gebhart/patrepeval huggingface dataset:
Forward Genetic Screening for the Improved Production of Fermentable Sugars from Plant Biomass (2013)

With their unique metabolism and the potential to produce large amounts of biomass, plants are an excellent bio-energy feedstock for a variety of industrial purposes. Here we developed a high-throughput strategy, using the model plant Arabidopsis thaliana, to identify mutants with improved sugar release from plant biomass. Molecular analysis indicates a variety of processes including starch degradation, cell wall composition and polar transport of the plant hormone auxin can contribute to this improved saccharification. To demonstrate translatability, polar auxin transport in maize was either genetically or chemical inhibited and this also resulted in increased sugar release from plant tissues. Our forward genetic approach using Arabidopsis not only uncovers new functions that contribute to cell wall integrity but also demonstrates that information gleaned from this genetic model can be directly translated to monocotyledonous crops such as maize to improve sugar extractability from biomass.
Recovery of Sugars from Ionic Liquid Biomass Liquor by Solvent Extraction (2010)

The dissolution of biomass into ionic liquids (ILs) has been shown to be a promising alternative biomass pretreatment technology, facilitating faster breakdown of cellulose through the disruption of lignin and the decrystallization of cellulose. Both biological and chemical catalysis have been employed to enhance the conversion of IL-treated biomass polysaccharides into monomeric sugars. However, biomass-dissolving ILs, sugar monomers, and smaller carbohydrate oligomers are all soluble in water. This reduces the overall sugar content in the recovered solid biomass and complicates the recovery and recycle of the IL. Near-complete recovery of the IL and the holocellulose is essential for an IL-based pretreatment technology to be economically feasible. To address this, a solvent extraction technique, based on the chemical affinity of boronates such as phenylboronic acid and naphthalene-2-boronic acid for sugars, was applied to the extraction of glucose, xylose, and cellobiose from aqueous mixtures of 1-ethyl-3-methylimidazolium acetate. It was shown that boronate complexes could extract up to 90% of mono- and disaccharides from aqueous IL solutions, 100% IL systems, and hydrolysates of corn stover containing IL. The use of boronate complexes shows significant potential as a way to recover sugars at several stages in ionic liquid biomass pretreatment processes, delivering a concentrated solution of fermentable sugars, minimizing toxic byproducts, and facilitating ionic liquid cleanup and recycle.
Graphene-Si Schottky IR Detector (2013)

This paper reports on photodetection properties of the graphene-Si schottky junction by measuring current–voltage characteristics under 1.55- <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\mu{\rm m}$</tex></formula> excitation laser. The measurements have been done on a junction fabricated by depositing mechanically exfoliated natural graphite on top of the pre-patterned silicon substrate. The electrical Schottky barrier height is estimated to be (0.44–0.47) eV with a minimum responsivity of 2.8 mA/W corresponding to an internal quantum efficiency of 10%, which is almost an order of magnitude larger than regular Schottky junctions. A possible explanation for the large quantum efficiency related to the 2-D nature of graphene is discussed. Large quantum efficiency, room temperature IR detection, ease of fabrication along with compatibility with Si devices can open a doorway for novel graphene-based photodetectors.
Early clinical experience with a candidate meningococcal B recombinant vaccine (rMenB) in healthy adults (2011)

Based on the immunogenicity and reactogenicity results in these participants, both rMenB and rMenB+OMVNW were promising candidates for further investigation.
Lightweight Real-time Makeup Try-on in Mobile Browsers with Tiny CNN Models for Facial Tracking (2019)

Recent works on convolutional neural networks (CNNs) for facial alignment have demonstrated unprecedented accuracy on a variety of large, publicly available datasets. However, the developed models are often both cumbersome and computationally expensive, and are not adapted to applications on resource restricted devices. In this work, we look into developing and training compact facial alignment models that feature fast inference speed and small deployment size, making them suitable for applications on the aforementioned category of devices. Our main contribution lies in designing such small models while maintaining high accuracy of facial alignment. The models we propose make use of light CNN architectures adapted to the facial alignment problem for accurate two-stage prediction of facial landmark coordinates from low-resolution output heatmaps. We further combine the developed facial tracker with a rendering method, and build a real-time makeup try-on demo that runs client-side in smartphone Web browsers. More results and demo are in our project page: http://research.modiface.com/makeup-try-on-cvprw2019/
Online BIST and BIST-based diagnosis of FPGA logic blocks (2004)

We present the first online built-in self-test (BIST) and BIST-based diagnosis of programmable logic resources in field-programmable gate arrays (FPGAs). These techniques were implemented and used in a roving self-testing areas (STARs) approach to testing and reconfiguration of FPGAs for fault-tolerant applications. The BIST approach provides complete testing of the programmable logic blocks (PLBs) in the FPGA during normal system operation. The BIST-based diagnosis can identify any group of faulty PLBs, then applies additional diagnostic configurations to identify the faulty look-up table or flip-flop within a faulty PLB. The ability to locate defective modules inside a PLB enables a new form of fault-tolerance that reuses partially defective PLBs in their fault-free modes of operation.
Expression and purification of human cholesterol 7 alpha-hydroxylase in Escherichia coli. (1994)

Cholesterol 7 alpha-hydroxylase (P450c7) is the first and rate-limiting enzyme in bile acid biosynthesis and is the product of a cytochrome P450 gene, CYP7. We have previously reported the cloning of a full-length human cholesterol 7 alpha-hydroxylase cDNA (Karam, W. G., and J. Y. L. Chiang. 1992. Biochem. Biophys. Res. Commun. 185: 588-595). Using this clone in a polymerase chain reaction, we have generated a cDNA (H7 alpha 1.5) in which the codons for the N-terminal 24 amino acid residues were deleted. The translational product of this cDNA would be a truncated protein, P450c7(delta 2-24) with a hydrophilic NH2-terminal sequence, Met-Ala-Arg-Arg-Arg-Gln... This cDNA was cloned into the expression vector pJL and the construct pJL/H7 alpha 1.5 was transformed into E. coli strain TOPP3. We have also ligated a truncated rat cholesterol 7 alpha-hydroxylase cDNA obtained previously (Li, Y. C., and J. Y. L. Chiang. 1991. J. Biol. Chem. 266: 19186-19191) into the pJL vector and have transformed this construct (pJL/R7 alpha 1.5) into E. coli strain MV1304. Both of these systems expressed functional cholesterol 7 alpha-hydroxylase in E. coli. A fivefold improvement in the expression of rat enzyme over the previous expression system was obtained. About 70-80% of the truncated human P450 in the clear lysate was localized in the cytosol. The truncated human and rat P450c7(delta 2-24) were purified to homogeneity. Reconstitution of cholesterol 7 alpha-hydroxylase activity using purified rat or human P450c7(delta 2-24) showed a similar Km of 6 and 7 microM for cholesterol, a Vmax of 0.13 and 0.14 nmol/min, and a turnover number of 1.3 and 1.5 per min, respectively. Immunoblotting experiment revealed that a polyclonal antibody raised against rat microsomal cholesterol 7 alpha-hydroxylase recognized both rat and human P450c7(delta 2-24). This expression system provides a method for isolation of a large quantity of purified and catalytically active cholesterol 7 alpha-hydroxylase for the study of structure and function of this important enzyme in bile acid synthesis and cholesterol homeostasis.
High thermoelectric performance of mechanically robust n-type Bi<sub>2</sub>Te<sub>3−x</sub>Se<sub>x</sub> prepared by combustion synthesis (2015)

Mechanically robust Bi<sub>2</sub>Te<sub>3</sub>-based materials with excellent thermoelectric performance are synthesized by ultra-fast self-propagating high-temperature synthesis in less than 20 min.
An Active Sequential Xampling Detector for Spectrum Sensing (2017)

Enabling low power wireless devices to adopt Nyquist sampling at high carriers is prohibitive. In spectrum sensing, this limit calls for an analog front-end that can sweep different bands quickly, in order to use the available spectrum opportunistically. In this paper we propose a new framework that allows to optimize a sub-Nyquist sampling front-end to combine the benefits of optimum sequential sensing with those of Compressive Spectrum Sensing (CSS). The sensing strategy we propose is formulated as a sequential utility optimization problem. The utility function decreases linearly with the number of measurements (accrued to make a decision) and increases as a function of the signal components binary states. The optimization selects the best linear combinations of sub-bands to mix, in order to accrue maximum utility. The structure of the utility represents the trade-off between exploration, exploitation and risk of making an error, that is characteristic of the spectrum sensing problem. We first present the analog front-end architecture, and then map the measurement model into the abstract optimization problem proposed, and analyzed, in the remainder of the paper. We characterize the optimal policy under constraints on the sensing matrix and derive the approximation factor of the greedy approach. Numerical simulations showcase the benefits of combining opportunistic spectrum sensing with sub-Nyquist sampling.
Rarity of CDK4 germline mutations in familial melanoma (2002)

To date, two genes have been implicated in melanoma pathogenesis. The first, CDKN2A, is a tumour suppressor gene with germline mutations detected in 20% of melanoma-prone families. The second, CDK4, is an oncogene with co-segregating germline mutations detected in only three kindreds worldwide. We examined 16 American melanoma-prone families for mutations in all coding exons of CDK4 and screened additional members of two previously reported families with the Arg24Cys germline CDK4 mutation to evaluate the penetrance of the mutation. No new CDK4 mutations were identified. In the two Arg24Cys families, the penetrance was estimated to be 63%. Overall, 12 out of 12 invasive melanoma patients, none out of one in situ melanoma patient, five out of 13 dysplastic naevi patients, two out of 15 unaffected family members, and none out of 10 spouses carried the Arg24Cys mutation. Dysplastic naevi did not strongly co-segregate with the Arg24Cys mutation. Thus the phenotype observed in melanoma-prone CDK4 families appears to be more complex than just the CDK4 mutation. Both genetic and environmental factors are likely to contribute to the occurrence of melanoma and dysplastic naevi in these families. In summary, although CDK4 is a melanoma susceptibility gene, it plays a minor role in hereditary melanoma.
TECHNICAL NOTE Prism fingerprint sensor that uses a holographic optical element (1996)

A prism fingerprint sensor is described that uses a holographic grating glued to a right-angled prism. A light source normally illuminates the hypotenuse side of the prism with the finger pressed against the grating. The ridges and valleys of the finger are sensed on the basis of the principle of total internal reflection. The grating is used essentially to correct the distortion usually present with prism sensors. The quality of the fingerprint is very good: the pores on the ridges can be seen.
Sampled grating tunable twin‐guide laser diodes with wide tuning range (≥40 nm) and large output power (≥10 mW) (2006)

The sampled grating tunable twin-guide (SG-TTG) laser diode is a DFB-like tunable laser that employs Vernier-effect tuning to achieve wide wavelength tuning. In contrast to most other monolithic widely tunable lasers (which are usually DBR-type lasers), a phase tuning section is not needed and, hence, the SG-TTG laser requires at least one tuning current less than comparable devices. The devices provide full wavelength coverage over a 40 nm-broad tuning range that is centered at 1.54 µm. Its tuning behavior is quasi-continuous with up to 8.2 nm broad continuous tuning regions. High side-mode suppression (SMSR ≥ 35 dB) as well as large output power (P ≥ 10 mW) are obtained over the whole wavelength range from 1520.5 to 1561.5 nm. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Measurement of the temperature dependence of Young's modulus of cartilage by phase-sensitive optical coherence elastography (2014)

The development of an effective system to monitor the changes in the elastic properties of cartilage tissue with increasing temperature in laser reconstruction is an urgent practical task. In this paper, the use of phase-sensitive optical coherence elastography for detection of elastic waves in the sample has allowed Young's modulus of cartilage tissue to be measured directly during heating. Young's modulus was calculated from the group velocity of propagation of elastic waves excited by means of a system supplying focused air pulses. The measurement results are in agreement with the results of measurements of the modulus of elasticity under mechanical compression. The technique developed allows for noninvasive measurements; its development is promising for the use in vivo.
Cellobiohydrolase and endoglucanase respond differently to surfactants during the hydrolysis of cellulose (2015)

The hydrolysis boosting effect of PEG appears to be specific for CBH I. The mechanism could be due to an increase in the apparent activity of the enzyme on the substrate surface. The addition of PEG increases the relaxation time of the liquid-phase water, which from the data presented points towards a mechanism related to PEG-water interactions rather than PEG-protein or PEG-substrate interactions.
Factors affecting immunodetection of hepatitis B surface antigen recombinant mutants (2007)

Immunoassays for hepatitis B surface antigen (HBsAg) capture antigen on a solid phase and then detect this immobilized antigen by a conjugate reagent that generates a signal. These capture and detection reagents can utilize either monoclonal antibody (single or multiple) or polyclonal antibodies or a combination of both. HBsAg capture and detection immunoreagents are usually directed against conformational epitopes of the “a” determinant. It is these same conformational epitopes that can be altered by mutations in HBsAg so that an immunoassay will return a false negative result if either the capture or detection immunoreagent is incapable of recognizing the viral mutant. The epitope recognition of capture or detection reagents is an important factor to consider when using an immunoassay to quantitate HBsAg mutants for use in testing panels. These quantitative concerns are compounded by our observation that production of recombinant HBsAg mutants can vary significantly in concentration when transfection variables are held constant. HBsAg mutant testing panels should be set at a concentration above the sensitivity endpoint of wildtype immunodetection so that a false negative due to reagent epitope recognition can be differentiated from a false negative due to assay sensitivity limitations. In this manner, recombinant HBsAg mutant panels can be used to estimate the ability of a particular immunoassay reagent configuration to detect altered HBsAg “a” determinant epitopes that may be encountered in actual clinical specimens. J. Med. Virol. 79:S47–S51, 2007. © 2007 Wiley-Liss, Inc.
Lignin Extraction from Black Liquor - Precipitation, filtration and washing (2008)

Various process streams in the pulp and/or paper mill contain valuable substances which can be converted into new products, e.g. lignin and xylane. Implementation of the most recently available technology allows sub-processes not only to produce new products but also to enhance the environmental performance of the mill as well as improve utilization of renewable resources. Extracting lignin from black liquor is one way of recovering valuable organic material. Lignin, which can be found in spent cooking liquor, is currently combusted in the recovery boiler to produce electricity and steam. Removing lignin decreases the overall heating value of the black liquor and, since the recovery boiler often is limited by the heat load, the throughput of black liquor can therefore be increased. Moreover, should the recovery boiler be a bottleneck in increasing the production of pulp, the removal of lignin would increase the capacity of the mill. Refined lignin can either be used as a solid biofuel or as a raw material for the production of other chemicals, e.g. active carbon and phenols.In this thesis, the extraction of lignin from black liquor using the “LignoBoost” process was investigated, with the primary focus being on increasing knowledge of the precipitation of lignin. The chemical reactions and the kinetics of the gas absorption process were studied and a mathematical model proposed that can describe the decrease in pH during the precipitation process by adjusting design parameters to experimental data. Several black liquors were used to study how different precipitation parameters and the chemical composition of the black liquors affected the absorption of gas into the black liquor and the filtration properties of the precipitated particles. In addition, the conditioning step after precipitation was also studied. During precipitation, it was found that the mixing speed affected the pH lowering rate below a pH value of about 10.5, indicating that above this level, the pH lowering rate may be controlled by the chemical reaction rate. This finding was consistent with the conclusions drawn from the work carried out on the mathematical model. It was also found that a higher mixing speed during precipitation increased the average specific filtration resistance of the precipitated particles. When a gas mixture with a low concentration CO2 was used, the pH lowering rate decreased significantly. The experiments using hardwood black liquors showed that the average specific filtration resistance was lowered considerably when the hemicelluloses were removed prior to precipitation.By using the “LignoBoost” concept on laboratory scale it was found that the lignin produced was excellent in terms of final purity and the yield losses during separation were very low. The process was also studied on both bench and pilot scales, with the focus being on the separation characteristics. In the pilot-scale experiments, 8 tonnes of lignin were produced with low levels of contamination (60%) and calorific value (LHV 25.4 MJ/kg).
A Wideband Injection Locked Quadrature Clock Generation and Distribution Technique for an Energy-Proportional 16–32 Gb/s Optical Receiver in 28 nm FDSOI CMOS (2016)

We present a novel frequency tracking method that exploits the dynamics of injection locking in a quadrature ring oscillator to increase the effective locking range from 5% (7-7.4 GHz) to 90% (4-11 GHz). The quadrature phase error between I and Q phases of an injection locked ring oscillator is derived and shown to contain frequency error information, both inside and outside the locking range. This error is utilized to form a first-order frequency tracking quadrature locked loop (QLL). This loop generates accurate clock phases for a 4-channel parallel optical receiver using a forwarded clock at quarter-rate. The QLL drives an ILO at each channel without any repeaters for local quadrature clock generation. Each local ILO has deskew capability for phase alignment. The receiver maintains a constant energy-per-bit consumption across 16-32 Gb/s by adaptive body biasing in a 28 nm FDSOI technology.
Streamer discharges for water purification (2004)

Summary form only given. Streamer discharges are considered to be an energy efficient alternative method for the biological and chemical decontamination of water. We have studied the generation of streamers in distilled and in tap water with a coaxial reactor of 50 mm diameter and 100 mm length. Voltage pulses of up to 100 kV amplitude and 500 ns duration have been applied. Electrical and optical diagnostics were used to investigate the spatial and temporal development of the streamers. With a straight wire of 75 /spl mu/m in diameter as the center electrode, an average of 3-4 streamers per cm wire length was observed. By enclosing the wire in a perforated insulating tube, a highly luminous plasma was generated in the pinhole perforations. The plasma spread along the outer surface of the tube, and served as a source of a multitude of secondary streamers. The high streamer density indicates a potential increase in bacterial and chemical decontamination efficiency over simple coaxial streamer reactors. The streamer density might be further enhanced by introducing dielectric pellets into the discharge volume. Experimental results on the bacterial decontamination effect of the various types of discharge will be presented.
Periodic retrieval of videos from disk arrays (2002)

A growing number of applications need access to video data stored in digital form on secondary storage devices (e.g., video-on-demand, multimedia messaging). As a result, video servers that are responsible for the storage and retrieval, at fixed rates, of hundreds of videos from disks are becoming increasingly important. Since video data tends to be voluminous, several disks are usually used in order to store the videos. A challenge is to devise schemes for the storage and retrieval of videos that distribute the workload evenly across disks, reduce the cost of the server and at the same time, provide good response times to client requests for video data. In this paper we present schemes that retrieve videos periodically from disks in order to provide better response times to client requests. We present two schemes that stripe videos across multiple disks in order to distribute the workload uniformly among them. For the two striping schemes, we show that the problem of retrieving videos periodically is equivalent to that of scheduling periodic tasks on a multiprocessor. For the multiprocessor scheduling problems, we present and compare schemes for computing start times for the tasks, if it is determined that they are schedulable.
A fuzzy genetic algorithm for automatic channel assignment for tactical HF radio networks (1997)

An innovative method for automatically allocating channels to groups of tactical HF radio nets is described. The method finds an optimal channel assignment that provides good propagation for each net, as determined by propagation prediction models, while avoiding channel interference. The method solves this difficult optimization problem using a genetic algorithm coupled with a set of goodness criteria that evaluate channel assignments using fuzzy logic. The method finds channel assignments similar to those created by expert human system designers.