gebhart/patrepeval huggingface dataset:
Functional Expression of a Fungal Laccase in <i>Saccharomyces cerevisiae</i> by Directed Evolution (2003)

Laccase from Myceliophthora thermophila (MtL) was expressed in functional form in Saccharomyces cerevisiae. Directed evolution improved expression eightfold to the highest yet reported for a laccase in yeast (18 mg/liter). Together with a 22-fold increase in k(cat), the total activity was enhanced 170-fold. Specific activities of MtL mutants toward 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) and syringaldazine indicate that substrate specificity was not changed by the introduced mutations. The most effective mutation (10-fold increase in total activity) introduced a Kex2 protease recognition site at the C-terminal processing site of the protein, adjusting the protein sequence to the different protease specificities of the heterologous host. The C terminus is shown to be important for laccase activity, since removing it by a truncation of the gene reduces activity sixfold. Mutations accumulated during nine generations of evolution for higher activity decreased enzyme stability. Screening for improved stability in one generation produced a mutant more stable than the heterologous wild type and retaining the improved activity. The molecular mass of MtL expressed in S. cerevisiae is 30% higher than that of the same enzyme expressed in M. thermophila (110 kDa versus 85 kDa). Hyperglycosylation, corresponding to a 120-monomer glycan on one N-glycosylation site, is responsible for this increase. This S. cerevisiae expression system makes MtL available for functional tailoring by directed evolution.
IgM Lymphocytotoxic Antibodies Following MultipleTransfusion (1971)

The immunoglobulin class of leucocyte antibodies occurring after multiple transfusion was investigated. In 7 of the 8 sera tested, both agglutinating and cytotoxic activity was found only in IgG-containing fractions .The 8th serum, from a patient with erythrogenesis imperfecta and haemochromatosis, showed weak agglutinating activity in IgG-containing fractions and strong cytotoxic activity in IgM-containing fractions.
Real-time intelligent pattern recognition algorithm for surface EMG signals (2007)

This study shows that ANFIS real-time learning method coupled with mixed time and time-frequency features as EMG features can provide acceptable results for designing sEMG pattern recognition system suitable for hand prosthesis control.
Heavy Duty Piston Rings - 1968 (1968)

<div class="htmlview paragraph">Refinements in heavy duty piston ring design to suit sealing requirements imposed by different engine designs are presented. Combinations of different individual ring designs used for optimum blowby and oil control in 1968 practice are reviewed. Requirements for piston ring facing materials and parameters for manufacturing processes for application of molybdenum to piston rings are presented. The further development of diesel engines, particularly in the high bmep area, requires further improved piston ring coatings in terms of high mechanical and bond strength, scuff, and wear resistance. The properties of new piston ring facing materials are discussed with particular emphasis on a new multiphase hard plasma-plied material.</div>
Reverse genetics system for introduction of site-specific mutations into the double-stranded RNA genome of infectious rotavirus (2006)

We describe here the successful establishment of a reverse genetics system for rotavirus (RV), a member of the Reoviridae family whose genome consists of 10-12 segmented dsRNA. The system is based on the recombinant vaccinia virus T7 RNA polymerase-driven procedure for supplying artificial viral mRNA in the cytoplasm. With the aid of helper virus (human RV strain KU) infection, intracellularly transcribed full-length VP4 mRNA of simian RV strain SA11 resulted in the rescue of the KU-based transfectant virus carrying the SA11 VP4 RNA segment derived from cDNA. In addition to the rescued transfectant virus with the authentic SA11 VP4 gene, three more infectious RV transfectants, into which silent mutation(s) were introduced to destroy both or one of the two restriction enzyme sites as gene markers in the SA11 VP4 genome, were also rescued with this method. The ability to artificially manipulate the RV genome will greatly increase the understanding of the replication and the pathogenicity of RV and will provide a tool for the design of attenuated vaccine vectors.
Activated mutant of G alpha 13 induces Egr-1, c-fos, and transformation in NIH 3T3 cells. (1994)

Expression of the constitutively activated mutant alpha-subunit of the heterotrimeric G protein G alpha 13 (alpha 13Q226L) leads to the transformation of NIH-3T3 cells. An analysis of the mitogenic pathway mediated by alpha 13Q226L indicated that the expression of the primary response genes, early growth response gene-1 (Egr-1, a nuclear transcription factor with zinc-finger motif) and c-fos (a leucine zipper transcription factor as well as a protooncogene) are constitutively activated in alpha 13Q226L-transformants. While ras-transformed cells did not express Egr-1, cells transformed by the GTPase deficient mutant alpha-subunit of G alpha 12 (alpha 12Q229L) exhibited a "weak" expression, suggesting that the induction of Egr-1 and c-fos is intrinsic to G alpha 13 signaling pathway and not a consequence of the transformed phenotype. Taken together, these results provide the first evidence that the G alpha 13 signaling pathway involves the activation of specific transcription factors and defines the expression of these nuclear transcription factors as a possible molecular mechanism in alpha 13Q226L-mediated cell proliferation and transformation.
The System for Secure Mobile PaymentTransactions (2013)

Secure mobile payment methods are typically needed in mobile access channels, it is vital toapply them when using mobile payment applications, which have arisen as a result of the increase of e-commerce. Currently, there are some payment methods that most of them can be used when conducting transactions but, they differ in terms of functionality, usability, costs or security. What makes mobile payment system more useful and necessary are the features and functionalities which are essentially based on customer needs that may differ in different market places, social categories and regions. In addition to payment system functionality, what mainly matters is securing payment methods with sufficient security protections. In this thesis, it is been tried to introduce some features currently lacking in mobile payment systems to propose a security architecture and then to present a solution for prospective problems with some current mobile payment systems and applications. The solution mainly implements what has been proposed and required to fulfill system requirements. The proposed security architecture supports already designed mobile payment system (SAFE) which typically interacts with the merchant and the customer for performing secure payment transactions. Mobile payment security architecture is designed, implemented and analyzed to be highly scalable and modular in addition to providing the desired security requirements set to it in this thesis work. The architecture is enhanced with mobile applications, so called SAFE apps, enabling securely authorizing e-commerce transactions. This report begins with introducing mobile payment system technologies, concept and architecture as the foundation for this work. The systems relevant to the one proposed in this thesis are briefly discussed in terms of functionality and security issues. System architecture and design of SAFE Mobile Payment System are briefly discussed as the core component of the settling e-commerce functions in a holistic view. The functionality and security issues ofthe system design and implementation are presented and finally the work is analyzed to determine how the project objectives were met.
Geometric Principles for Designing Highly Symmetric Self-Assembling Protein Nanomaterials (2017)

Emerging protein design strategies are enabling the creation of diverse, self-assembling supramolecular structures with precision on the atomic scale. The design possibilities include various types of architectures: finite cages or shells, essentially unbounded two-dimensional and three-dimensional arrays (i.e., crystals), and linear or tubular filaments. In nature, structures of those types are generally symmetric, and, accordingly, symmetry provides a powerful guide for developing new design approaches. Recent design studies have produced numerous protein assemblies in close agreement with geometric specifications. For certain design approaches, a complete list of allowable symmetry combinations that can be used for construction has been articulated, opening a path to a rich diversity of geometrically defined protein materials. Future challenges include improving and elaborating on current strategies and endowing designed protein nanomaterials with properties useful in nanomedicine and material science applications.
Studies with high-expansion foams for controlling experimental-coal-mine fires: a progress report (1958)

Lessons learnt during the pandemic should shape the future of the Italian health service. (www.actabiomedica.it).
The determination of the speed of sound in liquids using acoustic resonance in piezoelectric tubes (1999)

We developed a methodology based on acoustic resonance for determination of the speed of sound in various liquids. A frequency sweep of an annular piezoelectric transducer performed using an impedance analyser reveals the structural resonance frequency. Upon immersing the tube in a liquid the impedance curve obtained from the frequency sweep has an additional resonance peak. The peak is the result of the acoustic resonance in the tube that feeds back to the piezoelectric structure. By using the fundamental acoustic mode in pipes and accounting for end corrections and for the compliance of the piezoelectric tube, a formula for the intrinsic speed of sound in a liquid was determined. Several liquids were tested and the speed of sound was obtained. The comparison of the values obtained with literature data showed that the difference was less than 3%.
A comparison of bitemark injuries between fatal wolf and domestic dog attacks. (1999)

Bitemark patterns in adult human victims following a fatal wolf pack attack and a domestic dog pack attack are compared. Both victims exhibited a concentration of wounds to the extremities, left and right torso, but not to the groin or internal organs. The neck and face of the domestic dog attack victim were primary sites of attack while the feral wolf pack victim was spared damage to the neck, but had facial tissue destroyed postmortem. Most punctures were found on the ventral aspect of the domestic victim and dorsal aspect of the feral victim. It is speculated that most wounds were attributable to dominant animals of both packs and in both victims and this suggests a co-ordination of activity between. Differences in bitemark patterns may well have been caused in part by differences in genetics, training, breeding, socialization and impetus of attack between wolves and dogs. Distinct differences in bitemark patterns were found in these two human victims of a wolf and domestic dog attacks.
The Costs of Abusing Probationary Sentences: Overincarceration and the Erosion of Due Process (2010)

Something has gone terribly wrong in the American criminal justice system. In the process of moving from a system focused on the rehabilitative potential of the defendant to a system myopically focused on retribution, we have trampled not only upon our tool with the greatest rehabilitative potential, but also upon the due process protections that we supposedly hold most dear. By using probation as a default sentence for all of those whom we choose not to incarcerate, we have created burgeoning caseloads that prevent probation from serving any useful rehabilitative function. Many probationers go without any supervision whatsoever, and those who are in need of social services and support rarely get it. Not surprisingly, then, high percentages of probationers do not succeed on probation. Many of those wind up incarcerated, even though the system’s conclusion was that the underlying crime did not justify incarceration. The “crime” that we punish with incarceration is the inability to live up to the terms and conditions of probation, even if it was entirely unrealistic to expect the probationer to live up to those terms and conditions and entirely predictable that the probationer would fail. It may be hard to convince some constituencies to abandon the abuse of probation because they are wedded to what follows from that abuse: a shadow criminal justice system in which huge numbers of cases are processed not through the due process protections that come with the prosecution of a criminal charge, but through a probation violation hearing process that is devoid of virtually all of these protections. This process is certainly efficient, but does not reflect the values of justice that our system is supposed to represent. It is simply inappropriate to hold a violation hearing at which a criminal charge is adjudicated not through a criminal trial replete with protections for the innocent, but rather through a truncated procedure designed for a very different purpose. This article proposes the use of probation only in the limited circumstances in which it can serve a useful rehabilitative function, and only in numbers that will allow for appropriate supervision and services. And perhaps more importantly, this article proposes the abandonment of a system in which a probation violation hearing acts as a substitute for a criminal trial. The author proposes a far more logical system in which we use probation only when it can serve a legitimate function, we allow probation officers to actually do their jobs, we deal with future criminality on its own terms, and we honor and respect traditional notions of due process when we adjudicate criminal charges.
Elevated phenylalanine levels interfere with neurite outgrowth stimulated by the neuronal cell adhesion molecule L1 in vitro (2006)

Elevated levels of phenylalanine (Phe) as observed in patients with phenylketonuria interfere with proper neuronal development, leading to severe psychomotor deficits and mental retardation. We have analyzed the effects of Phe on neurite outgrowth in vitro. When expressed in fibroblasts, the neuronal cell adhesion molecules L1 and plexin B3 strongly increase the length of neurites emanating from cerebellar neurons in co-culture experiments. Elevated Phe blocks L1-mediated, but not plexin B3-mediated outgrowth, whereas tyrosine is ineffective. Elevated Phe also interferes with aggregation of fibroblasts overexpressing L1, suggesting that the pathological effect of elevated Phe occurs by interfering with L1-mediated cell adhesion.
Physisorption and Chemisorption of Alkanethiols and Alkyl Sulfides on Au(111) (1998)

The energetics and kinetics of the adsorption of a variety of sulfur-containing hydrocarbons onto Au(111) have been explored using helium beam reflectivity and temperature-programmed desorption (TPD) techniques. Simple alkanethiols as well as dialkyl sulfides, dialkyl disulfides, and other sulfur-containing organics were found to adsorb with a low coverage physisorption enthalpy about 20% greater than the heat of vaporization in the bulk. In contrast to the dialkyl sulfides that only physisorb, alkanethiols and dialkyl disulfides also interact chemically with the gold with a chemisorption enthalpy of 126 kJ/mol that is independent of alkyl chain length. The presence of sterically hindering substituent groups on the carbon atom adjacent to the sulfur atom produces, however, a reduction in the chemisorption enthalpy of up to 15%. Temperature-programmed desorption of nonequilibrated, high exposure layers of alkanethiols with eight carbon atoms or longer displayed a second, higher energy, chemisorption peak at 148 kJ/mol which could be eliminated by annealing, leaving only the lower energy chemisorption peak. The chemisorption rate of molecules in the physisorbed precursor state has also been measured. Arrhenius plots for the chemisorption of a series of alkanethiols from their physisorbed precursors show that the chemisorption activation energy is 28.8 kJ/mol and is independent of chain length.
Synthesis of 3,6‐Dibromopyrazine‐2,5‐dicarbonitrile [1] (2012)

Abstract Symmetrically functionalized pyrazine of 3,6‐dibromopyrazine‐2,5‐dicarbonitrile was synthesized in three or four steps from 3‐aminopyrazinecarbonitrile or its 6‐bromo derivatives.
Continuous-Bed Columns Containing Sol-Gel Bonded Packing Materials for Capillary Electrochromatography (2000)

Sol-gel bonded packing materials in continuous-bed columns have been prepared for capillary electrochromatography (CEC). Three packing materials were investigated: small-pore Spherisorb ODS1 (3 μm, 80 Å) with octadecyl as stationary phase, small-pore mixed-mode Spherisorb ODS/SCX (3 μm, 80 Å) with octadecyl and propyl sulfonic acid as stationary phases, and large-pore Nucleosil ODS (7 μm, 1 400 Å) with octadecyl as stationary phase. The characteristics of these columns were compared in terms of electroosmotic flow, efficiency, inertness, and retention factors. In contrast to columns containing sol-gel bonded ODS, columns containing sol-gel bonded mixed-mode ODS/SCX generated nearly pH independent electroosmotic flow (EOF) over pH 2–9. Columns containing sol-gel bonded large-pore ODS produced nearly three times lower reduced plate height than those containing small-pore ODS. Efficiencies of 220,000 plates per meter and 175,000 plates per meter were obtained from columns containing sol-gel bonded 7 μm, 1 400 Å ODS and columns containing sol-gel bonded 3 μm, 80 Å ODS, respectively, which are among the highest reported efficiencies for continuous-bed columns. In CEC, over one million plates per meter and pH independent EOF are expected from continuous-bed columns containing sol-gel bonded 1.5 μm particles with large pores and mixed-mode stationary phases.
AWARE (Asymmetric Write Architecture With REdundant Blocks): A High Write Speed STT-MRAM Cache Architecture (2013)

Spin-transfer torque magnetic RAM (STT-MRAM) is a promising memory technology for lower level caches because of its high density and nonvolatile nature. However, the high write latency is a bottleneck to its widespread adoption as the future on-chip memory. In this paper, we propose a new cache architecture-asymmetric write architecture with redundant blocks (AWARE)-that can improve the write latency by taking advantage of the asymmetric write characteristics of 1T-1MTJ STT-MRAM bit-cells. Due to the nature of the storage element in STT-MRAM, the time required for the two-state transitions ( 1→ 0 and 0→ 1) is not identical. In other words, one of the state transitions is slower than the other direction. In conventional cache architecture, the overall write latency is limited by the slower transition. However, the AWARE cache design introduces redundant blocks in each row, and they are preset to the initial state that enables the faster transition. Hence the write operations performed in these redundant blocks are much faster than the conventional write scheme. The write latency in AWARE is improved by 30% over conventional cache architecture with no area penalty in the data array. Moreover, the additional tag bits introduced in this technique result in penalty on the total cache area. In addition, the write energy increases modestly by 7% in the proposed cache design. However, this write-energy increase can be mitigated by sacrificing the cache capacity.
Supervised Reinforcement Learning with Recurrent Neural Network for Dynamic Treatment Recommendation (2018)

Dynamic treatment recommendation systems based on large-scale electronic health records (EHRs) become a key to successfully improve practical clinical outcomes. Prior relevant studies recommend treatments either use supervised learning (e.g. matching the indicator signal which denotes doctor prescriptions), or reinforcement learning (e.g. maximizing evaluation signal which indicates cumulative reward from survival rates). However, none of these studies have considered to combine the benefits of supervised learning and reinforcement learning. In this paper, we propose Supervised Reinforcement Learning with Recurrent Neural Network (SRL-RNN), which fuses them into a synergistic learning framework. Specifically, SRL-RNN applies an off-policy actor-critic framework to handle complex relations among multiple medications, diseases and individual characteristics. The "actor'' in the framework is adjusted by both the indicator signal and evaluation signal to ensure effective prescription and low mortality. RNN is further utilized to solve the Partially-Observed Markov Decision Process (POMDP) problem due to lack of fully observed states in real world applications. Experiments on the publicly real-world dataset, i.e., MIMIC-3, illustrate that our model can reduce the estimated mortality, while providing promising accuracy in matching doctors' prescriptions.
Minimal Solvers for 3D Geometry from Satellite Imagery (2015)

We propose two novel minimal solvers which advance the state of the art in satellite imagery processing. Our methods are efficient and do not rely on the prior existence of complex inverse mapping functions to correlate 2D image coordinates and 3D terrain. Our first solver improves on the stereo correspondence problem for satellite imagery, in that we provide an exact image-to-object space mapping (where prior methods were inaccurate). Our second solver provides a novel mechanism for 3D point triangulation, which has improved robustness and accuracy over prior techniques. Given the usefulness and ubiquity of satellite imagery, our proposed methods allow for improved results in a variety of existing and future applications.
Some observations on EEG response to photic flicker stimulation. (1961)

By applying a combined method of crosscorrelation and frequency analysis to EEG tracings, the average response patterns to photic flicker stimulation with a frequency in the alpha wave range were sorted out, even when the application of the frequency analysis only could not separate the response from the irrelevant oscillations to the stimulation. During the stimulation, low volage fast pattern (alpha blocking state), in which the response was hard to recognize by visual inspection of the tracing, occurred in the EEG tracings from time to time. In the frequency spectra of them, however, not only a peak at the stimulating frequency, but the other ones at slightly higher frequency and sometimes with subharmonic frequency were appeared to suggest they are the response to the stimulation, though they are far lower than the peak of the dominant alpha wave before the initiation of the stimulation, rised up at the stimulating frequency in the power spectra of the crosscorrelogram between the stimula-tion and the tracing to indicate the other peaks were not related response, at least directly, to the stimulation, but by others. It is well recognized that the electroencephalogram (EEG) is driven by a photic flicker stimulation with a frequency of alpha wave is estimated in many cases (ADRIAN AND MATTHEWS&apos;) 1934, DURUP AND