gebhart/patrepeval huggingface dataset:
Genetic reductionist approach for dissecting individual roles of GGDEF proteins within the c-di-GMP signaling network in <i>Salmonella</i> (2009)

Bacteria have developed an exclusive signal transduction system involving multiple diguanylate cyclase and phosphodiesterase domain-containing proteins (GGDEF and EAL/HD-GYP, respectively) that modulate the levels of the same diffusible molecule, 3'-5'-cyclic diguanylic acid (c-di-GMP), to transmit signals and obtain specific cellular responses. Current knowledge about c-di-GMP signaling has been inferred mainly from the analysis of recombinant bacteria that either lack or overproduce individual members of the pathway, without addressing potential compensatory effects or interferences between them. Here, we dissected c-di-GMP signaling by constructing a Salmonella strain lacking all GGDEF-domain proteins and then producing derivatives, each restoring 1 protein. Our analysis showed that most GGDEF proteins are constitutively expressed and that their expression levels are not interdependent. Complete deletion of genes encoding GGDEF-domain proteins abrogated virulence, motility, long-term survival, and cellulose and fimbriae synthesis. Separate restoration revealed that 4 proteins from Salmonella and 1 from Yersinia pestis exclusively restored cellulose synthesis in a c-di-GMP-dependent manner, indicating that c-di-GMP produced by different GGDEF proteins can activate the same target. However, the restored strain containing the STM4551-encoding gene recovered all other phenotypes by means of gene expression modulation independently of c-di-GMP. Specifically, fimbriae synthesis and virulence were recovered through regulation of csgD and the plasmid-encoded spvAB mRNA levels, respectively. This study provides evidence that the regulation of the GGDEF-domain proteins network occurs at 2 levels: a level that strictly requires c-di-GMP to control enzymatic activities directly, restricted to cellulose synthesis in our experimental conditions, and another that involves gene regulation for which c-di-GMP synthesis can be dispensable.
Monolithic III–V on Silicon Plasmonic Nanolaser Structure for Optical Interconnects (2015)

Monolithic integration of III-V semiconductor lasers with Si circuits can reduce cost and enhance performance for optical interconnects dramatically. We propose and investigate plasmonic III-V nanolasers as monolithically integrated light source on Si chips due to many advantages. First, these III-V plasmonic light sources can be directly grown on Si substrates free of crystallographic defects due to the submicron cavity footprint (250 nm × 250 nm) being smaller than the average defect free region size of the heteroepitaxial III-V material on Si. Secondly, the small lateral and vertical dimensions facilitate process co-integration with Si complementary metal-oxide-semiconductor (CMOS) in the front end of the line. Thirdly, combining with monolithically integrated CMOS circuits with low device capacitance and parasitic capacitance, the nano-cavity optoelectronic devices consume orders of magnitude less power than the conventional lasers and reduce the energy consumption. Fourthly, the modulation bandwidth of the plasmonic light-sources is enhanced to significantly higher than conventional lasers due to enhanced photon state density and transition rate. In addition, we show that these device performance are very robust after taking into account the surface recombination and variations in device fabrication processes.
Pseudo-elliptic in-line filters with dielectric resonators in propagating waveguide (2015)

In this paper a new class of in-line filters with pseudoelliptic responses exploiting the TE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01δ</sub> dielectric mode is presented. The basic structure consists of a single resonant dielectric puck placed into a rectangular propagating waveguide. Couplings are controlled by a proper positioning of the puck, and no irises are required. The fundamental propagating mode of the waveguide is exploited to bypass the resonator so as to obtain couplings between non adjacent resonators, allowing responses with a number of zeros equal to the number of poles. Direct input-to-output coupling is incorporated, resulting in very selective responses. With respect to classical waveguide filters, the maximum number of transmission zeros is obtained in a more compact waveguide section while not sacrificing the quality factor. Furthermore, in contrast with conventional dielectric resonator filters, which are limited to very narrow band applications, filters having a FBW up to 2% (or more) can be designed with the proposed approach. Higher order filters are obtained by cascading singlets, resulting in designs with high modularity. The connection between singlets is accurately taken into account in the equivalent circuit and no further optimization is required after the cascade, also allowing an exact positioning of the transmission zeros. Design of three pole filters demonstrate the flexibility of the proposed approach, while the measurement of a manufactured filter with a FBW of 2,3% demonstrate its feasibility.
Layout Decomposition and Legalization for Double-Patterning Technology (2013)

The use of multiple-patterning (MP) optical lithography for sub-20 nm technologies has inevitably become slow to adopt the next generation of lithography systems. The biggest technical challenge of MP is failure to reach a manufacturable layout-coloring solution, especially in dense layouts. This paper offers a post layout solution for the removal of conflicts, i.e., patterns that cannot be assigned to different masks without violating spacing rules. The proposed method essentially consists of three steps: 1) layout coloring; 2) exposure layers; 3) geometric rules definition; and 4) layout legalization using compaction and MP rules as constraints. The method is general and can be used for different MP technologies, including lithography-etch, lithography-etch double-patterning (DP), triple patterning/MP (i.e., multiple litho-etch steps), and self-aligned DP (SADP). For demonstration purposes, we apply the proposed method in this paper to remove conflicts in DP. We offer an <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</i> ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> ) layout-coloring heuristic algorithm for DP, which is up to 80× faster than the integer linear program-based approach. The conflict-removal problem is formulated as a linear program, which permits an extremely fast runtime (less than 1 min in real time for macro layouts). The method was tested on standard cells and macro layouts from a commercial 22-nm library designed without any MP awareness. For many cells, the method removes all conflicts without any area increase. For some complex cells and macros, the method still removes all conflicts but with a modest 6% average increase in area.
Synthesis of a New Explosive Compound, Trans-1,4,5,8-Tetranitro-1,4,5,8- Tetraazadecalin (1981)

Abstract : The synthesis of a new explosive compound, trans-1,4,5,8-tetranitro- 1,4,5,8-tetraazadecalin, is described. The compound has several physical properties which are superior to those of HDX (1,3,5,7-tetranitro-1,3,5,7- tetraazacyclooctane) and RDX (1,3,5-trinitro-1,3,5-hexahydrotriazine). These superior physical properties include heat stability and insensitivity to impact.
Polarization characteristics of LiNbO3 channel waveguide directional couplers (1983)

Measurements are described on Z-LiNbO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> , single-mode, channel waveguide directional couplers for the TE- and TM-mode polarizations at 0.83- and 1.3-μm wavelengths. The coupling characteristics for each polarization are strongly dependent on the mode confinement, and, hence, on the mode dispersion, and also vary differently with changes in mode dispersion. With particular waveguide fabrication parameters, the TE- and TM-mode coupling coefficients are equal for any waveguide spacing; for other fabrication conditions, the coupling coefficients are always unequal or equal at only one spacing. Theoretical calculations, based on experimentally determined diffusion parameters, follow the trend of measured values in most cases and correctly predict the effect on the coupling characteristics of changes in waveguide fabrication.
Defining agonist peptides of human interleukin-1 beta. (1989)

The structure-function relationship in the human IL-1 beta protein has been analyzed by means of computer prediction, synthesis of peptides and use of monoclonal antibodies of predetermined specificity. A nine amino acid-long fragment (VQGEESNDK), corresponding to the human IL-1 beta sequence in position 163-171, was shown to possess only some of the IL-1 activities, i.e. those directed to the immune system, while being devoid of IL-1-like inflammatory effects. It is thus proposed that discrete domains within the IL-1 beta protein might be responsible for the different biological activities of the molecule and that the 163-171 fragment may represent one of the immunostimulatory sites of IL-1 beta.
Four-dimensional IMRT treatment planning using a DMLC motion-tracking algorithm (2009)

The purpose of this study is to develop a four-dimensional (4D) intensity-modulated radiation therapy (IMRT) treatment-planning method by modifying and applying a dynamic multileaf collimator (DMLC) motion-tracking algorithm. The 4D radiotherapy treatment scenario investigated is to obtain a 4D treatment plan based on a 4D computed tomography (CT) planning scan and to have the delivery flexible enough to account for changes in tumor position during treatment delivery. For each of 4D CT planning scans from 12 lung cancer patients, a reference phase plan was created; with its MLC leaf positions and three-dimensional (3D) tumor motion, the DMLC motion-tracking algorithm generated MLC leaf sequences for the plans of other respiratory phases. Then, a deformable dose-summed 4D plan was created by merging the leaf sequences of individual phase plans. Individual phase plans, as well as the deformable dose-summed 4D plan, are similar for each patient, indicating that this method is dosimetrically robust to the variations of fractional time spent in respiratory phases on a given 4D CT planning scan. The 4D IMRT treatment-planning method utilizing the DMLC motion-tracking algorithm explicitly accounts for 3D tumor motion and thus hysteresis and nonlinear motion, and is deliverable on a linear accelerator.
Development of an Automated Patient-recognition Method for Digital Chest Radiographs Using Edge-enhanced Images (Originals) (2003)

It is important that all images in a picture archiving and communication system (PACS) environment should be stored in the correct location, e.g., in the proper patient's folder. However, if patient information, such as identification number or patient name, has been entered incorrectly, the image may be stored in the wrong place. We are developing an automated patient recognition method for chest radiographs based on a template-matching technique to prevent such filing errors. To further improve the performance of our method, we investigated the usefulness of a new automated patient-recognition method based on a template-matching technique by using edge-enhanced and smoothed images. We found that the relationship between the correlation values obtained with and without the edge-enhancement technique tended to provide different criteria for identifying correct or incorrect patients. When we combined the two methods to distinguish the images by a rule-based method, 67.1% of wrongly identified patients in our database could be identified as wrongly identified, without any false warnings for correctly identified patients. We consider that this automated method for patient recognition based on edge-enhanced images would be useful in preventing "wrong" images from being stored in a PACS environment.
RINGS: a new search/match database for identification by polycrystalline electron diffraction (2002)

RINGS is a relational database built from NIST Crystal Data for the identification of polycrystalline solids by selected area electron diffraction (SAED) and elemental analysis using Microsoft Access 97 (subsequently converted to Access 2000 ). Experimental d spacings are matched against values calculated from reduced unit cells, thereby fully and rigorously incorporating the effects of double diffraction. A total of 79136 inorganic phases are included with original Crystal Data reference codes, allowing access to all the information in NIST Crystal Data. Specific examples illustrate the advantages over previous approaches to the problem. This database will be most useful to researchers in mineralogy, metallurgy, materials science, forensics and analytical chemistry who seek to identify well characterized phases with known unit cells.
Aziridinyldinitrobenzamides:  Synthesis and Structure−Activity Relationships for Activation by <i>E. </i><i>coli</i> Nitroreductase (2004)

The 5-aziridinyl-2,4-dinitrobenzamide CB 1954 is a substrate for the oxygen-insensitive nitroreductase (NTR) from E. coli and is in clinical trial in combination with NTR-armed adenoviral vectors in a GDEPT protocol; CB 1954 is also of interest for selective deletion of NTR-marked cells in normal tissues. Since little further drug development has been carried out around this lead, we report here the synthesis of more soluble variants and regioisomers and structure-activity relationship (SAR) studies. The compounds were primarily prepared from the corresponding chloro(di)nitroacids through amide side chain elaboration and subsequent aziridine formation. One-electron reduction potentials [E(1)], determined by pulse radiolysis, were around -400 mV, varying little for aziridinyldinitrobenzamide regioisomers. Cytotoxicity in a panel of NTR-transfected cell lines showed that in the CB 1954 series there was considerable tolerance of substituted CONHR side chains. The isomeric 2-aziridinyl-3,5-dinitrobenzamide was also selective toward NTR+ve lines but was approximately 10-fold less potent than CB 1954. Other regioisomers were too insoluble to evaluate. While CB 1954 gave both 2- and 4-hydroxylamine metabolites in NTR+ve cells, related analogues with substituted carboxamides gave only a single hydroxylamine metabolite possibly because the steric bulk in the side chain constrains binding within the active site. CB 1954 is also a substrate for the two-electron reductase DT-diaphorase, but all of the other aziridines (regioisomers and close analogues) were poorer substrates with resulting improved specificity for NTR. Bystander effects were determined in multicellular layer cocultures and showed that the more hydrophilic side chains resulted in a modest reduction in bystander killing efficiency. A limited number of analogues were tested for in vivo activity, using a single ip dose to CD-1 nude mice bearing WiDr-NTR(neo) tumors. The most active of the CB 1954 analogues was a diol derivative, which showed a substantial median tumor growth delay (59 days compared with >85 days for CB 1954) in WiDr xenografts comprising 50% NTR+ve cells. The diol is much more soluble and can be formulated in saline for administration. The results suggest there may be advantages with carefully selected analogues of CB 1954; the weaker bystander effect of its diol derivative may be an advantage in the selective cell ablation of NTR-tagged cells in normal tissues.
Closed-form supervised dimensionality reduction with generalized linear models (2008)

We propose a family of supervised dimensionality reduction (SDR) algorithms that combine feature extraction (dimensionality reduction) with learning a predictive model in a unified optimization framework, using data- and class-appropriate generalized linear models (GLMs), and handling both classification and regression problems. Our approach uses simple closed-form update rules and is provably convergent. Promising empirical results are demonstrated on a variety of high-dimensional datasets.
Developing a Multi-Joint Upper Limb Exoskeleton Robot for Diagnosis, Therapy, and Outcome Evaluation in Neurorehabilitation (2012)

Arm impairments in patients post stroke involve the shoulder, elbow and wrist simultaneously. It is not very clear how patients develop spasticity and reduced range of motion (ROM) at the multiple joints and the abnormal couplings among the multiple joints and the multiple degrees-of-freedom (DOF) during passive movement. It is also not clear how they lose independent control of individual joints/DOFs and coordination among the joints/DOFs during voluntary movement. An upper limb exoskeleton robot, the IntelliArm, which can control the shoulder, elbow, and wrist, was developed, aiming to support clinicians and patients with the following integrated capabilities: 1) quantitative, objective, and comprehensive multi-joint neuromechanical pre-evaluation capabilities aiding multi-joint/DOF diagnosis for individual patients; 2) strenuous and safe passive stretching of hypertonic/deformed arm for loosening up muscles/joints based on the robot-aided diagnosis; 3) (assistive/resistive) active reaching training after passive stretching for regaining/improving motor control ability; and 4) quantitative, objective, and comprehensive neuromechanical outcome evaluation at the level of individual joints/DOFs, multiple joints, and whole arm. Feasibility of the integrated capabilities was demonstrated through experiments with stroke survivors and healthy subjects.
Thermally expandable microcapsules for polymer foaming—Relationship between expandability and viscoelasticity (2009)

Abstract A new thermally expandable microcapsule was developed for use with foaming polypropylene (PP) by injection molding and extrusion processes at operating temperatures above 200°C. The microcapsule consists of a blowing agent as the core and a shell polymer. The rheological properties of the shell polymer were controlled by a crosslinking agent to design the expandability and shrinkage. The effects of rheological properties on the expandability and the surface appearance of foam products were thoroughly investigated. It was found that storage modulus G ′ and tan δ significantly affected the expandability and shrinkage and were controllable through crosslinking polymerization. Visual observation of batch foaming, rheological measurement, and experiments of foam injection molding and extrusion elucidated the existence of the optimal degree of crosslinking that could realize more than 30% density reduction while maintaining a smoothsurface at PP foam injection molding and extrusion. POLYM. ENG. SCI., 2010. © 2009 Society of Plastics Engineers
Vertically Integrated Reconfigurable Nanowire Arrays (2018)

This letter discusses a feasible variant of vertically integrated reconfigurable field effect transistors (RFET) based on top-down nanowires. The structures were studied by 3-D device simulations. Subdividing the structure into two vertical pillars allows a lean technological realization as well as simple access to the electrodes. In addition of enabling p- and n-FET operations like a horizontal RFET, the device delivers higher performance. We show that by the integration of additional vertical pillars and select gates, a higher device functionality and flexibility in interconnection are provided.
Automated extraction of fracture network from 3D poststack seismic data for fracture and fault characterization and modeling (2013)

This article describes a new, efficient, and effective method for natural fracture interpretation with exploration and reservoir applications. The method automatically extracts, controls the quality of, and characterizes seismic-scale fracture networks, including fracture corridors and faults. The extracted 3D fracture networks are the basis of an innovative workflow for modeling subseismic fracture networks. Extracted and modeled 3D fracture networks can be analyzed as planes, sets, and even as 3D networks to aid the interpretation of naturally fractured reservoirs. In addition to conventional fracture-plane characteristics (orientation, distribution, density, etc.), the extracted networks can provide additional properties (fracture length, fracture plane area, aspect ratio, intersection type, intersection length, intersection vector, etc.) to improve the description of the fracture network.
Investigation of signal-to-noise ratio in frequency-domain multiphoton fluorescence lifetime imaging microscopy (2016)

Multiphoton microscopy (MPM) combined with fluorescence lifetime imaging microscopy (FLIM) has enabled three-dimensional quantitative molecular microscopy in vivo. The signal-to-noise ratio (SNR), and thus the imaging rate of MPM-FLIM, which is fundamentally limited by the shot noise and fluorescence saturation, has not been quantitatively studied yet. In this paper, we investigate the SNR performance of the frequency-domain (FD) MPM-FLIM with two figures of merit: the photon economy in the limit of shot noise, and the normalized SNR in the limit of saturation. The theoretical results and Monte Carlo simulations find that two-photon FD-FLIM requires 50% fewer photons to achieve the same SNR as conventional one-photon FLIM. We also analytically show that the MPM-FD-FLIM can exploit the DC and higher harmonic components generated by nonlinear optical mixing of the excitation light to improve SNR, reducing the required number of photons by an additional 50%. Finally, the effect of fluorophore saturation on the experimental SNR performance is discussed.
Sequential logic optimization by redundancy addition and removal (1993)

This paper presents a method of multi-level logic optimization for combinational and synchronous sequential logic. The circuits are optimized through iterative addition and removal of redundancies. Among the large number of possible connections that can be added, the proposed method can efficiently identify those connections that would create more redundancies and, thus, would result in a smaller network. This is done with the use of combinational and sequential ATPG techniques based up the concept of mandatory assignments. Experiments on ISCAS-85 combinational benchmark circuits show that best results are obtained for most of them. For sequential circuits, experimental results on MCNC FSM benchmarks and ISCAS-89 sequential benchmark circuits show that a significant amount of area reduction can be achieved beyond combinational optimization and sequential redundancy removal.
Dehydrogenation of ammonia-borane by Shvo's catalyst (2010)

Shvo's cyclopentadienone-ligated ruthenium complex is an efficient catalyst for the liberation of exactly two molar equivalents of hydrogen from ammonia-borane, a prospective hydrogen storage medium. The mechanism for the dehydrogenation features a ruthenium hydride resting state from which dihydrogen loss is the rate-determining step.
Covalent chemical functionalization of semiconducting layered chalcogenide nanosheets (2019)

The covalent functionalization of the surfaces of transition metal dichalcogenide and pnictogen chalcogenide materials is demonstrated using aryl diazonium chemistry.