gebhart/patrepeval huggingface dataset:
X’tal Cube PET Detector Composed of a Stack of Scintillator Plates Segmented by Laser Processing (2014)

We have developed a three-dimensional (3-D) position-sensitive radiation detector named X'tal cube, which can be applied to a PET detector. The X'tal cube is composed of a scintillation crystal block and multi-pixel photon counters (MPPCs). The crystal block is segmented three-dimensionally into small cubes by optical discontinuity (3-D segmentation) and no reflector is inserted inside. Scintillation light originating in a segment then spreads three-dimensionally so that the MPPCs are set on all six surfaces of the crystal block to detect the light. Regarding the 3-D segmentation of the crystal block, we have already succeeded in getting the segmentation inside of a monolithic scintillator block by a laser processing technique instead of the general way, arranging small cubic scintillator elements into a 3-D array. We have confirmed that utilizing the laser processing technique not only eliminates the difficulty of handling the small scintillator elements but also improves detector performance. As a new trial, we considered fabrication of the crystal block by stacking the scintillator plates which were segmented two-dimensionally by the laser processing technique (2-D segmentation). Plates are also easier to handle and for the laser processing, 2-D segmentation is simpler than 3-D segmentation. In this study, we prepared the X'tal cube with the scintillator plates (Plate-XC) and evaluated its performance to confirm its technical feasibility. For the Plate-XC, we segmented 18 mm × 18 mm × 2.0 mm LYSO plates two-dimensionally by laser processing so as to make a 9 × 9 array of 2.0 mm × 2.0 mm segments. The crystal block was composed of 9 stacked LYSO plates without using coupling material but with air gaps. The Plate-XC showed sufficient crystal identification performance when 662 keV gamma-rays were irradiated. Furthermore, to understand the characteristics of the Plate-XC, we also analyzed the scintillation light distribution in the crystal block. Results indicated that light spread from outer segments was influenced by the segment boundary conditions, air gaps or laser-processed gaps, while the spread from the center segment did not seem to have such an influence. Regarding energy performance, we obtained around 10% energy resolution for the outer segments as well as for the center segment.
Identification of amplified restriction fragment polymorphism (AFLP) markers tightly linked to the tomato <i>Cf‐9</i> gene for resistance to <i>Cladosporium fulvum</i> (1995)

Using the technique of amplified restriction fragment polymorphism (AFLP) analysis, and bulked segregant pools from F2 progeny of the cross Lycopersicon esculentum (Cf9) x L. pennellii, approximately 42,000 AFLP loci for tight linkage to the tomato Cf-9 gene for resistance to Cladosporium fulvum have been screened. Analysis of F2 recombinants identified three markers which co-segregated with Cf-9. The Cf-9 gene has recently been isolated by transposon tagging using the maize transposon Dissociation (Ds). Analysis of plasmid clones containing Cf-9 shows that two of these markers are located on opposite sides of the gene separated by 15.5 kbp of intervening DNA. AFLP analysis provides a rapid and efficient technique for detecting large numbers of DNA markers and should expedite plant gene isolation by positional cloning and the construction of high-density molecular linkage maps of plant genomes.
Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals (2017)

Naturally, many aerobic organisms degrade lignin-derived aromatics through conserved intermediates including protocatechuate and catechol. Employing this microbial approach offers a potential solution for valorizing lignin into valuable chemicals for a potential lignocellulosic biorefinery and enabling bioeconomy. In this study, two hybrid biochemical routes combining lignin chemical depolymerization, plant metabolic engineering, and synthetic pathway reconstruction were demonstrated for valorizing lignin into value-added products. In the biochemical route 1, alkali lignin was chemically depolymerized into vanillin and syringate as major products, which were further bio-converted into cis, cis-muconic acid (ccMA) and pyrogallol, respectively, using engineered Escherichia coli strains. In the second biochemical route, the shikimate pathway of Tobacco plant was engineered to accumulate protocatechuate (PCA) as a soluble intermediate compound. The PCA extracted from the engineered Tobacco was further converted into ccMA using the engineered E. coli strain. This study reports a direct process for converting lignin into ccMA and pyrogallol as value-added chemicals, and more importantly demonstrates benign methods for valorization of polymeric lignin that is inherently heterogeneous and recalcitrant. Our approach also validates the promising combination of plant engineering with microbial chassis development for the production of value added and speciality chemicals.
CFO mitigation using adaptive frequency-domain decision feedback equalization for uplink SC-FDMA (2015)

To mitigate Inter-Carrier Interference (ICI) due to large Carrier Frequency Offset (CFO) in an uplink Single- Carrier Frequency Division Multiple Access system, a 3-tap Adaptive Frequency Domain Decision Feedback Equalizer (AFD- DFE) is designed in this work by exploiting the banded and sparse structure of the equivalent channel matrix. The block Recursive Least Squares (RLS) algorithm is used for adaptation and both the feedforward and feedback filters are implemented in the frequency-domain. Consequently, the complexity of the block RLS, by exploiting the matrix structure in the frequency-domain, is reduced substantially when compared to its time-domain counterpart. Ultimately, it will be shown that the proposed AFD- DFE exhibits significant excellent performance improvement when compared to a 1-tap AFD-DFE while still enjoying a low computational complexity.
Inline Pump Sharing Architecture for Remotely-Pumped Pre- and Post-Amplifiers (2007)

A new transmission link configuration with remote Er post- and pre-amplifiers where pump power is shared between a pair of fibers carrying traffic in opposite directions is proposed. A budget increase of >4dB is demonstrated.
Interspecies gene transfer provides soybean resistance to a fungal pathogen (2015)

Fungal pathogens pose a major challenge to global crop production. Crop varieties that resist disease present the best defence and offer an alternative to chemical fungicides. Exploiting durable nonhost resistance (NHR) for crop protection often requires identification and transfer of NHR-linked genes to the target crop. Here, we identify genes associated with NHR of Arabidopsis thaliana to Phakopsora pachyrhizi, the causative agent of the devastating fungal disease called Asian soybean rust. We transfer selected Arabidopsis NHR-linked genes to the soybean host and discover enhanced resistance to rust disease in some transgenic soybean lines in the greenhouse. Interspecies NHR gene transfer thus presents a promising strategy for genetically engineered control of crop diseases.
Nitrated Indenoisoquinolines as Topoisomerase I Inhibitors:  A Systematic Study and Optimization (2007)

The biological activity of indenoisoquinoline topoisomerase I (Top1) inhibitors can be greatly enhanced depending on the choice of substituents on the aromatic rings and lactam side chain. Previously, it was discovered that a 3-nitro group and a 9-methoxy group afforded enhanced biological activity. In the present investigation, indenoisoquinoline analogues were systematically prepared using combinations of nitro groups, methoxy groups, and hydrogen atoms in an effort to understand the contribution of each group toward cytotoxicity and Top1 inhibition. Analysis of the biological results suggests that the nitro group is important for Top1 inhibition and the methoxy group improves cytotoxicity. In addition, previously identified structure-activity relationships were utilized to select favorable lactam side chain functionalities for incorporation on the aromatic skeleton of analogues in this study. As a result, this investigation has provided optimal Top1 inhibitors equipotent to camptothecin that demonstrate low nanomolar cytotoxicities toward cancer cells.
Target Cell Cyclophilin A Modulates Human Immunodeficiency Virus Type 1 Infectivity (2004)

The peptidyl-prolyl isomerase cyclophilin A (CypA) increases the kinetics by which human immunodeficiency virus type 1 (HIV-1) spreads in tissue culture. This was conclusively demonstrated by gene targeting in human CD4(+) T cells, but the role of CypA in HIV-1 replication remains unknown. Though CypA binds to mature HIV-1 capsid protein (CA), it is also incorporated into nascent HIV-1 virions via interaction with the CA domain of the Gag polyprotein. These findings raised the possibility that CypA might act at multiple steps of the retroviral life cycle. Disruption of the CA-CypA interaction, either by the competitive inhibitor cyclosporine (CsA) or by mutation of CA residue G89 or P90, suggested that producer cell CypA was required for full virion infectivity. However, recent studies indicate that CypA within the target cell regulates HIV-1 infectivity by modulating Ref1- or Lv1-mediated restriction. To examine the relative contribution to HIV-1 replication of producer cell CypA and target cell CypA, we exploited multiple tools that disrupt the HIV-1 CA-CypA interaction. These tools included the drugs CsA, MeIle(4)-CsA, and Sanglifehrin; CA mutants exhibiting decreased affinity for CypA or altered CypA dependence; HeLa cells with CypA knockdown by RNA interference; and Jurkat T cells homozygous for a deletion of the gene encoding CypA. Our results clearly demonstrate that target cell CypA, and not producer cell CypA, is important for HIV-1 CA-mediated function. Inhibition of HIV-1 infectivity resulting from virion production in the presence of CsA occurs independently of the CA-CypA interaction or even of CypA.
A High-Resolution Planar Hall Effect Magnetometer for Ultra-Low Frequencies (2016)

Recent reports have demonstrated field resolutions of planar Hall effect magnetometers in the picotesla range. Here, we report a significant improvement in the field resolution of these sensors by decreasing their preamplifier white noise and the sensing element 1/f noise. We design, build, and test a miniature transformer-matched amplifier with a record noise level of 200 pV/√Hz and improve the fabrication process of the sensing element to increase its volume and reduce its associated 1/f noise. The magnetometer exhibits a magnetic resolution of ~ 200 pT/√Hz at 1 Hz and ~ 600 pT/√Hz at 0.1 Hz. These values are threefold better than previously reported results. The obtained resolution may enable applications for which high-end magnetometers, such as fluxgates, are currently used. We discuss routes for the further improvement of the magnetic field resolution.
Isolation of Fibroblast Growth Factor from Bovine Adrenal Gland: Physicochemical and Biological Characterization* (1986)

The angiogenic growth factors present in the bovine adrenal gland have been purified by a combination of differential salt precipitation, ion exchange chromatography, and heparin-Sepharose chromatography. They consist of 2 single chain polypeptides with apparent mol wt of 16,000 and 15,000. Sequence analysis of the first 14 residues of both peptides identified the sequences as Pro-Ala-Leu-Pro-Glu-Asp-Gly-Gly-Ser-Gly-Ala-Phe-Pro-Pro for 1 of the peptides and His-Phe-Lys-Asp-Pro-Lys-Arg-Leu-Tyr-x-Lys-Asn-Gly-Gly for the other. The first sequence is identical to residues 1-14 of bovine pituitary and brain fibroblast growth factor (FGF), while the second is identical to residues 1-14 of the corpus luteum (CL) FGF, which is an amino-terminally truncated form of FGF and is otherwise similar, if not identical, to FGF. The biological activity of adrenal FGF is indistinguishable from that of pituitary or brain FGF and CL FGF. They are highly active in triggering the proliferation of culture bovine vascular endothelial cells derived from either large vessels (aortic arch) or CL and adrenal cortex capillaries (half-maximal stimulation at 20-40 pg/ml and saturation at 400-600 pg/ml). In vivo implants containing 50 ng to 1 microgram adrenal-derived growth factors stimulate neovascularization in the chorioallantoic membrane of the chick embryo. In addition to being mitogenic for vascular endothelial cells, adrenal FGFs stimulate the proliferation of a wide variety of mesoderm- and neuroectoderm-derived cells, including vascular smooth muscle cells, granulosa and adrenal cortex cells, rabbit costal chondrocytes, and corneal endothelial cells.
Navigating a 2D Virtual World Using Direct Brain Stimulation (2016)

Can the human brain learn to interpret inputs from a virtual world delivered directly through brain stimulation? We answer this question by describing the first demonstration of humans playing a computer game utilizing only direct brain stimulation and no other sensory inputs. The demonstration also provides the first instance of artificial sensory information, in this case depth, being delivered directly to the human brain through noninvasive methods. Our approach utilizes transcranial magnetic stimulation (TMS) of the human visual cortex to convey binary information about obstacles in a virtual maze. At certain intensities, TMS elicits visual percepts known as phosphenes, which transmits information to the subject about their current location within the maze. Using this computer-brain interface (CBI), five subjects successfully navigated an average of 92% of all the steps in a variety of virtual maze worlds. They also became more accurate in solving the task over time. These results suggest that humans can learn to utilize information delivered directly and noninvasively to their brains to solve tasks that cannot be solved using their natural senses, opening the door to human sensory augmentation and novel modes of human-computer interaction.
Watermarking spot colors in packaging (2015)

In January 2014, Digimarc announced Digimarc® Barcode for the packaging industry to improve the check-out efficiency and customer experience for retailers. Digimarc Barcode is a machine readable code that carries the same information as a traditional Universal Product Code (UPC) and is introduced by adding a robust digital watermark to the package design. It is imperceptible to the human eye but can be read by a modern barcode scanner at the Point of Sale (POS) station. Compared to a traditional linear barcode, Digimarc Barcode covers the whole package with minimal impact on the graphic design. This significantly improves the Items per Minute (IPM) metric, which retailers use to track the checkout efficiency since it closely relates to their profitability. Increasing IPM by a few percent could lead to potential savings of millions of dollars for retailers, giving them a strong incentive to add the Digimarc Barcode to their packages. Testing performed by Digimarc showed increases in IPM of at least 33% using the Digimarc Barcode, compared to using a traditional barcode. A method of watermarking print ready image data used in the commercial packaging industry is described. A significant proportion of packages are printed using spot colors, therefore spot colors needs to be supported by an embedder for Digimarc Barcode. Digimarc Barcode supports the PANTONE spot color system, which is commonly used in the packaging industry. The Digimarc Barcode embedder allows a user to insert the UPC code in an image while minimizing perceptibility to the Human Visual System (HVS). The Digimarc Barcode is inserted in the printing ink domain, using an Adobe Photoshop plug-in as the last step before printing. Since Photoshop is an industry standard widely used by pre-press shops in the packaging industry, a Digimarc Barcode can be easily inserted and proofed.
Intracellular Viral Processing, Not Single-Stranded DNA Accumulation, Is Crucial for Recombinant Adeno-Associated Virus Transduction (2004)

Adeno-associated virus (AAV) is a unique gene transfer vector which takes approximately 4 to 6 weeks to reach its expression plateau. The mechanism for this slow-rise expression profile was proposed to be inefficient second-strand DNA synthesis from the input single-stranded (ss) DNA viral genome. In order to clarify the status of ss AAV genomes, we generated AAV vectors labeled with bromodeoxyuridine (BrdU), a nucleotide analog that can be incorporated into the AAV genome and packaged into infectious virions. Since BrdU-DNA can be detected only by an anti-BrdU antibody when DNA is in an ss form, not in a double-stranded (ds) form, ss AAV genomes with BrdU can be readily tracked in situ. Although ss AAV DNA was abundant by Southern blot analysis, free ss AAV genomes were not detectable after AAV transduction by this new detection method. Further Southern blot analysis of viral DNA and virions revealed that ss AAV DNA was protected within virions. Extracted cellular fractions demonstrated that viral particles in host cells remained infectious. In addition, a significant amount of AAV genomes was degraded after AAV transduction. Therefore, we conclude that the amount of free ss DNA is not abundant during AAV transduction. AAV transduction is limited by the steps that affect AAV ss DNA release (i.e., uncoating) before second-strand DNA synthesis can occur. AAV ss DNA released from viral uncoating is either converted into ds DNA efficiently or degraded by cellular DNA repair mechanisms as damaged DNA. This study elucidates a mechanism that can be exploited to develop new strategies to improve AAV vector transduction efficiency.
Design Considerations for Vanadium Redox Flow Battery (1991)

Materials and design of the vanadium redox battery are different from most conventional batteries. Conductive plastics make it light weight and easy to manufacture while the modular design allows flexibility and many ways of integrating the battery. The vanadium redox battery will provide advantages for stationary applications such as stand-by power units, load levelling, storage units for solar electricity as well as mobile applications in vehicles for recreational, industrial and city transports wherever pollution-free operation is required.
A novel high-speed piezoelectric deformable varifocal mirror for optical applications (2003)

We describe the characteristics of a microelectromechanical deformable optical component: a parabolic focusing mirror having a focal length that is controlled by piezoelectric actuation of thin-film PZT. Devices of two different sizes were tested and have resonant frequencies in the low MHz range, nominal focal lengths between 1500 and 2000 /spl mu/m and numerical apertures of approximately 0.10 and 0.05. Tuning ranges of several hundred microns have been demonstrated. Finite element modeling is described and compared to measured results. The equations required for device scaling are provided to show some of the tradeoffs that can be made between aperture size, mechanical bandwidth and focal length tuning range.
Dynamics of domain wall depinning driven by a combination of direct and pulsed currents (2008)

The current-induced depinning of a domain wall from an artificial pinning site is investigated in Permalloy nanowires. The depinning probability exhibits an oscillatory dependence on the current pulse length, which is, surprisingly, reduced when a dc current of the same polarity is added to the current pulse. By contrast, the depinning probability increases when dc and pulsed currents have opposite polarities even though the total current flowing though the device is smaller. These results are understood within an analytical one-dimensional model of the domain wall dynamics.
Numerical Study of Microwave Scattering in Breast Tissue via Coupled Dielectric and Elastic Contrasts (2008)

A computational investigation of microwave scattering in mechanically (or acoustically) excited breast tissue is conducted to explore the feasibility of combining dielectric and elastic properties contrasts to enhance breast cancer detection. The mechanical excitation induces tissue-dependent displacements in the heterogeneous breast interior, which modulate the scattered microwave signals. Sheet boundary conditions are implemented using the finite-difference time-domain (FDTD) method to efficiently compute the Doppler component of the scattered microwave signals. Simulation results for a 2D numerical phantom testbed demonstrate increased microwave scattering contrast between malignant and normal fibroglandular inclusions when elastic properties are exploited.
Active Compressive Sensing via Pyroelectric Infrared Sensor for Human Situation Recognition (2016)

Conventional pyroelectric infrared (PIR) motion sensors use paired elements for the detection of moving targets. This method makes them incapable of measuring thermal signals from static targets. We need an active sensor that can detect static thermal subjects. This paper presents our design of active PIR sensors. The proposed PIR sensing systems can actively detect static thermal targets by using three methods that are suitable to different applications: 1) a sensor that can be rotated by a self-controlled servo motor for the detection of moving or static thermal subjects nearby; 2) a sensor that is equipped with a mask for low-complexity posture recognition; and 3) a sensor that can be worn on the wrist for the recognition of surrounding subjects (this sensor is especially useful for blind users). Compressive sensing (CS) theory indicates that random down-sampling method can capture more accurate information of the original signal than the evenly spaced sampling. Based on CS theory, we have developed the random sampling structures for the active PIR systems, and have built a statistical feature space for human scenario recognition. The experimental results demonstrate that the active sensing system can efficiently measure the static thermal targets, and the random sampling scheme has a better recognition performance than the even sampling scheme.
LiDARsim: Realistic LiDAR Simulation by Leveraging the Real World (2020)

We tackle the problem of producing realistic simulations of LiDAR point clouds, the sensor of preference for most self-driving vehicles. We argue that, by leveraging real data, we can simulate the complex world more realistically compared to employing virtual worlds built from CAD/procedural models. Towards this goal, we first build a large catalog of 3D static maps and 3D dynamic objects by driving around several cities with our self-driving fleet. We can then generate scenarios by selecting a scene from our catalog and "virtually" placing the self-driving vehicle (SDV) and a set of dynamic objects from the catalog in plausible locations in the scene. To produce realistic simulations, we develop a novel simulator that captures both the power of physics-based and learning-based simulation. We first utilize raycasting over the 3D scene and then use a deep neural network to produce deviations from the physics-based simulation, producing realistic LiDAR point clouds. We showcase LiDARsim's usefulness for perception algorithms-testing on long-tail events and end-to-end closed-loop evaluation on safety-critical scenarios.
Virus-Induced Gene Silencing (2003)

In the postgenomic era, large-scale functional genomic approaches are necessary for converting sequence information into functional information. A para-genetic approach, called virus-induced gene silencing (VIGS), offers a rapid means of gaining insight into gene function in plants. VIGS system could be used to suppress endogenous gene expression by infecting plants with a recombinant virus vector (VIGS vector) carrying host-derived sequence. Here, we describe the use of tobacco rattle virus (TRV)-based VIGS technique to study gene function in Nicotiana benthamiana and tomato.