gebhart/patrepeval huggingface dataset:
Modification of Flower Colour using Genetic Engineering (1994)

(1994). Modification of Flower Colour using Genetic Engineering. Biotechnology and Genetic Engineering Reviews: Vol. 12, No. 1, pp. 63-88.
Engineering resistance against <i>Tomato yellow leaf curl virus</i> via the CRISPR/Cas9 system in tomato (2018)

CRISPR/Cas systems confer molecular immunity against phages and conjugative plasmids in prokaryotes. Recently, CRISPR/Cas9 systems have been used to confer interference against eukaryotic viruses. Here, we engineered Nicotiana benthamiana and tomato (Solanum lycopersicum) plants with the CRISPR/Cas9 system to confer immunity against the Tomato yellow leaf curl virus (TYLCV). Targeting the TYLCV genome with Cas9-single guide RNA at the sequences encoding the coat protein (CP) or replicase (Rep) resulted in efficient virus interference, as evidenced by low accumulation of the TYLCV DNA genome in the transgenic plants. The CRISPR/Cas9-based immunity remained active across multiple generations in the N. benthamiana and tomato plants. Together, our results confirmed the efficiency of the CRISPR/Cas9 system for stable engineering of TYLCV resistance in N. benthamiana and tomato, and opens the possibilities of engineering virus resistance against single and multiple infectious viruses in other crops.
Optimal Link Weights for Maximizing QoS Traffic (2007)

In this paper we explore the optimal weight setting to maximize QoS traffic admissible to a hop-by-hop routing network (such as the Internet). We try to answer the following questions: (1) How much ingress and egress traffic can be admitted to a hop-by-hop routing network (such as the Internet) without causing congestion of any link, and (2) what is the optimal link weight setting that can maximize the amount of traffic admissible to the network? We first present a mixed-integer programming formulation to compute the optimal link weights that can maximize the ingress and egress QoS traffic admissible to a hop-by-hop routing network. We then present a heuristic search algorithm to find the optimal weights. The heuristic algorithm has a performance comparable to the optimal link weights, but its computation complexity is much lower.
Learning Concept Templates from Web Images to Query Personal Image Databases (2007)

With the proliferation of digital cameras, the size of personal media data such as digital photos, videos, etc. has grown extremely large. The personal nature of the data has heightened the demands for a media management system on personal desktops. Existing solutions for media management target mostly server-based Web databases and rely on extensive metadata (i.e., labels) generation to aid retrieval. Personal media databases, on the other hand, have very limited labels generated by the end users themselves. This paper introduces a method for learning concept templates from web images to query personal image databases. The proposed method has the advantage of leveraging Web resources to ease personal photo retrieval in order to avoid costly annotation of personal image databases.
SpoIIE Regulates Sporulation but Does Not Directly Affect Solventogenesis in <i>Clostridium acetobutylicum</i> ATCC 824 (2005)

Using gene expression reporter vectors, we examined the activity of the spoIIE promoter in wild-type and spo0A-deleted strains of Clostridium acetobutylicum ATCC 824. In wild-type cells, the spoIIE promoter is active in a transient manner during late solventogenesis, but in strain SKO1, where the sporulation initiator spo0A is disrupted, no spoIIE promoter activity is detectable at any stage of growth. Strains 824(pMSpo) and 824(pASspo) were created to overexpress spoIIE and to decrease spoIIE expression via antisense RNA targeted against spoIIE, respectively. Some cultures of strains 824(pMSpo) degenerated during fermentations by losing the pSOL1 megaplasmid and hence did not produce the solvents ethanol, acetone, and butanol. The frequent degeneration event was shown to require an intact copy of spoIIE. Nondegenerate cultures of 824(pMSpo) exhibited normal growth and solvent production. Strain 824(pASspo) exhibited prolonged solventogenesis characterized by increased production of ethanol (225%), acetone (43%), and butanol (110%). Sporulation in strains harboring pASspo was significantly delayed, with sporulating cells exhibiting altered morphology. These results suggest that SpoIIE has no direct effect on the control of solventogenesis and that the changes in solvent production in spoIIE-downregulated cells are mediated by effects on the cell during sporulation.
A method for the calibration of magnetic force microscopy tips (2000)

A method is presented for the analysis of magnetic force microscopy (MFM) measurements that allows the quantitative determination of the sample stray field. It is shown how measurements on an easily obtainable calibration sample can be used to calibrate the MFM measurement as a function of the wavelength of the sample stray field at the tip apex. It is demonstrated that the thus obtained MFM calibration can be used to determine the stray field distribution of the tip. Furthermore, the effect of the tip on the MFM imaging mechanism is analyzed by comparing it to some simple tip models. From the analysis, it is shown that the point–monopole and dipole models do not accurately describe the MFM imaging mechanism.
Acylhydrazones as Antifungal Agents Targeting the Synthesis of Fungal Sphingolipids (2018)

The incidence of invasive fungal infections has risen dramatically in recent decades. Current antifungal drugs are either toxic, likely to interact with other drugs, have a narrow spectrum of activity, or induce fungal resistance. Hence, there is a great need for new antifungals, possibly with novel mechanisms of action. Previously our group reported an acylhydrazone called BHBM that targeted the sphingolipid pathway and showed strong antifungal activity against several fungi. In this study, we screened 19 derivatives of BHBM. Three out of 19 derivatives were highly active against <i>Cryptococcus neoformans</i><i>in vitro</i> and had low toxicity in mammalian cells. In particular, one of them, called D13, had a high selectivity index and showed better activity in an animal model of cryptococcosis, candidiasis, and pulmonary aspergillosis. D13 also displayed suitable pharmacokinetic properties and was able to pass through the blood-brain barrier. These results suggest that acylhydrazones are promising molecules for the research and development of new antifungal agents.
Molecular basis of weak D expression in the Indian population and report of a novel, predominant variant <i>RHD</i> allele (2018)

We describe a major novel, variant RHD allele in Indians that can be easily identified routinely by implementing a simple genotyping assay. Although we may consider this variation as a weak partial D variant, further studies and observations are needed to confirm the same. These findings may contribute to improve significantly Rh blood group diagnostics in more than one billion Indians.
Optimizing computing costs using divisible load analysis (1998)

A bus oriented network where there is a charge for the amount of divisible load processed on each processor is investigated. A cost optimal processor sequencing result is found which involves assigning load to processors in nondecreasing order of the cost per load characteristic of each processor. More generally, one can trade cost against solution time. Algorithms are presented to minimize computing cost with an upper bound on solution time and to minimize solution time with an upper bound on cost. As an example of the use of this type of analysis, the effect of replacing one fast but expensive processor with a number of cheap but slow processors is also discussed. The type of questions investigated here are important for future computer utilities that perform distributed computation for some charge.
Geoacoustic modeling of the seafloor—Recent experimental work (1993)

Over the past decade a number of new techniques have been developed for measuring the geoacoustic properties of seafloor sediments. Several of these methods utilize sensors that are deployed on the seafloor and respond to seismic waves generated by different kinds of source including explosives and mechanical impact as well as the ambient pressure fluctuations generated by wave motion at the sea surface. Since the motion that is sensed at the seafloor is a combination of many different kinds of interface and body waves (i.e., Scholte waves, Love waves, p, sv, and sh refractions and reflections, etc.), inversion to obtain a geoacoustic model is a complex task that must be tailored to each individual experiment taking into account the bandwidth of the signal and the interaction between the various types of wave. This paper summarizes some of the recent field experiments and the methods that are being used to interpret the data. [Work supported by ONR codes 1125OA and 1125GG.]
Piezoelectric crystal composite for high frequency ultrasound application (2010)

Electromechanical coupling coefficient of piezoelectric materials determines the energy conversion efficiency between electrical and acoustic energies and vice versa. A high electromechanical coupling coefficient is essential to the performance of an ultrasound transducer. High frequency piezoelectric single crystal 1-3 composite was fabricated using etch-and-fill method. Crystal composite has superior piezoelectric properties compared to the monolithic single crystals. In addition, piezoelectric composites using PMN-PT binary crystal and PIN-PMN-PT ternary crystal were fabricated, with coupling coefficient greater than 0.8. Ternary piezoelectric crystals PIN-PMN-PT have improved thermal and electrical stability compared to the binary PMN-PT. Such improvements are useful especially for high frequency applications.
Time of Flight Measurements in Real-Time Ultrasound Signatures of Aluminum Spot Welds: An Image Processing Approach (2011)

Ultrasonic testing is one of the most popular non-destructive methods to determine the quality in spot welds. The next step of this technology is to be able to determine the quality while the weld is being made, this advance can have a great impact on the quality assurance of joints in materials like aluminum, where the spot welding process is a difficult task. In our approach, a state-of-the-art ultrasound transducer assembly is installed in one of the welding electrodes. Working in pulse-echo mode, the system collects A-scans of the waves passing through the welded plates in the direction perpendicular to the plate’s surface. A-scans are gated to allow stack-up front and back wall reflections to be recorded. Such setup has allowed the acquisition of real-time ultrasonic signatures composed of multiple A-scans for each spot weld. Eventually the signature should be processed to extract information about the weld quality. During the welding process temperature gradually increases within the aluminum plates; as sound speed in metals is inversely proportional to the temperature, the time of flight will increase during welding. The change in time of flight of the ultrasonic wave during the whole welding process is a good indicator of the heating rate in the weld and can be a good judge of weld quality. Unfortunately, electrode deterioration, industrial noises and pulse changes due to frequency dependent attenuation make signal detection a challenging task. To overcome this difficulty the system treats B-scan as an image instead of a set of separate A-scans. With such approach, the weak signal detection (in
ChemInform Abstract: Aromatase Inhibition by 5‐Substituted Pyrimidines and Dihydropyrimidines. (1988)

Abstract Reaction of 5‐lithio pyrimidine, prepared in situ from the corresponding 5‐bromo derivative (I), with the ketones (II) gives the pyrimidinyl carbinols (III).
Optical pulse shaping system based on aperture-coupled striplines for OMEGA pulse shaping applications (1999)

An optical pulse shaping system based on an aperture-coupled stripline electrical waveform generator is discussed. Shaped electrical and optical pulses have been produced. The measured pulse shapes agree well with our models.
Cooperative upconversion lasers and nonlinear dynamics (1992)

Here we describe a class of cw upconversion lasers in which inversion is due exclusively to cooperative interactions of rare earth ions in highly doped solids, resulting in unique opportunities for output wavelength agility, large upconversion factors, and high quantum efficiencies through nonlinear dynamics. We have isolated capabilities of the cooperative mechanism by performing experiments in Er:CaF 2 and Er:LiYF 4 with infrared pumping of the first Er 3+ resonance at 1.53 μm. At liquid helium temperatures, laser action at 544 nm was achieved in an astigmatically compensated, three-mirror cavity with 5% efficiency in LiYF 4 . The upconversion factor (ratio of pump to laser wavelength) was 2.81, to our knowledge the highest ever reported for cw upconversion lasers. At 77 K, laser action at 551 nm was observed. Surprisingly, output at both 544 and 551 nm was truly cw with cooperative pumping, unlike earlier green erbium lasers, which exhibited self-pulsing. Also at 77 K, near infrared laser action was obtained at 0.855 pm with exceptionally high efficiency in CaF 2 (28%) and LiYF 4 (20%) on self-quenching transitions. Successful demonstration of cw laser action on such transitions also suggests a means whereby quantum efficiencies may exceed unity. The lower laser level in such cases is the origin of cooperative pumping to the upper laser level, but also receives population as the result of stimulated emission. Hence population can be recycled for enhanced quantum efficiency. Additionally, population pulsations can occur and sustained oscillations in laser output have been observed in a cooperative erbium upconversion laser at 2.8 μm.
Viral Vascular Endothelial Growth Factor Plays a Critical Role in Orf Virus Infection (2000)

Infection by the parapoxvirus orf virus causes proliferative skin lesions in which extensive capillary proliferation and dilation are prominent histological features. This infective phenotype may be linked to a unique virus-encoded factor, a distinctive new member of the vascular endothelial growth factor (VEGF) family of molecules. We constructed a recombinant orf virus in which the VEGF-like gene was disrupted and show that inactivation of this gene resulted in the loss of three VEGF activities expressed by the parent virus: mitogenesis of vascular endothelial cells, induction of vascular permeability, and activation of VEGF receptor 2. We used the recombinant orf virus to assess the contribution of the viral VEGF to the vascular response seen during orf virus infection of skin. Our results demonstrate that the viral VEGF, while recognizing a unique profile of the known VEGF receptors (receptor 2 and neuropilin 1), is able to stimulate a striking proliferation of blood vessels in the dermis underlying the site of infection. Furthermore, the data demonstrate that the viral VEGF participates in promoting a distinctive pattern of epidermal proliferation. Loss of a functional viral VEGF resulted in lesions with markedly reduced clinical indications of infection. However, viral replication in the early stages of infection was not impaired, and only at later times did it appear that replication of the recombinant virus might be reduced.
Performance Improvement of a High Mobility Vehicular Communications System Using Fuzzy-Decision Viterbi Decoder (2006)

A fuzzy-decision Viterbi decoder is proposed for a dedicated short-range communications (DSRC) system to combat the effect of a time-varying fading channel. The performance of the DSRC system using the proposed fuzzy-decision Viterbi decoder is compared with both the hard-decision and soft-decision Viterbi decoder. The simulation results show that the gain in performance of the proposed fuzzy-decision Viterbi decoder with respect to the hard-decision and soft-decision Viterbi decoder is significantly increased
Structure-activity studies of vasoactive intestinal polypeptide. (1991)

This report explores the potential side-chain functional groups required for interaction of the bronchodilator neuropeptide, vasoactive intestinal peptide (VIP), with its receptor. The binding affinity and biological activity of native VIP have been found to be sensitive to the removal of amino- and carboxyl-terminal residues. This data suggests that elements within the entire primary sequence of the VIP molecule appear to be necessary for recognition by VIP receptors. The introduction of alanine residues substituted into the VIP molecule is utilized to probe for side-chain functional groups that are crucial for eliciting high receptor binding affinity in vitro and high biological potency in vivo. The VIP pharmacophore appears to be identical in guinea pig lung and human lung and consists of multiple binding sites most likely involving positions Asp3, Phe6, Thr7, Tyr10, Tyr22, and Leu23. These findings could be exploited to enhance the biological potency of VIP by increasing the binding energy at these positions.
Deep Feature Flow for Video Recognition (2016)

Deep convolutional neutral networks have achieved great success on image recognition tasks. Yet, it is non-trivial to transfer the state-of-the-art image recognition networks to videos as per-frame evaluation is too slow and unaffordable. We present deep feature flow, a fast and accurate framework for video recognition. It runs the expensive convolutional sub-network only on sparse key frames and propagates their deep feature maps to other frames via a flow field. It achieves significant speedup as flow computation is relatively fast. The end-to-end training of the whole architecture significantly boosts the recognition accuracy. Deep feature flow is flexible and general. It is validated on two recent large scale video datasets. It makes a large step towards practical video recognition.
Biocompatible Nickel-Prussian Blue@Silver Nanocomposites Show Potent Antibacterial Activities (2017)

Herein, we report a simple and cost-effective method for the synthesis of nickel-prussian blue@silver nanocomposites. The nanocomposite is highly stable and shows biocompatibility observed by <i>in vitro</i> assay and by <i>ex vivo</i> chicken embryonic angiogenesis assay. The nanocomposite exhibits profound antibacterial activity toward Gram-negative (<i>Escherichia coli</i>) and Gram-positive (<i>Bacillus subtillus</i>) bacteria. The results altogether suggest the future potential applications of nickel-prussian blue@silver nanocomposite as an antibacterial agent.
Characterization of antibodies that inhibit HIV gp120 antigen processing and presentation (2005)

Antibodies to the CD4-binding site (CD4bs) of HIV-1 envelope gp120 have been shown to inhibit MHC class II presentation of this antigen, but the mechanism is not fully understood. To define the key determinants contributing to the inhibitory activity of these antibodies, a panel of anti-CD4bs monoclonal antibodies with different affinities was studied and compared to antibodies specific for the chemokine receptor-binding site or other gp120 regions. Anti-CD4bs antibodies that completely obstruct gp120 presentation exhibit three common properties: relatively high affinity for gp120, acid-stable interaction with gp120, and the capacity to slow the kinetics of gp120 proteolytic processing. None of these antibodies prevents gp120 internalization into APC. Notably, the broadly virus-neutralizing anti-CD4bs IgG1b12 does not block gp120 presentation as strongly, because although IgG1b12 has a relatively high affinity, it dissociates from gp120 more readily at acidic pH and only moderately retards gp120 proteolysis. Other anti-gp120 antibodies, regardless of their affinities, do not affect gp120 presentation. Hence, high-affinity anti-CD4bs antibodies that do not dissociate from gp120 at endolysosomal pH obstruct gp120 processing and prevent MHC class II presentation of this antigen. The presence of such antibodies could contribute to the dearth of anti-gp120 T helper responses in chronically HIV-1-infected patients.
Faceted Design of Channels for Low-Dispersion Electrokinetic Flows in Microfluidic Systems (2003)

A novel methodology for designing microfluidic channels for low-dispersion, electrokinetic flows is presented. The technique relies on trigonometric relations that apply for ideal electrokinetic flows, allowing faceted channels to be designed using common drafting software and a hand calculator. Flows are rotated and stretched along the abrupt interface between adjacent regions having differing specific permeability--a quantity with dimensions of length that we introduce to derive the governing equations. Two-interface systems are used to eliminate hydrodynamic rotation of bands injected into channels. Regions bounded by interfaces form faceted flow "prisms" with uniform velocity fields that can be combined with other prisms to obtain a wide range of turning angles and expansion ratios. Lengths of faceted prisms can be varied arbitrarily, simplifying chip layout and allowing the ability to reduce unwanted effects such as transverse diffusion and Joule heating for a given faceted prism. Designs are demonstrated using two-dimensional numerical solutions of the Laplace equation.
Haploinsufficiency of Anx7 tumor suppressor gene and consequent genomic instability promotes tumorigenesis in the Anx7(+/-) mouse (2003)

Annexin 7 (ANX7) acts as a tumor suppressor gene in prostate cancer, where loss of heterozygosity and reduction of ANX7 protein expression is associated with aggressive metastatic tumors. To investigate the mechanism by which this gene controls tumor development, we have developed an Anx7(+/-) knockout mouse. As hypothesized, the Anx7(+/-) mouse has a cancer-prone phenotype. The emerging tumors express low levels of Anx7 protein. Nonetheless, the wild-type Anx7 allele is detectable in laser-capture microdissection-derived tumor tissue cells. Genome array analysis of hepatocellular carcinoma tissue indicates that the Anx7(+/-) genotype is accompanied by profound reductions of expression of several other tumor suppressor genes, DNA repair genes, and apoptosis-related genes. In situ analysis by tissue imprinting from chromosomes in the primary tumor and spectral karyotyping analysis of derived cell lines identify chromosomal instability and clonal chromosomal aberrations. Furthermore, whereas 23% of the mutant mice develop spontaneous neoplasms, all mice exhibit growth anomalies, including gender-specific gigantism and organomegaly. We conclude that haploinsufficiency of Anx7 expression appears to drive disease progression to cancer because of genomic instability through a discrete signaling pathway involving other tumor suppressor genes, DNA-repair genes, and apoptosis-related genes.
Development of cell culture monitoring system and novel non-contact pH measurement (2011)

This paper describes a cell culture monitoring system for regenerative medicine. To realize this monitoring system, a new culture vessel and a removable measurement unit were proposed. The measurement unit was installed in the culture vessel and it was used to measure important cell culture parameters (e.g., temperature, CO(2) level, and pH). Thus, the status of the culture could be monitored. In addition, we developed a novel noninvasive method based on spectrophotometry for measuring pH. This method is a non-contact method that permits noninvasive and contamination-free pH measurement. The spectroscopic pH measurements agreed well with pH measurements using an electrode. The error was within 0.02; thus, the new pH measurement method is sufficiently accurate for cell culture. This new system is expected to contribute to advances in tissue engineering and regenerative medicine.