gebhart/patrepeval huggingface dataset:
Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers (2012)

Considerable evidence suggests that during the progression of complex diseases, the deteriorations are not necessarily smooth but are abrupt, and may cause a critical transition from one state to another at a tipping point. Here, we develop a model-free method to detect early-warning signals of such critical transitions, even with only a small number of samples. Specifically, we theoretically derive an index based on a dynamical network biomarker (DNB) that serves as a general early-warning signal indicating an imminent bifurcation or sudden deterioration before the critical transition occurs. Based on theoretical analyses, we show that predicting a sudden transition from small samples is achievable provided that there are a large number of measurements for each sample, e.g., high-throughput data. We employ microarray data of three diseases to demonstrate the effectiveness of our method. The relevance of DNBs with the diseases was also validated by related experimental data and functional analysis.
Myocardial regeneration (2002)

The mechanism of pathological myocardial growth involves myocyte hypertrophy and proliferation. However, the origin of replicating myocytes in the human heart remains to be identified. The major challenging question is whether the myocardium possesses a subpopulation of myocytes that are not terminally differentiated or whether primitive cells reside in the heart and undergo lineage commitment generating amplifying cells. The possibility is advanced that cells expressing surface antigens commonly found in stem cells are stored in the adult heart and, following stimulation, can give rise to myocytes and vascular structures. Thus, the damaged heart has the potential to repair itself.
S‐[<sup>18</sup>F]Acetylcyclofoxy: a useful probe for the visualization of opiate receptors in living animals (1984)

A fluoro-analogue of the potent narcotic antagonist, naltrexone, was synthesized and shown to bind with high affinity to opiate receptors in vitro. 3-[18F]acetylcyclofoxy was prepared via a one-step triflate displacement reaction with the positron emitting 18F ion from tetraethylammonium [18F] fluoride. 3-[18F]acetylcyclofoxy accumulation in opiate receptor rich brain regions of both rat and baboon is shown to be completely displaced by the active enantiomer of naloxone [-)-naloxone) while the identical dose of the pharmacologically inert (+)-naloxone has no detectable effect. Moreover, both rat and baboon brain showed the well documented, typical opiate receptor distribution so that basal ganglia and thalamus are clearly visible in the living baboon brain up to 95 min after intravenous injection of 3-[18F] acetylcyclofoxy. We expect that 3-[18F )acetylcyclofoxy will be a useful probe for visualizing opiate receptors in living humans.
Expression of the <i>Bs2</i> pepper gene confers resistance to bacterial spot disease in tomato (1999)

The Bs2 resistance gene of pepper specifically recognizes and confers resistance to strains of Xanthomonas campestris pv. vesicatoria that contain the corresponding bacterial avirulence gene, avrBs2. The involvement of avrBs2 in pathogen fitness and its prevalence in many X. campestris pathovars suggests that the Bs2 gene may be durable in the field and provide resistance when introduced into other plant species. Employing a positional cloning strategy, the Bs2 locus was isolated and the gene was identified by coexpression with avrBs2 in an Agrobacterium-mediated transient assay. A single candidate gene, predicted to encode motifs characteristic of the nucleotide binding site-leucine-rich repeat class of resistance genes, was identified. This gene specifically controlled the hypersensitive response when transiently expressed in susceptible pepper and tomato lines and in a nonhost species, Nicotiana benthamiana, and was designated as Bs2. Functional expression of Bs2 in stable transgenic tomatoes supports its use as a source of resistance in other Solanaceous plant species.
Highly efficient organic electroluminescent device with modified cathode (2006)

One of the key parameters for high efficiency organic electrophosphorescent light emitting diodes is charge injection into the phosphorescence compound. By introducing a hybrid device architecture, and incorporating electron and hole interfacial layers with lowest unoccupied molecular orbital and highest occupied molecular orbital levels similar to that of the phosphorescence compound, on the cathode and the anode side of the device, respectively, charge injection properties were improved. A green electrophosphorescence device with luminous efficacy of 50lm∕W at luminance efficiency reaching 55cd∕A was demonstrated.
Regulation of leukocyte adhesion molecule-1 (TQ1, Leu-8) expression and shedding by normal and malignant cells. (1991)

The human leukocyte adhesion molecule-1 (LAM-1, TQ1, Leu-8) is involved in the binding of human leukocytes to high endothelial venules (HEV) of peripheral lymph nodes (LN). The regulation of LAM-1 expression is unique in that leukocyte stimulation induces a rapid down-modulation of LAM-1 from the cell surface. In this study, the regulation and function of LAM-1 was studied in detail in normal lymphocytes and compared with the LAM-1 of malignant leukocytes. Modulation of LAM-1 from the cell surface occurred concomitantly with the appearance of LAM-1 in the culture medium indicating that LAM-1 is cleaved from the cell surface. Shedding of LAM-1 was decreased in the presence of protein kinase C (PKC) inhibitors. As with normal lymphocytes, cells transfected with the LAM-1 cDNA and chronic lymphocytic leukemia (CLL) cells also shed LAM-1 following phorbol myristate acetate (PMA) exposure. CLL cells expressed the same Mr LAM-1 protein as normal lymphocytes and LAM-1+ CLL cells were able to specifically bind to HEV. In addition, normal lymphocytes and LAM-1+ CLL cells were capable of binding polyphosphomonester core polysaccharide (PPME) derived from yeast cell wall, a carbohydrate which mimics an essential component of the natural ligand for LAM-1, and PPME and HEV binding was specifically blocked by a new monoclonal antibody (mAb) reactive with LAM-1. The expression of LAM-1 and other adhesion molecules was examined on cells of 118 hematopoietic malignancies. LAM-1 was most frequently expressed on CLL and follicular or diffuse small cleaved cell lymphomas, whereas most other malignancies were LAM-1-. Thus, most CLL cells and some non-Hodgkin's lymphoma cells express a functionally active LAM-1 molecule which may correlate with their capacity to migrate through the circulation and disseminate into peripheral LN.
Wavelength tuning in active surface-emitting harmonic generators and applications for spatially addressable coherent detection (1992)

Active surface-emitting harmonic generators based on monolithic integration of InGaAs/GaAs single-quantum-well (SQW) lasers with multilayered nonlinear waveguides have been fabricated. Wavelength tuning of the integrated SQW laser in active/passive segmented devices has been investigated and used to control the emission angle of the harmonic light for application as spatially addressable coherent detectors.
Few-cycle THz generation for imaging and tomography applications (2002)

The methods for generating few-cycle THz radiation from semiconductors without external applied fields are reviewed. Their spectral characteristics, efficiency and prospects for imaging and tomography at terahertz frequencies are discussed.
Microstructure Control of Barium Titanate – Potassium Niobate Solid Solution System Ceramics by MPB Engineering and their Piezoelectric Properties (2011)

Effect of the microstructural homogeneity of 0.5 BaTiO 3 - 0.5 KNbO 3 (0.5BT-0.5KN) solid solution ceramics on the dielectric and piezoelectric properties was investigated. Microstructure of a sample prepared by a conventional sintering method was homogenous, and the room temperature crystal structure was assigned to cubic Pm3m symmetry and therefore the sample was paraelectric. On the other hand, microstructure of samples prepared by a two-step sintering method was inhomogeneous, that is, it was made of BT and KN grains. The large electric field piezoelectric constant d 33 * increased with increasing interface area.
Very Low Cost Gyroscopes (2006)

This paper was invited as part of discussion on the extent to which gyroscope cost and performance are influenced by micromachining. The contribution here addresses a very low cost segment enabled by integrating mechanisms and electronics. The resulting IC's are also packaged and tested with standard technology. The paper outlines some of the corresponding design challenges and the methods used to overcome them in a commercial process
Low-power acoustic harvesting of aerosols (2002)

A new acoustic device for levitation and/or concentration of aerosols and small liquid/solid samples (up to several millimeters in diameter) in air has been developed. The device is inexpensive, low-power, and, in its simplest embodiment, does not require accurate alignment of a resonant cavity. It is constructed from a cylindrical PZT tube of outside diameter D=19.0 mm and thickness-to-radius ratio h/a /spl sim/0.03. The lowest-order breathing mode of the tube is tuned to match a resonant mode of the interior air-filled cylindrical cavity. A high Q cavity results that can be driven efficiently. An acoustic standing wave is created in the interior cavity of the cylindrical shell where particle concentration takes place at the nodal planes of the field. It is shown that drops of water in excess of 1 mm in diameter may be levitated against the force of gravity for approximately 100 mW of input electrical power. The main objective of the research is to implement this low-power device to concentrate and harvest aerosols in a flowing system. Several different cavity geometries are presented for efficient collection of the concentrated aerosols. Concentration factors greater than 40 are demonstrated for particles of size 0.7 /spl mu/ in a flow volume of 50 L/minute.
Atypical Li[sub 1.1]V[sub 3]O[sub 8] Prepared by a Novel Synthesis Route (2006)

International audience
A High-Throughput Screen Identifies a New Natural Product with Broad-Spectrum Antibacterial Activity (2012)

Due to the inexorable invasion of our hospitals and communities by drug-resistant bacteria, there is a pressing need for novel antibacterial agents. Here we report the development of a sensitive and robust but low-tech and inexpensive high-throughput metabolic screen for novel antibiotics. This screen is based on a colorimetric assay of pH that identifies inhibitors of bacterial sugar fermentation. After validation of the method, we screened over 39,000 crude extracts derived from organisms that grow in the diverse ecosystems of Costa Rica and identified 49 with reproducible antibacterial effects. An extract from an endophytic fungus was further characterized, and this led to the discovery of three novel natural products. One of these, which we named mirandamycin, has broad-spectrum antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Vibrio cholerae, methicillin-resistant Staphylococcus aureus, and Mycobacterium tuberculosis. This demonstrates the power of simple high throughput screens for rapid identification of new antibacterial agents from environmental samples.
System Applies Polymer Powder To Filament Tow (1993)

Polymer powder applied uniformly and in continuous manner. Powder-coating system applies dry polymer powder to continuous fiber tow. Unique filament-spreading technique, combined with precise control of tension on fibers in system, ensures uniform application of polymer powder to web of spread filaments. Fiber tows impregnated with dry polymer powders (towpregs) produced for preform-weaving and composite-material-molding applications. System and process valuable to prepreg industry, for production of flexible filament-windable tows and high-temperature polymer prepregs.
Towards methionine overproduction in Corynebacterium glutamicum - methanethiol and dimethyldisulfide as reduced sulfur sources (2010)

In the present work, methanethiol and dimethyldisulfide were investigated as sulfur source for methionine synthesis in Corynebacterium glutamicum. In silico pathway analysis has predicted a high methionine yield for these reduced compounds provided that they can be utilized. Wild type cells were able to grow on methanethiol and on dimethyldisulfide as sole sulfur source, respectively. Isotope labeling studies with mutant strains exhibiting targeted modification of methionine biosynthesis gave detailed insight into the underlying pathways involved in assimilation of methanethiol and dimethyldisulfide. Both sulfur compounds are incorporated as entire molecule, adding the terminal S-CH3 group to O-acetylhomoserine. In this reaction, methionine is directly formed. MetY (O-acetylhomoserine sulfhydrylase) was identified as enzyme catalyzing this reaction. Deletion of metY resulted in methionine auxotrophic strains grown on methanethiol or dimethyldisulfide as sole sulfur source. Plasmid based overexpression of metY in the delta metY background restored the capability to grow on methanethiol or dimethyldisulfide as sole sulfur source. In vitro studies with the C. glutamicum wild type revealed a relatively low activity of MetY for methanethiol (63 mU/mg) and dimethyldisulfide (61 mU/mg). Overexpression of metY increased the in vitro activity to 1780 mU/mg and was beneficial for methionine production, since the intracellular methionine pool was increased two-fold in the engineered strain. This positive effect was limited by depletion of the metY substrate O-acetylhomoserine, requesting for further metabolic engineering targets towards competitive production strains.
A New Azimuthal Deep-Reading Resistivity Tool for Geosteering and Advanced Formation Evaluation (2009)

Summary Drilling services and oil companies have long been interested in acquiring the capability of landing a well accurately in a hydrocarbon reservoir and remaining in it for optimal drainage. Although traditional logging-while-drilling (LWD) propagation resistivity tools can help to achieve this goal, their overall effectiveness is not satisfactory because they lack azimuthal sensitivity. Ideally, geosteering and advanced formation-evaluation methods, such as anisotropy calculations, require azimuthally sensitive measurements. This paper discusses a newly developed propagation resistivity tool that is designed to be azimuthally sensitive for use in geosteering and formation evaluation while drilling. It uses the tilted-antenna concept to produce directionally sensitive measurements that are lacking in traditional LWD propagation tools. This paper also discusses the theory and the development of this tool, as well as the experimentation and numerical-modeling data used to characterize its azimuthal capability. Advanced application algorithms used to calculate the horizontal and the vertical resistivity (anisotropy calculation), as well as dipping angle, will be explained in detail. Finally, the paper presents and discusses field examples to demonstrate that this newly developed tool is a two-in-one service: geosteering and advanced formation evaluation. The azimuthal deep-reading resistivity is shown to bear promise for use in optimization of well trajectory and well placement and in advanced formation evaluation while drilling. This newly developed tool is superior to traditional propagation tools in locating bed boundaries and in keeping the well in the desired pay zone. In addition to providing traditional multiple-depth-of-investigation resistivity measurements, this new tool provides multiple-depth-of-investigation azimuthal resistivity measurements.
Efficient Convergent Synthesis of Bi-, Tri-, and Tetra-antennary Complex Type <i>N</i>-Glycans and Their HIV-1 Antigenicity (2013)

The structural diversity of glycoproteins often comes from post-translational glycosylation with heterogeneous N-glycans. Understanding the complexity of glycans related to various biochemical processes demands a well-defined synthetic sugar library. We report herein a unified convergent strategy for the rapid production of bi-, tri-, and tetra-antennary complex type N-glycans with and without terminal N-acetylneuraminic acid residues connected via the α-2,6 or α-2,3 linkages. Moreover, using sialyltransferases to install sialic acid can minimize synthetic steps through the use of shared intermediates to simplify the complicated procedures associated with conventional sialic acid chemistry. Furthermore, these synthetic complex oligosaccharides were compiled to create a glycan array for the profiling of HIV-1 broadly neutralizing antibodies PG9 and PG16 that were isolated from HIV infected donors. From the study of antibody PG16, we identified potential natural and unnatural glycan ligands, which may facilitate the design of carbohydrate-based immunogens and hasten the HIV vaccine development.
Monitoring Technique using Acoustic Emission and Microseismic Event (2008)

Acoustic emission (AE) and Microseimsic (MS) activities are law-energy seismic events associated with a sudden inelastic deformation such as the sudden movement of existing fractures, the generation of new fractures or the propagation of fractures. These events rapidly increase before major failure and happen within a given rock volume and radiate detectable seismic waves. The main difference between AE and MS signals is that the seismic motion frequencies of AE signals are higher than those of MS signals. As the failure of geotechnical structures usually happens as a high velocity and small displacement, it is nat easy ta determine the precursor and initiation stress level of failure in displacement detection method. To overcame this problem, AE/MS techniques far detection of structure failure and damage have recently adapt in civil engineering. This study deal with the basic theory of AE/MS and state of arts in monitoring technique using AE/MS.
Waterfilling-Based Proportional Fairness Scheduler for Downlink Non-Orthogonal Multiple Access (2017)

In this letter, a low-complexity waterfilling-based power allocation (PA) technique, incorporated within the proportional fairness scheduler, is proposed and applied to a non-orthogonal multiple access (NOMA) scheme in a cellular downlink system. The aim of the proposed joint PA and scheduling scheme is to maximize the achieved average throughput through a quasi-optimal repartition of the transmit power among subbands, while guaranteeing a high level of fairness in resource allocation. Extensive simulation results show that the proposed technique enhances both system capacity and user fairness, when compared to either orthogonal signaling or NOMA with static PA.
Interferometric synthetic aperture microscopy (2007)

Interferometric synthetic aperture microscopy provides high-resolution three-dimensional optical images of semitransparent samples with large depth of field without scanning the focal plane. ISAM theory and experiments will be discussed.
Unique optical properties of organic semiconductor lasers (1998)

Summary form only given. We have studied the optical properties of two different organic semiconductor laser (OSL) structures: a waveguide edge-emitting OSL and an organic vertical-cavity surface-emitting laser (OVCSEL). The optically pumped edge-emitting OSL consists of a 3000 /spl Aring/ thick organic film vacuum-deposited onto a [100] InP substrate precoated with a 2-/spl mu/m thick layer of SiO/sub 2/. The organic films were grown in high vacuum by thermal coevaporation of tris(8-hydroxyquinoline) aluminum (Alq/sub 3/) and DCM molecules at mass ratios from 10:1 to 200:1. The organic film forms a slab optical waveguide with the SiO/sub 2/ cladding layer on one side and air on the other. The laser optical cavity is formed by the 7% reflective facets of the as-deposited organic film, which conforms to the cleaved parallel edges of the substrate. Unique optical and electronic properties of these OSLs such as thermal stability of emission wavelength, lasing threshold and output power, extremely narrow linewidth combined with a low material cost, and ease of integration of amorphous organic films with other optoelectronic devices make these lasers attractive for a number of applications, such as optical communication, optical sensing, and memory.
<i>Z</i>-Selectivity in Olefin Metathesis with Chelated Ru Catalysts: Computational Studies of Mechanism and Selectivity (2012)

The mechanism and origins of Z-selectivity in olefin metathesis with chelated Ru catalysts were explored using density functional theory. The olefin approaches from the "side" position of the chelated Ru catalysts, in contrast to reactions with previous unchelated Ru catalysts that favor the bottom-bound pathway. Steric repulsions between the substituents on the olefin and the N-substituent on the N-heterocyclic carbene ligand lead to highly selective formation of the Z product.
Numerical investigation on high power mid-infrared supercontinuum fiber lasers pumped at 3 µm (2013)

High power mid-infrared (mid-IR) supercontinuum (SC) laser sources in the 3-12 µm region are of great interest for a variety of applications in many fields. Although various mid-IR SC laser sources have been proposed and investigated experimentally and theoretically in the past several years, power scaling of mid-IR SC lasers beyond 3 μm with infrared edges extending beyond 7 μm are still challenges because the wavelengths of most previously used pump sources are below 2 μm. These problems can be solved with the recent development of mode-locked fiber lasers at 3 μm. In this paper, high power mid-IR SC laser sources based on dispersion engineered tellurite and chalcogenide fibers and pumped by ultrafast lasers at 3 µm are proposed and investigated. Our simulation results show that, when a W-type tellurite fiber with a zero dispersion wavelength (ZDW) of 2.7 µm is pumped at 2.78 μm, the power proportion of the SC laser beyond 3 µm can exceed 40% and the attainable SC output power of the proposed solid-cladding tellurite fiber is one order of magnitude higher than that of existing microstructured tellurite fibers. Our calculation also predicts that a very promising super-broadband mid-IR SC fiber laser source covering two atmospheric windows and molecules' "fingerprint" region can be obtained with a microstructured As<sub>2</sub>Se<sub>3</sub> chalcogenide fiber pumped at 2.78 μm.
Dual-domain point diffraction interferometer (1999)

The phase-shifting point diffraction interferometer has recently been developed and implemented at Lawrence Berkeley National Laboratory to meet the significant metrology challenge of characterizing extreme ultraviolet projection lithography systems. Here we present a refined version of this interferometer that overcomes the original design's susceptibility to noise attributed to scattered light. The theory of the new hybrid spatial- and temporal-domain (dual-domain) point diffraction interferometer is described in detail and experimental results are presented.
Use of GSO for inelastic gamma-ray spectroscopy measurements in the borehole (1992)

Gadolinium oxyorthosilicate (GSO) with its high density, high effective Z, fast decay time and good performance at high temperature, is the scintillation detector of choice for a new generation of neutron-induced, inelastic gamma-ray spectroscopy tools for borehole measurements, specifically aimed at measuring the carbon and oxygen content from the region surrounding the borehole. The ratio of the carbon and oxygen gamma-ray yields are transformed into formation oil saturation. To get the maximum benefit from GSO, the data acquisition, choice of materials, and measurement geometry were optimized for a small diameter tool at elevated temperatures and crystal characteristics. The large neutron cross section of the gadolinium in the scintillation crystal, its second decay constant, and the desired precision of the oil saturation measurement had important consequences in the tool design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>