gebhart/patrepeval huggingface dataset:
Performance of dual axes confocal microscope for in vivo molecular and cellular imaging (2004)

The application of conventional confocal microscopes with high numerical aperture (NA) to in vivo imaging is limited by the objectiveís large physical dimensions and short working distance. We are developing a confocal microscope that uses simple low NA lenses oriented in a dual axes configuration for miniaturization and in vivo imaging. This architecture achieves a long working distance, micron level axial resolution, and reduced noise from scattered light outside the focal volume. Combined with the novel method of post-objective scanning, this design can be scaled down to millimeter dimensions. We derive the dual axes response from diffraction theory, and construct two tabletop prototypes to demonstrate the performance of this approach. We collect images from freshly excised biopsy specimens of human esophagus and transgenic mouse cerebellum expressing GFP. With horizontal cross-sectional images, we achieve 1 to 2 μm resolution and collect reflectance and fluorescence images. With vertical cross-sectional images, we achieve 4 to 5 μm resolution, dynamic range of 70 dB, and tissue penetration over 1 mm. An instrument miniaturized with this configuration could be used for in vivo cellular and molecular imaging.
Coloured Petri Nets: A High Level Language for System Design and Analysis (1993)

This paper describes how Coloured Petri Nets (CP-nets) have been developed - from being a promising theoretical model to being a full-fledged language for the design, specification, simulation, validation and implementation of large software systems (and other systems in which human beings and/or computers communicate by means of some more or less formal rules). First CP-nets are introduced by means of a small example and a formal definition of their structure and behaviour is presented. Then we describe how to extend CP-nets by a set of hierarchy constructs (allowing a hierarchical CP-net to consist of many different subnets, which are related to each other in a formal way). Next we describe how to analyse CP-nets, how to support them by various computer tools, and we also describe some typical applications. Finally, a number of future extensions are discussed (of the net model and the supporting software).
Reconstruction of uniform sensitivity emission image with partially known axial attenuation information in PET-CT scanners (2012)

In PET-CT the axial length of image reconstruction is defined by the CT scan, which delivers an axial extend-dependent radiation dose. The beginning and end scanning points for CT and therefore PET scans are typically chosen in such a way that the PET scan is performed with a particular number of beds. While PET bed overlapping is optimized to achieve uniform image sensitivity, the whole volume edge planes suffer from low sensitivity, since only direct plane LORs are available from the acquisition. This problem can be solved through object over scanning by additional bed acquisitions. This does not result in an additional PET radiation dose. Still, the edge planes will have lower sensitivity due to the absence of oblique LOR attenuation factors. ACFs are necessary for sensitivity restoration of oblique LORs and are accumulated over the attenuation map image beyond CT scanning points. Recent theoretical investigations concluded that both activity and attenuation distributions can be obtained from PET emission TOF data alone with knowledge of the sinogram scaling parameter. In this work we consider an easier problem for the above-mentioned application. ACFs, converted to 511 energy units, are partially known and scatter distribution is already estimated based on direct plane LORs. The iterative algorithm to reconstruct only the emission image, with estimation of partially unknown ACFs, is presented. The estimation of ACFs is a sub-product of emission activity reconstruction. The algorithm is of a similar complexity to commonly used ML-EM. Initial investigations of experimental data show that partial ACF knowledge restores attenuation information necessary for the uniform sensitivity of PET reconstructed volume edge planes.
Size variation of the M protein in group A streptococci. (1985)

In addition to the type-specific antigenic variation that is a well-known characteristic for the group A streptococcal M protein, we have now found that the M molecules vary with respect to their molecular size, both between M types and within an M type. By the use of an M6 monoclonal antibody, which crossreacts with 20 different M protein types, and antibodies to the N-acetyl glucosamine determinant of the cell wall, we have been able to identify the M protein molecules released from the streptococcal cell wall with muralytic enzymes, particularly group C phage-associated lysin. Immunoblot analysis of the cell extract identified M protein molecules bound to various cell wall fragments, suggesting a peptidoglycan linkage for the M molecule. M protein extracted from 20 different streptococcal serotypes revealed size variations from 41,000 to 80,000 in molecular weight. This extreme variation is unusual for related proteins. Similar size variations in the M molecule were also found in random clinical isolates of type 6 streptococci. No size change was seen in M6 protein isolated from: (a) strains within a limited epidemic, (b) a strain passaged in mice 192 times, and (c) a strain passaged in the laboratory for 156 generations, suggesting that the observed variation is not a rapid process. The results indicate that, within the broad limits observed in this study, the size of the M protein may not be critical to the antiphagocytic activity of the molecule.
Closing-Down Optimization for Single-Arm Cluster Tools Subject to Wafer Residency Time Constraints (2020)

A kind of facilities for wafer fabrication, cluster tools (CTs) need to close down to an idle state from time to time because of periodical maintenance and switches from one type of lots to another, which is called a normal close-down process (NCDP). It is crucial to optimize such a transient process since it tends to occur more and more frequently due to customization. Also, process modules (PMs) in CTs are known to be failure-prone. Once a PM failure occurs, a tool needs to close down to an idle state as well, which is different from NCDP and is called a failure close-down process (FCDP). With wafer residency time constraints (WRTCs) being imposed, close-down process optimization for such a tool is challenging, since one needs to not only finish this process as soon as possible but also meet WRTCs during this transient process. In order to tackle this problem, this article first introduces steady state scheduling problems. Then, with a presented backward robot task sequence, a linear programming model is first proposed to optimize NCDP. To deal with the PM failures, efficient PM failure response policies are formulated for the cases in which a PM fails. Then, four linear programs are proposed to optimize an FCDP. Finally, industrial case studies are given to show the usefulness of the proposed approaches.
CEST MRI Reporter Genes (2010)

In recent years, several reporter genes have been developed that can serve as a beacon for non-invasive magnetic resonance imaging (MRI). Here, we provide a brief summary of recent advances in MRI reporter gene technology, as well as detailed "hands-on" protocols for cloning, expression, and imaging of reporter genes based on chemical exchange saturation transfer (CEST).
Towards a Universal FPGA Matrix-Vector Multiplication Architecture (2012)

We present the design and implementation of a universal, single-bit stream library for accelerating matrix-vector multiplication using FPGAs. Our library handles multiple matrix encodings ranging from dense to multiple sparse formats. A key novelty in our approach is the introduction of a hardware-optimized sparse matrix representation called Compressed Variable-Length Bit Vector (CVBV), which reduces the storage and bandwidth requirements up to 43% (on average 25%) compared to compressed sparse row (CSR) across all the matrices from the University of Florida Sparse Matrix Collection. Our hardware incorporates a runtime-programmable decoder that performs on-the-fly-decoding of various formats such as Dense, COO, CSR, DIA, and ELL. The flexibility and scalability of our design is demonstrated across two FPGA platforms: (1) the BEE3 (Virtex-5 LX155T with 16GB of DRAM) and (2) ML605 (Virtex-6 LX240T with 2GB of DRAM). For dense matrices, our approach scales to large data sets with over 1 billion elements, and achieves robust performance independent of the matrix aspect ratio. For sparse matrices, our approach using a compressed representation reduces the overall bandwidth while also achieving comparable efficiency relative to state-of-the-art approaches.
Controlled dither in 90 nm digital to time conversion based direct digital synthesizer for spur mitigation (2010)

Dithering is used in many discrete to continuous value conversion functions to provide an effective fractional value. This paper reviews the application of dither to a digital-to-time converter (DTC) based digital synthesizer suitable for many common wireless communication systems. Measurements of a 90 nm CMOS implementation using a 5 bit DTC show extension to effective 8 bits.
Optimization of glucose feeding approaches for enhanced glucosamine and <i>N</i>-acetylglucosamine production by an engineered <i>Escherichia coli</i> (2011)

In this work, a recombinant Escherichia coli was constructed by overexpressing glucosamine (GlcN) synthase and GlcN-6-P N-acetyltransferase for highly efficient production of GlcN and N-acetylglucosamine (GlcNAc). For further enhancement of GlcN and GlcNAc production, the effects of different glucose feeding strategies including constant-rate feeding, interval feeding, and exponential feeding on GlcN and GlcNAc production were investigated. The results indicated that exponential feeding resulted in relatively high cell growth rate and low acetate formation rate, while constant feeding contributed to the highest specific GlcN and GlcNAc production rate. Based on this, a multistage glucose supply approach was proposed to enhance GlcN and GlcNAc production. In the first stage (0-2 h), batch culture with initial glucose concentration of 27 g/l was conducted, whereas the second culture stage (2-10 h) was performed with exponential feeding at μ (set) = 0.20 h⁻¹, followed by feeding concentrated glucose (300 g/l) at constant rate of 32 ml/h in the third stage (10-16 h). With this time-variant glucose feeding strategy, the total GlcN and GlcNAc yield reached 69.66 g/l, which was enhanced by 1.59-fold in comparison with that of batch culture with the same total glucose concentration. The time-dependent glucose feeding approach developed here may be useful for production of other fine chemicals by recombinant E. coli.
Regulation of the Human FcεRI α-Chain Distal Promoter (2003)

The alpha-chain of the high affinity receptor for IgE (Fc epsilon RI) is essential for cell surface expression of Fc epsilon RI and binding of the IgE Ab. The human alpha-chain gene possesses two promoters: the proximal promoter, which is highly conserved with that of rodent; and the distal promoter, the structure and role of which are largely unknown. Transcriptional regulation of the alpha-chain distal promoter was investigated in this study. Transient reporter assay revealed critical region for transcription activity located within -27/-17. EMSA identified Elf-1, YY1, and PU.1 as transcription factors binding to this region. In contrast to the proximal promoter, which was trans-activated by YY1 and PU.1, these transcription factors exhibited repressive function on this promoter. Addition of IL-4 caused a marked increase in transcription from the distal promoter and subsequently increased the intracellular production of the alpha-chain. These results indicate that IL-4-dependent up-regulation of the human alpha-chain was due to enhancement of distal promoter activity and suggests that the two promoters have different regulatory mechanisms for alpha-chain expression.
A novel analytical approach for the simultaneous measurement of nitrate and DOC in soil water (2020)

Abstract. In this paper, we present a novel approach, enabling the measurement of nitrate concentrations in natural soil porewater containing natural soil dissolved organic carbon (DOC). The method is based on UV absorbance spectroscopy, combined with fluorescence spectroscopy, for simultaneous analysis of DOC and nitrate concentrations. The analytical procedure involves deduction of the absorption caused by the DOC from the total absorbance in the UV range that is attributed to both DOC and nitrate in the water solution. The analytical concept has been successfully tested in soil water samples obtained from five agricultural sites, as well as in water samples obtained from a commercial hummus soil mixture. We believe that the new analytical concept can provide a scientific foundation for developing a sensor for real-time nitrate concentration measurements in agricultural soils. As such, it can play a significant role in reducing nitrate pollution in water resources, optimizing input application in agriculture, and decreasing food production costs.
Spectrophotometric intracutaneous analysis: a new technique for imaging pigmented skin lesions (2002)

This first clinical trial with SIAscopy has yielded very promising results and delivers new, useful information to the clinician diagnosing pigmented skin lesions.
Pseudomorphic growth of Ge<i>x</i>Si1−<i>x</i> on silicon by molecular beam epitaxy (1984)

GexSi1−x layers are grown on Si substrates over the full range of alloy compositions at temperatures from 400–750 °C by means of molecular beam epitaxy. At a given growth temperature films grow in a smooth, two-dimensional manner up to a critical germanium fraction xc. Beyond xc growth is rough. xc increases from 0.1 at 750 °C to 1.0 at ∼550 °C. Rutherford ion backscattering measurements indicate good crystallinity over a wide range of growth conditions. Transmission electron microscopy reveals that in thin films, the lattice mismatch between the GexSi1−x and Si layers can be accommodated by lattice distortion rather than by misfit dislocation formation. This pseudomorphic growth condition can persist to alloy thicknesses as large as l/4 μm.
Reduction of threading dislocation density in GaN using an intermediate temperature interlayer (2000)

GaN thin films with a reduced threading dislocation density have been produced by organometallic vapor phase epitaxy using an intermediate temperature interlayer. A description of the growth process is presented with characterization results. Reduction of the dislocation density was obtained by insertion of a single thin interlayer grown at an intermediate temperature after the initial growth at high temperature. A large percentage of the threading dislocations present in the first GaN epilayer are found to bend in the interlayer and do not propagate in the top layer grown at higher temperature in a lateral growth mode.
Efficient writing of Bragg gratings through the coating of various optical fibers (2014)

We report on the efficient direct inscription through the polymer coating of fundamental order fiber Bragg gratings (FBGs) with high refractive index modulation. This direct inscription was performed through fiber jackets made of various polymers including acrylate, polyimide and silicone, for optical fiber diameters ranging from 50 to 250 µm and for various glass compositions such as H2-loaded and unloaded germanosilicate, pure silica, fluorides and chalcogenides.
ASPHALTENE CHARACTERISATION USING SPECTRAL ANALYSIS SYSTEM (2004)

Asphaltenes are the heaviest hydrocarbon component of crude oil and remain in colloidal suspension under reservoir temperature and pressure conditions. These materials may flocculate and deposit as a result of pressure, temperature and compositional changes, and consequently, disrupt production operations. This disruption can have severe implications, particularly in an offshore subsea environment. In these circumstances, it is imperative to understand the fundamental behaviour of asphaltenes prior to the development phase of any field under consideration. In this paper, we present a novel methodology to understand the thermodynamic asphaltene instability conditions using near infrared and spectral analysis system (SAS) techniques. Using the SAS technique, we were able to estimate the asphaltene particle size and growth behaviour as functions of pressure and time. Asphaltene particle size determined at the onset of asphaltene flocculation is in the order of 0.25 µm for a pressure-compensated sample. On the other hand, the asphaltene particle size is determined to be about 0.8 µm at the onset pressure using a conventional sample. Results also indicate that the particles from the pressure-compensated sample had a slower initial growth rate compared to the particles growth rate estimated from the non-pressure compensated sample. These results demonstrate the importance of representative sampling on asphaltene characterisation.
Design of a High Power Microwave Applicator for the Control of Insects in Stored Products (2003)

Recent tests of infested, freely flowing, hard red wheat, in a 28GHz microwave applicator indicate that abounding energy input of 56.8 J/g will produce a mortality of 99% for the least vulnerable species and agelevel of each of the three major grain pests tested, i.e. hard red wheat, Triticum aestivum (L.), infested withpupae, young larvae and eggs of the rice weevil Sitophilus oryzae (L), the red flour beetle Triboliumcastaneum (Herbst), and the lesser grain borer Rhizopertha dominica (F.). A 200kW prototype unit is nowbeing developed for testing at throughput rate of 24 tonne/h. Technical specifications for this unit aredescribed herein.
Hybrid Molecule–Nanocrystal Photon Upconversion Across the Visible and Near-Infrared (2015)

The ability to upconvert two low energy photons into one high energy photon has potential applications in solar energy, biological imaging, and data storage. In this Letter, CdSe and PbSe semiconductor nanocrystals are combined with molecular emitters (diphenylanthracene and rubrene) to upconvert photons in both the visible and the near-infrared spectral regions. Absorption of low energy photons by the nanocrystals is followed by energy transfer to the molecular triplet states, which then undergo triplet-triplet annihilation to create high energy singlet states that emit upconverted light. By using conjugated organic ligands on the CdSe nanocrystals to form an energy cascade, the upconversion process could be enhanced by up to 3 orders of magnitude. The use of different combinations of nanocrystals and emitters shows that this platform has great flexibility in the choice of both excitation and emission wavelengths.
Surface passivation: a new way to reduce self-output in LiMn{sub 2}O{sub 4}/Li lithium ion rechargeable batteries; Passivation de surface: une nouvelle voie pour reduire l`autodecharge dans les batteries rechargeables a ions lithium LiMn{sub 2}O{sub 4}/Li (1996)

The new generation of performing rechargeable lithium-ion batteries (``rocking-chair``-type) are penalized by important self-output phenomena linked with the use of highly oxidizing positive electrodes. In order to limit this problem in LiMn{sub 2}O{sub 4}/C batteries, two different passivation techniques were used in order to limit the surface contact between the positive electrode and the electrolyte. Thanks to these treatments, a significant reduction of the percentage of irreversible capacity losses is effectively observed. (J.S.) 3 refs.
Improving virtual machine performance using a cross-run profile repository (2005)

Virtual machines for languages such as the Java programming language make extensive use of online profiling and dynamic optimization to improve program performance. But despite the important role that profiling plays in achieving high performance, current virtual machines discard a program's profile data at the end of execution, wasting the opportunity to use past knowledge to improve future performance. In this paper, we present a fully automated architecture for exploiting cross-run profile data in virtual machines. Our work addresses a number of challenges that previously limited the practicality of such an approach.We apply this architecture to address the problem of selective optimization, and describe our implementation in IBM's J9 Java virtual machine. Our results demonstrate substantial performance improvements on a broad suite of Java programs, with the average performance ranging from 8.8% -- 16.6% depending on the execution scenario.
Cytosolic 5′‐nucleotidase 1A autoimmunity in sporadic inclusion body myositis (2012)

Autoantibodies against cN1A are common in and highly specific to IBM among muscle diseases, and may provide a link between IBM's dual processes of autoimmunity and myodegeneration. Blood diagnostic testing is feasible and should improve early and reliable diagnosis of IBM.
Delta opioidmimetic antagonists: prototypes for designing a new generation of ultraselective opioid peptides. (1995)

Dmt-Tic opioidmimetic peptides represent a highly potent class of opioid peptide antagonists with greater potency than the nonopioid delta antagonist naltrindole and have potential application as clinical and therapeutic compounds.
Azo-Functionalized Silk as a Biocompatible Material for Low Power Holography and Nonlinear Optics (2010)

Azobenzene modified silk, a biocompatible material suitable for applications in biomedicine is shown to display photo-effects such as optically induced birefringence, suitability as a holographic recording material and photoinduction of surface relief features.
Accurate Resampling of Top-<inline-formula> <tex-math notation="LaTeX">$k$ </tex-math> </inline-formula> Monitoring Reports Using Unreported Residual Resource Consumption (2018)

Top-k reports are compound metrics that provide useful information when diagnosing problems in a system, e.g., to identify persistent CPU usage by a process. In large systems, these reports are collected at regular intervals and need to be resampled to reduce the bitrate of the data, to answer user queries for different sampling periods, or to save space and make it possible to keep historical data for long term performance analysis. However, resampling top-k reports, i.e., aggregating several reports collected for small time intervals into a single top-k report can introduce inaccuracies. For example, a process that consistently uses CPU over the aggregation interval but is not included in the short term top-k reports will be missing from the aggregated report. In this paper, we present an algorithm that collects top-k reports at regular intervals and can aggregate them with little or no error. This is accomplished by including residual resource consumption of unreported, but potentially significant entities in the top-k reports, and using these residual values during aggregation. We show different approaches to including residual resource consumption in individual top-k reports, analyze the error introduced, the parameters with which the algorithm's efficiency can be tuned, and demonstrate the effectiveness of the algorithm in a real-world scenario.
An analytical iterative statistical algorithm for image reconstruction from projections (2014)

Abstract The main purpose of the paper is to present a statistical model-based iterative approach to the problem of image reconstruction from projections. This originally formulated reconstruction algorithm is based on a maximum likelihood method with an objective adjusted to the probability distribution of measured signals obtained from an x-ray computed tomograph with parallel beam geometry. Various forms of objectives are tested. Experimental results show that an objective that is exactly tailored statistically yields the best results, and that the proposed reconstruction algorithm reconstructs an image with better quality than a conventional algorithm with convolution and back-projection.