gebhart/patrepeval huggingface dataset:
Engineering a Reduced <i>Escherichia coli</i> Genome (2002)

Our goal is to construct an improved Escherichia coli to serve both as a better model organism and as a more useful technological tool for genome science. We developed techniques for precise genomic surgery and applied them to deleting the largest K-islands of E. coli, identified by comparative genomics as recent horizontal acquisitions to the genome. They are loaded with cryptic prophages, transposons, damaged genes, and genes of unknown function. Our method leaves no scars or markers behind and can be applied sequentially. Twelve K-islands were successfully deleted, resulting in an 8.1% reduced genome size, a 9.3% reduction of gene count, and elimination of 24 of the 44 transposable elements of E. coli. These are particularly detrimental because they can mutagenize the genome or transpose into clones being propagated for sequencing, as happened in 18 places of the draft human genome sequence. We found no change in the growth rate on minimal medium, confirming the nonessential nature of these islands. This demonstration of feasibility opens the way for constructing a maximally reduced strain, which will provide a clean background for functional genomics studies, a more efficient background for use in biotechnology applications, and a unique tool for studies of genome stability and evolution.
Optimum Catalyst Size for Slurry Bubble Column Reactors (2005)

A mathematical model to describe the hydrodynamics of the slurry bubble-column reactor (SBCR) for converting synthesis gas into liquid fuels has been developed. This model includes the complete granular temperature balance based on the kinetic theory of granular flow. The kinetic theory model and the computer code1 were extended to include the effect of the mass-transfer coefficient between the liquid and gas and the water gas shift reaction in the Air Products/DOE LaPorte SBCR. In this model, the mass-transfer coefficient is an input. It was estimated from a relationship between the fundamental equations of the boundary layers and the turbulent kinetic energy of particles (granular temperature) computed by the hydrodynamic model with no reaction. We have varied the particle size from 20 to 100 μm and discovered a maximum in the granular temperature. For the particles over this range, the mass-transfer coefficient has the highest values. With reaction, this model was used to predict the slurry height, gas holdup, and rate of methanol production of the Air Products/DOE LaPorte SBCR. The computed granular temperature was around 30 cm2/s2, and the computed catalyst viscosity was close to 1.0 cP, as shown by Wu and Gidaspow (Chem. Eng. Sci. 2000, 55, 573). The estimated volumetric mass-transfer coefficient has a good agreement with experimental values shown in the literature. A critical issue in the SBCR that has not been addressed in the literature is that of optimum particle size. The optimum size was determined for maximum methanol production in a SBCR. The size was about 60−70 μm, which was found for maximum granular temperature in the model with no reaction.
Intersubband electroluminescence from long-side-cleaved quantum-cascade lasers above threshold: Investigation of phonon bottleneck effects (2000)

A technique is reported which allows the observation of intersubband spontaneous emission in unipolar quantum-cascade lasers above threshold. The technique consists of cleaving the laser stripe in the direction perpendicular to its facets. This does not negatively affect the operation of the lasers thanks to their unipolar nature. To show the potential of the method, we apply it to superlattice quantum-cascade (QC) lasers with various active region designs. We directly observe the saturation of the luminescence intensity at the laser transition, and a bottleneck effect for transitions separated from the lasing one by less than one optical phonon. This technique should help in the optimization of QC lasers.
Advanced broadband optical access networks (2009)

Optical fiber-based access networks are being deployed to address the increasing demand for bandwidth and help to support multiple services. As for the future optical access networks, different technologies have been proposed and under investigations, including WDM-based passive optical networks (WDM-PON), optical coding division multiplexing —based PON (OCDM-PON), and orthogonal frequency division multiplexing —based PON (OFDM-PON). Compared with other PON technologies, OFDM-PON shows some very promising features, e.g. dynamic bandwidth allocation, network privacy and support of multiple services. Here we will show the principles, and experimental testings of an OFDM-PON and further talk about virtual PON scheme using OFDM technologies.
Structural Contributions to Hydrodynamic Diameter for Quantum Dots Optimized for Live-Cell Single-Molecule Tracking (2018)

Quantum dots are fluorescent nanoparticles with narrow-band, size-tunable, and long-lasting emission. Typical formulations used for imaging proteins in cells are hydrodynamically much larger than the protein targets, so it is critical to assess the impact of steric effects deriving from hydrodynamic size. This report analyzes a new class of quantum dots that have been engineered for minimized size specifically for imaging receptors in narrow synaptic junctions between neurons. We use fluorescence correlation spectroscopy and transmission electron microscopy to calculate the contributions of the crystalline core, organic coating, and targeting proteins (streptavidin) to the total hydrodynamic diameter of the probe, using a wide range of core materials with emission spanning 545-705 nm. We find the contributing thickness of standard commercial amphiphilic polymers to be ~8 to ~14 nm, whereas coatings based on the compact ligand HS-(CH<sub>2</sub>)<sub>11</sub> <sup>-</sup> (OCH<sub>2</sub>CH<sub>2</sub>)<sub>4</sub>-OH contribute ~6 to ~9 nm, reducing the diameter by ~2 to ~5 nm, depending on core size. When the number of streptavidins for protein targeting is minimized, the total diameter can be further reduced by ~5 to ~11 nm, yielding a diameter of 13.8-18.4 nm. These findings explain why access to the narrow synapse derive primarily from the protein functionalization of commercial variants, rather than the organic coating layers. They also explain why those quantum dots with size around 14 nm with only a few streptavidins can access narrow cellular structures for neuronal labeling, whereas those >27 nm and a large number of streptavidins, cannot.
Molecular regulation of nicotine biosynthesis (2005)

Nicotine is most familiar to us as a principal pharmacologically active component of cigarettes. This alkaloid is synthesized in the root in response to insect damage and then transported to the aerial parts of tobacco plants. In this short review, we summarize enzymes and genes involved in nicotine biosynthesis, regulatory mechanisms of gene expression involving the NIC regulatory loci and jasmonic acid, and finally metabolic engineering of nicotine formation.
Integrated segmentation of cellular structures (2011)

Automatic segmentation of cellular structures is an essential step in image cytology and histology. Despite substantial
progress, better automation and improvements in accuracy and adaptability to novel applications are needed. In
applications utilizing multi-channel immuno-fluorescence images, challenges include misclassification of epithelial and
stromal nuclei, irregular nuclei and cytoplasm boundaries, and over and under-segmentation of clustered nuclei.
Variations in image acquisition conditions and artifacts from nuclei and cytoplasm images often confound existing
algorithms in practice. In this paper, we present a robust and accurate algorithm for jointly segmenting cell nuclei and
cytoplasm using a combination of ideas to reduce the aforementioned problems. First, an adaptive process that includes
top-hat filtering, Eigenvalues-of-Hessian blob detection and distance transforms is used to estimate the inverse
illumination field and correct for intensity non-uniformity in the nuclei channel. Next, a minimum-error-thresholding
based binarization process and seed-detection combining Laplacian-of-Gaussian filtering constrained by a distance-map-based
scale selection is used to identify candidate seeds for nuclei segmentation. The initial segmentation using a local
maximum clustering algorithm is refined using a minimum-error-thresholding technique. Final refinements include an
artifact removal process specifically targeted at lumens and other problematic structures and a systemic decision process
to reclassify nuclei objects near the cytoplasm boundary as epithelial or stromal. Segmentation results were evaluated
using 48 realistic phantom images with known ground-truth. The overall segmentation accuracy exceeds 94%. The
algorithm was further tested on 981 images of actual prostate cancer tissue. The artifact removal process worked in 90%
of cases. The algorithm has now been deployed in a high-volume histology analysis application.
Optical Properties of Intact Leaves for Estimating Chlorophyll Concentration (2002)

Changes in leaf chlorophyll content can serve as relative indicators of plant vigor and environmental quality. This study identified reflectance, transmittance, and absorptance wavebands and band ratios within the 400- to 850-nm range for intact leaves that could be used to estimate extracted leaf chlorophyll per unit leaf area (areal concentration) with minimal error. Leaf optical properties along with chlorophyll a, b, and a + b concentrations were measured for the planar-leaved sweetgum (Liquidambar styraciflua L.), red maple (Acer rubrum L.), wild grape (Vitis rotundifolia Michx.), and switchcane [Arundinaria gigantea (Walter) Muhl.], and for needles of longleaf pine (Pinus palustris Miller). Generally, reflectance, transmittance, and absorptance corresponded most precisely with chlorophyll concentrations at wavelengths near 700 nm, although regressions were also strong in the 550- to 625-nm range. A power function was superior to a simple linear function in yielding low standard deviations of the estimate (s). When data were combined among the planar-leaved species, s values were low at approximately 50 mumol/m2 out of a 940 mumol/m2 range in chlorophyll a + b at best-fit wavelengths of 707 to 709 nm. Minimal s values for chlorophyll a + b ranged from 32 to 62 mumol/m2 across species when band ratios having numerator wavelengths of 693 to 720 nm were used with the application of a power function. Optimal denominator wavelengths for the band ratios were 850 nm for reflectance and transmittance and 400 nm for absorptance. This information can be applied in designing field portable chlorophyll meters and in the landscape-scale remote sensing of plant responses to the environment.
Translating test programs using a model-based process (1999)

The authors apply model-based techniques as a mechanism for rehosting a test program designed for operation on one type of automatic test equipment so that it can be used with different automatic test equipment. The paper describes the necessary steps to enact the translation process: extracting existing test strategy/replaceable item callouts/code segments, deriving an inference model from the existing test strategy, converting the inference model into a new test strategy, translating the individual code segments and, finally, merging the model-based test strategy with the translated code segments. The proposed interchange mechanisms for the model and test strategy data are the Enhanced Diagnostic Inference Model and Fault Tree Model schemata of the IEEE Standard 1232: Artificial Intelligence Exchange and Service Tie to All Test Environments (Al-ESTATE). The process takes advantage of the separation of the test strategy and the encapsulated tests inherent in model-based diagnostics as a basis for performing the test program translation.
Optical Force Sensor Based on Whispering Gallery Mode Resonators (2006)

This paper discusses a novel micro-optical force sensor based on dielectric microspheres that are excited by coupling light from optical fibers. The technique exploits the morphology-dependent shifts in resonant frequencies that are commonly referred to as the whispering gallery modes (WGM). A small change in the size, shape or optical constants of the microsphere causes a shift in the resonant frequency (or the WGM). For example, a compression force applied to the microsphere will lead to a change in both its shape and its index of refraction distribution. These changes will result in a shift of the WGM. By monitoring this shift, the magnitude of the applied force can be determined. The WGM shifts are observed by scanning a tunable diode laser that is coupled into the optical fiber on one end and monitoring the transmission spectrum by a photo diode on the other end. When the microsphere is in contact with a bare section of the fiber, the optical modes are observed as dips (due to destructive interference) in the intensity of the light transmitted through the fiber. Current results demonstrate the WGM shifts due to compression force applied to micro-spheres along the polar direction. The measurements also indicate a force measurement resolution of ~ 10 N with the current sensor design.
The Structural Basis of Effective LOX-1 Inhibition (2022)

Along with other scavenger receptors, splice variants of LOX-1 play an important role in modulating numerous subcellular mechanisms such as normal cell development, differentiation and growth in response to physiological stimuli. Thus, LOX-1 activity is a key regulator in determining the severity of many genetic, metabolic, cardiovascular, renal, and neurodegenerative diseases and/or cancer. Increased expression of LOX-1 precipitates pathological disorders during the aging process. Therefore, it becomes important to develop novel LOX-1 inhibitors based on its ligand binding polarity and/or affinity and disrupt the uptake of its ligand: oxidized low-density lipoproteins (ox-LDL). In this review, we shed light on the presently studied and developed novel LOX-1 inhibitors that may have potential for treatment of diseases characterized by LOX-1 activation.
Analyzing High-Density ECG Signals Using ICA (2008)

The analysis of ECG signals is of fundamental importance for cardiac diagnosis. Conventional ECG recordings, however, use a limited number of channels (12) and each records a mixture of activities generated in different parts of the heart. Therefore, direct observation of the ECG signals collected on the body surface is likely an inefficient way to study and diagnose cardiac abnormalities. This study describes new experimental and analytical methods to capture more meaningful ECG component signals, each representing more directly a physical cardiac source. This study first describes a simply applied method for collecting high-density ECG signals. The recorded signals are then separated by independent component analysis (ICA) to obtain spatially fixed and temporally independent component activations. Results from five subjects show that P-, QRS-, and T-waves can be clearly separated from the recordings, suggesting ICA might be an effective and useful tool for high-density ECG analysis, interpretation, and diagnosis.
Preclinical Evaluation of Illudins as Anticancer Agents: Basis for Selective Cytotoxicity (1990)

Illudins are potent natural products derived from Omphalotus illudens and related fungi. The chemical structure of illudins differs from that of other conventional chemotherapeutic agents. While illudins are toxic to most tumor cells after prolonged exposure (greater than or equal to 48 hr), with shorter exposure times (less than or equal to 2 hr), they show selective toxicity for human myelocytic leukemia and epidermoid, lung, ovarian, and breast carcinoma cells of various species of origin. The apparent histologic specificity of illudin S toxicity is based on an energy-dependent transport mechanism present in sensitive cells, but absent in cells relatively resistant to illudin S. For human myeloid leukemia HL60 cells, the Michaelis constant was 4.2 microM and the maximum velocity was 12.2 pmol/minute per 10 million cells or 730 pmol/hour per 10 million cells. The energy-dependent transport mechanism was detected in other mammalian tumor cells.
Geo-Intelligence based fiber fault localization system for rural India (2015)

This study paper proposes Geo-Intelligence based algorithmic development of fiber fault localization system (FFLS) for rural India. This research is to support fiber fault localization for 2, 50,000 Gram Panchayats (GP) under Govt. Of India NOFN (National Optical Fiber Network) project. In absence of basic infrastructure facilities in rural areas e.g. approaching road etc., the biggest challenge for this technical work is to digitize existing fiber based infrastructure i.e. fiber with attributes, join boxes, telephone exchanges along with incremental fiber approaching towards GPs. Geo-Intelligence based FFLS require accurate Geographical Information System (GIS) mapping of fiber with junction boxes and other important places i.e. exchanges, BTSs, FPOI(Fiber Point Of Interconnect) etc. For PON (Passive Optical Network) (as GPON network has been selected as choice for network), the fiber link is point to multipoint topology. Traditional OTDR cannot be used for fault localization in GPON (tree topology) because OTDR is designed for point to point topology. Since GPON is point to multipoint (tree topology) technology, hence present algorithmic development for fault detection is useful for traditional OTDR. The development of FFLS algorithms includes a). Extraction of technology based topological GIS mapped fiber sections (from central office to CPE) b). Extracting equipment components (active and passive) inventory c). Predicting extra fiber length between two nodes i.e. fiber spool. d). Co-relation of OTDR traces with alarm based information and Utilizing images for referencing above information. In present study ITU-T G.984.x Gigabit Passive Optical Network (GPON) based practical FFLS system has been demonstrated in lab environment.
Wind type tone synthesizer adapted for simulating a conical resonance tube (1995)

First Page
Organic Dye-Doped Polymer Optical Fiber Amplifier (1993)

There has been great interest in development of polymer optical fibers (POFs) for local area networks (LANs), datalinks, applications for automobile and medical applications etc., because of virtues, such as easy processing, handling, low cost and large diameter, enabling high efficiencies of fiber coupling and beam insertion. (1) In those days, highly developed Er 3+ -doped optical fiber amplifier can obtain much more functional applications. On the other hand, until now, POF system has no amplifying element, so applications of POFs are positioned in hopeless situation. Our proposals and experiment presented in this paper concerning graded-index (GI) Rhodamine B doped POF-Amplifiers (POFA) could give a break-through on such situation. The POFA gave sufficient gain with extremely short length of fiber for its large cross sections. Also, high-power amplification was tried with large core diameter fiber.
Catalysis of Hydrosilylation by Well‐Defined Surface Rhodium Siloxide Phosphine Complexes (2009)

Abstract Surface rhodium siloxide phosphine complexes have been synthesized directly by condensation of the molecular precursor Rh(cod)(PR 3 )(OSiMe 3 ) [R=Cy ( 1 ), Ph ( 2 ), i Pr( 3 ); cod=1,5‐cyclooctadiene] with silanol groups on silica (Aerosil 200) and their structures have been characterized by 13 C, 29 Si, and 31 P cross‐polarization magic‐angle spinning (CP/MAS) NMR spectroscopy. Such single‐site complexes have been tested for their activity in hydrosilylation of olefins with heptamethyltrisiloxane and poly(hydromethyl‐ co ‐dimethyl)siloxane. The immobilized catalysts 1 – 3 all retained their effectiveness even after recycling up to at least five times and mostly up to ten times. Based on the results of CP/MAS NMR measurements, a mechanism of hydrosilylation catalysis by single‐site rhodium siloxide phosphine complexes is proposed, which involves concurrent pathways of oxidative addition and replacement of phosphine by olefins.
A cell surface glycoprotein expressed by colorectal carcinomas including poorly differentiated, noncarcinoembryonic antigen-producing colorectal tumors. (1988)

A monoclonal antibody to a cell surface glycoprotein on human colorectal carcinomas was raised using the undifferentiated colon carcinoma cell line MIP 101 as the immunogen. This antibody, ND4, is an IgG2a which does not cross-react with carcinoembryonic antigen (CEA), non-specific cross-reacting antigen, or blood group substances A, B, and H. Immunoprecipitation using lysates of cells grown in [35S]methionine or [3H]glucosamine and lysates of cells surface labeled with 125I showed binding to a cell surface glycoprotein with a molecular weight of approximately 160,000. Indirect immunofluorescence showed binding to the cell surface of 14 of 15 human colorectal carcinoma cell lines including six of six that do not secrete CEA. Two of seven human noncolorectal carcinoma lines and one of six nonhuman cell lines also bound antibody. Immunoperoxidase staining of formalin-fixed tissues showed prominent antibody binding with 19 of 33 (58%) human colorectal carcinomas, including five of six poorly differentiated tumors, five of 43 (12%) normal colonic mucosal biopsies, and one of 17 (6%) normal noncolonic tissues. One of 11 (9%) noncolonic tumors, a gastric adenocarcinoma, stained with ND4. Preliminary data obtained by a nonquantitative nitrocellulose dot-immunoassay have tentatively identified this glycoprotein in the serum of 15 of 37 (41%) patients with colorectal cancer. Three of the 15 patients had early stage disease and normal CEA levels (less than 2.5 ng/ml). Three patients had circulating antigen detectable preoperatively but not after tumor resection. Only one of 11 (9%) sera samples from normal subjects was positive. The characteristics of ND4 suggest that it may be of value in monitoring patients with colorectal carcinomas who do not have plasma CEA elevations. It may also be of value in the differential diagnosis of metastatic, poorly differentiated adenocarcinomas of unknown primary origin.
Discovery of GS-9973, a Selective and Orally Efficacious Inhibitor of Spleen Tyrosine Kinase (2014)

Spleen tyrosine kinase (Syk) is an attractive drug target in autoimmune, inflammatory, and oncology disease indications. The most advanced Syk inhibitor, R406, 1 (or its prodrug form fostamatinib, 2), has shown efficacy in multiple therapeutic indications, but its clinical progress has been hampered by dose-limiting adverse effects that have been attributed, at least in part, to the off-target activities of 1. It is expected that a more selective Syk inhibitor would provide a greater therapeutic window. Herein we report the discovery and optimization of a novel series of imidazo[1,2-a]pyrazine Syk inhibitors. This work culminated in the identification of GS-9973, 68, a highly selective and orally efficacious Syk inhibitor which is currently undergoing clinical evaluation for autoimmune and oncology indications.