DPSK modulation can equalize an accumulated chromatic dispersion of 4000 ps/nm. In addition, we discuss in this paper different MLSE schemes applied to 2 times 10.7-Gb/s DQPSK modulation. It is shown that a joint-symbol MLSE (JS-MLSE) on the balanced outputs of the in-phase and quadrature components gives the best performance.
Ablation of sensory neurons in a genetic model of pancreatic ductal adenocarcinoma slows initiation and progression of cancer (2016)

Pancreatic ductal adenocarcinoma (PDAC) is characterized by an exuberant inflammatory desmoplastic response. The PDAC microenvironment is complex, containing both pro- and antitumorigenic elements, and remains to be fully characterized. Here, we show that sensory neurons, an under-studied cohort of the pancreas tumor stroma, play a significant role in the initiation and progression of the early stages of PDAC. Using a well-established autochthonous model of PDAC (PKC), we show that inflammation and neuronal damage in the peripheral and central nervous system (CNS) occurs as early as the pancreatic intraepithelial neoplasia (PanIN) 2 stage. Also at the PanIN2 stage, pancreas acinar-derived cells frequently invade along sensory neurons into the spinal cord and migrate caudally to the lower thoracic and upper lumbar regions. Sensory neuron ablation by neonatal capsaicin injection prevented perineural invasion (PNI), astrocyte activation, and neuronal damage, suggesting that sensory neurons convey inflammatory signals from Kras-induced pancreatic neoplasia to the CNS. Neuron ablation in PKC mice also significantly delayed PanIN formation and ultimately prolonged survival compared with vehicle-treated controls (median survival, 7.8 vs. 4.5 mo; P = 0.001). These data establish a reciprocal signaling loop between the pancreas and nervous system, including the CNS, that supports inflammation associated with oncogenic Kras-induced neoplasia. Thus, pancreatic sensory neurons comprise an important stromal cell population that supports the initiation and progression of PDAC and may represent a potential target for prevention in high-risk populations.