gebhart/patrepeval huggingface dataset:
Frequency dependencies of power noise (2002)

In this paper, frequency dependencies of delta-I noise caused by variations of the on-chip switching activity have been analyzed by simulations for a complex computer system board with multi-chip module, especially the impact of coincidences with resonances of the power distribution system. The switching frequency and the noise source waveform have been varied in case of a single delta-I step. For repeated delta-I steps the power noise dependencies on the repetition frequency, the duty cycle and the damping of the resonant loop have been analyzed. Simulations using switching current sources for on-chip switching have been confirmed by simulations with switching resistors plus de voltage source. Mid-frequency noise simulations using SPEED2000 and noise voltage measurements yield the same results within 6% for the first and second voltage droops and overshoots, if the real resistance of power/ground vias and module pins are included in the simulation.
Studies of Acetylperoxy Radicals Produced by Photolysis of Biacetyl in Aerated Benzene Solutions. Ion-Pair Formation with Tetramethyl-p-phenylenediamine (1996)

Spin-trapping studies of the radicals produced by photolysis of biacetyl in degassed benzene confirmed the formation of acetyl radicals as a major product and methyl radicals as a minor one. In aerated benzene, the trapped radicals are ascribed to the acetylperoxy radical yielded by the reaction of the acetyl radical and oxygen. The laser photolysis studies of biacetyl in aerated benzene containing tetramethyl-p-phenylenediamine, TMPD, demonstrate that the acetylperoxy radicals react with TMPD to give the weakly interacting complex which turns to the ion-pair complex with the rate constant 6.7 × 105 s-1. The absorption spectrum of the ion-pair complex resembles that of the cation radical of TMPD. The quantum yield for the formation of the acetylperoxy radicals produced by photolysis of biacetyl in benzene is estimated as 0.41. The addition of cyclohexene and norbornadiene is found to increase the rate for the formation of the ion-pair complex, indicating that the acetylperoxy radicals react with these olefins: the rate constants are 2.1 × 106 M-1 s-1 for cyclohexene and 1.8 × 107 M-1 s-1 for norbornadiene.
Antimicrobial sesquiterpenoids from Laurencia obtusa Lamouroux (2017)

Abstract Purification of the organic extract of Laurencia obtusa Lamouroux by column chromatography and preparative thin layer chromatography provided four new compounds: a eudesmane-type sesquiterpenoid [eudesma-4(15),11-diene-5,7-diol ( 1 )], a cuparane-type sesquiterpenoid [10-hydroxycuparaldehyde ( 2 )], and two nor -cuparanes [3-hydroxy-15- nor -cuparan-10β-ol ( 3 ) and 2-bromo-3-hydroxy-15- nor -cuparan-10β-ol ( 4 )]. Structural identification was made possible by comparison of spectral data with those reported in the literature. Compounds 3 and 4 are significant as nor -cuparanes are rarely isolated from marine environment. 1 showed moderate anticandidal activity, whereas 2 exhibited reasonable antibacterial activity against multidrug-resistant bacteria (especially Gram-positive). All the compounds are nontoxic to Artemia salina .
The Organic Diamond Disk (ODD) for Dressing Polishing Pads of Chemical Mechanical Planarization (2007)

Diamond pad conditioners can determine the efficiency of CMP processes and the quality of polished wafers. The polishing rate of a wafer is dependent on the amplitude (height) of pad asperities. The polishing uniformity is controlled by the frequency (density) of such asperities. Current diamond pad conditioners cannot dress the pad to produce microns sized asperities at high density. This is because the tips of diamond grits cannot be leveled to the same height so the grooved pad top is uneven with excessive asperities that may ruin the wafer and under sized asperities that is easily glazed. New designs of diamond pad conditioners have markedly improved the leveling of diamond tips. Organic diamond disks (ODD) are manufactured by reverse casting of polymers. Due to the uniform spacing of diamond grits and their controlled tip heights, none of the diamond grits will be overly stressed. Moreover, all diamond grits are sharing the dressing work. Consequently, the number of working grits of ODD is significantly higher than conventional designs. Moreover, because no diamond will cut pad unnecessarily, the pad life is greatly lengthened. Furthermore, due to the uniform distribution of pad asperities, the slurry will be held efficiently so the run off is avoided. As a result, the slurry usage is reduced. ODD is therefore a significant savor of CMP consumables for semiconductor manufacture.
Open World Recognition (2015)

As humans, we encounter countless objects daily. We effortlessly recognize object across variations despite the fact that the objects might vary in size, scale, translation or rotation. Humans can identify previously seen objects and posses the ability to learn new instances with minimal or no supervision. Human visual system continues to learn and adapt to ever changing surroundings. In recent years, there have been significant advances in the field of computer based recognition systems. While significant strides have been made towards building automated recognition systems, these systems face multiple challenges when operating in evolving environments. Operational issues such as changing data distributions, perturbations in input/output conditions and ever changing requirements of the system users, pose challenges in operational environments. In this work we highlight specific operational challenges such as handling partial information, incremental model adaptation, large-scale classification and propose solutions towards addressing these challenges iii Dedication This thesis is dedicated to my family for their love, constant support, encouragement and patience. iv Acknowledgements
Healthcare ex Machina: Are conversational agents ready for prime time? (Preprint) (2018)

<sec> <title>UNSTRUCTURED</title> Conversational agents are computer software capable of having a natural conversation. They are increasingly used in healthcare, but research in this field is very scarce. . If chatbots are to be safely used by a large number of patients, they must be evaluated like a medical device, or even a drug. </sec>
Formal Communication Modeling and Refinement (2006)

In this chapter we applied Action Systems formalism to the specification and refinement of communication channels between digital system components, within the larger concept of platform-based design. Issues such as abstraction level — reflected in the representation of the communication channels, and asynchronous as well as synchronous communication schemes were addressed. The refinement techniques were used to correctly transform the initial abstract specification into a more concrete form, closer to implementation level. While the communication platform was analyzed in more detail, the actual computation units were only viewed as communication partners. Hence, their individual internal behavior can be analyzed and specified later, as a separate refinement process that preserves the external behavior established earlier.
Palidis: fast discovery of novel insertion sequences (2022)

Abstract The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognises insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterised. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences. Data Summary Palidis is available here: github.com/blue-moon22/palidis The Insertion Sequence Catalogue is available to download here: https://github.com/blue-moon22/ISC The raw reads from the Human Microbiome Project can be retrieved using the download links provided in Supplementary Data 1 The analysis for this paper is available here: github.com/blue-moon22/palidis_paper_analysis The output of Palidis that was run on these reads is available in Supplementary Data 2 Impact Statement Insertion sequences are a class of transposable element that play an important role in the dissemination of antimicrobial resistance genes. However, it is challenging to completely characterise the transmission dynamics of insertion sequences and their precise contribution to the spread of antimicrobial resistance. The main reasons for this are that it is impossible to identify all insertion sequences based on limited reference databases and that de novo computational methods are ill-equipped to make fast or accurate predictions based on incomplete genomic assemblies. Palidis generates a larger, more comprehensive catalogue of insertion sequences based on a fast algorithm harnessing genomic diversity in mixed microbial communities. This catalogue will enable genomic epidemiologists and researchers to annotate genomes for insertion sequences more extensively and advance knowledge of how insertion sequences contribute to bacterial evolution in general and antimicrobial resistance spread across microbial lineages in particular. This will be useful for genomic surveillance, and for development of microbiome engineering strategies targeting inactivation or removal of important transposable elements carrying antimicrobial resistance genes.
Nonlinear two-dimensional impurity diffusion in semiconductors: A quasi-linear numerical analysis (1984)

A two-dimensional numerical simulation program is proposed which enables the concentration profiles of diffused dopants in semiconductors to be calculated. This program takes the nonlinear phenomena typical of high concentrations into account; however, since the corresponding nonlinear diffusion model is made quasi-linear by means of a suitable transformation of the variable, it becomes almost as easy and efficient as a linear numerical simulation program. The numerical algorithm developed is based on the finite difference Alternating Direction Implicit (ADI) method proposed by Peaceman and Rachford. As a practical application, the two-dimensional doping profiles of arsenic into silicon are calculated for a predeposition process and for a drive-in process following an ion implantation.
Penicillin-Binding Proteins and Alternative Dual-Beta-Lactam Combinations for Serious Enterococcus faecalis Infections with Elevated Penicillin MICs (2023)

Ampicillin-ceftriaxone has become a first-line therapy for Enterococcus faecalis endocarditis. We characterized the penicillin-binding protein (PBP) profiles of various E. faecalis strains and tested for synergy to better inform beta-lactam options for the treatment of E. faecalis infections. We assessed the affinity of PBP2B from elevated-MIC strain E. faecalis LS4828 compared to type strain JH2-2 using the fluorescent beta-lactam Bocillin FL. We also characterized <i>pbp4</i> and <i>pbpA</i> structures and PBP4 and PBP2B expression and used deletion and complementation studies to assess the impact of PBP2B on the levels of resistance. We tested penicillin-susceptible and -resistant E. faecalis isolates against ceftriaxone or ceftaroline combinations with other beta-lactams in 24-h time-kill studies. Two penicillin-susceptible strains (JH2-2 and L2052) had identical <i>pbp</i> sequences and similar PBP expression levels. One reduced-penicillin-susceptibility strain (L2068) had <i>pbp</i> sequences identical to those of the susceptible strains but expressed more PBP4. The second decreased-penicillin-susceptibility strain (LS4828) had amino acid substitutions in both PBP4 and PBP2B and expressed increased quantities of both proteins. PBP2B did not appear to contribute significantly to the elevated beta-lactam MICs. No synergy was demonstrable against the strains with both mutated PBPs and increased expression (L2068 and LS4828). Meropenem plus ceftriaxone or ertapenem plus ceftriaxone demonstrated the most consistent synergistic activity. PBP2B of strain LS4828 does not contribute significantly to reduced penicillin susceptibility. Neither the MIC nor the level of PBP expression correlated directly with the identified synergistic combinations when tested at static subinhibitory concentrations.
Vibration from a riveting hammer causes severe nerve damage in the rat tail model (2011)

Shock-wave vibration causes severe nerve damage. Frequency weighting seriously underestimates the risk of nerve injury with impact tools.
Imaging of Condensed Matter Magnetism Using an Atomic-Sized Sensor (2018)

The development of increasingly sensitive scanning techniques has enabled valuable insights into the physics of interacting condensed matter systems. Recently a new kind of local probe based on Nitrogen-Vacancy (NV) centers in diamond has emerged as a powerful magnetic imaging platform. The NV center has been used for a variety of local measurements including measurements of magnetic fields, imaging of single electron spins with nanometer resolution, magnetic resonance detection of single nuclear spins, as well as measurements of temperature and electric fields. However, imaging an a priori unknown static magnetization structure using a NV center magnetometer is inherently difficult because infinitely many magnetization patterns can produce identical local magnetic fields. In this work I use a scanning NV center magnetometer to image topologically non-trivial magnetization patterns in stacks of thin magnetic films, in which skyrmions had been predicted. I will summarize the details of the experiment crucial to obtaining these data as well as our method for extracting the underlying magnetization structure. As a result of this experiment, we discover a never-before observed type of skyrmion tube whose structure rotates from top to bottom, which has since been confirmed by another technique.
Structure and Reaction Mechanism of Phosphoethanolamine Methyltransferase from the Malaria Parasite Plasmodium falciparum (2011)

In the malarial parasite Plasmodium falciparum, a multifunctional phosphoethanolamine methyltransferase (PfPMT) catalyzes the methylation of phosphoethanolamine (pEA) to phosphocholine for membrane biogenesis. This pathway is also found in plant and nematodes, but PMT from these organisms use multiple methyltransferase domains for the S-adenosylmethionine (AdoMet) reactions. Because PfPMT is essential for normal growth and survival of Plasmodium and is not found in humans, it is an antiparasitic target. Here we describe the 1.55 Å resolution crystal structure of PfPMT in complex with AdoMet by single-wavelength anomalous dispersion phasing. In addition, 1.19-1.52 Å resolution structures of PfPMT with pEA (substrate), phosphocholine (product), sinefungin (inhibitor), and both pEA and S-adenosylhomocysteine bound were determined. These structures suggest that domain rearrangements occur upon ligand binding and provide insight on active site architecture defining the AdoMet and phosphobase binding sites. Functional characterization of 27 site-directed mutants identifies critical active site residues and suggests that Tyr-19 and His-132 form a catalytic dyad. Kinetic analysis, isothermal titration calorimetry, and protein crystallography of the Y19F and H132A mutants suggest a reaction mechanism for the PMT. Not only are Tyr-19 and His-132 required for phosphobase methylation, but they also form a "catalytic" latch that locks ligands in the active site and orders the site for catalysis. This study provides the first insight on this antiparasitic target enzyme essential for survival of the malaria parasite; however, further studies of the multidomain PMT from plants and nematodes are needed to understand the evolutionary division of metabolic function in the phosphobase pathway of these organisms.
Global observation of the ionospheric electronic response to solar events using ground and LEO GPS data (1998)

We present in this work the temporal evolution of the three‐dimensional electron density at global scale during two ionospheric storms (October 18–19, 1995, and January 10, 1997) computed using only actual Global Positioning System data. The tomographic model is solved by means of a Kaiman filtering with a filter updating time of 1 hour in a Sun‐fixed reference frame, and with a resolution of 10 × 10 deg in latitude/local time and 100 km in height including also a protonospheric component (eight layers). The data set contains the data from the International GPS Service IGS (with more than 100 ground GPS stations worldwide distributed) and the GPS/MET low orbiting GPS receiver (both positive and negative elevation observations are used). This means for each storm 1,000,000 of delays, 400 occultations and 3000 unknowns per batch. The International Reference Ionosphere and data coming from the ionosonde of the Ebre observatory are used to show the reliability of the results.
Phased arrays: A strategy to lower the energy threshold for neutrinos (2017)

In-ice radio arrays are optimized for detecting the highest energy, cosmogenic neutrinos expected to be produced though cosmic ray interactions with background photons. However, there are two expected populations of high energy neutrinos: the astrophysical flux observed by IceCube (~1 PeV) and the cosmogenic flux (~ 1017 eV or 100 PeV). Typical radio arrays employ a noise-riding trigger, which limits their minimum energy threshold based on the background noise temperature of the ice. Phased radio arrays could lower the energy threshold by combining the signals from several channels before triggering, thereby improving the signal-to-noise at the trigger level. Reducing the energy threshold would allow radio experiments to more efficiently overlap with optical Cherenkov neutrino telescopes as well as for more efficient searches for cosmogenic neutrinos. We discuss the proposed technique and prototypical phased arrays deployed in an anechoic chamber and at Greenland’s Summit Station.
Pharmacokinetics of novel antimicrobial cationic peptides NAB 7061 and NAB 739 in rats following intravenous administration (2009)

While both compounds had generally similar pharmacokinetics to colistin, even minor alterations in the chemical structures appear to have an impact on their pharmacokinetics, especially on their clearance by the kidney. There are also substantial differences in relation to the relative contributions of renal and non-renal clearance to overall elimination from the body.
Development and validation of a production process of platelet lysate for autologous use (2010)

Growth factors (GF) contained in platelets are a potential source to improve wound healing by the stimulation and acceleration of soft tissue and bone healing. This resulted in the idea that autologous platelet-rich plasma or platelet lysate (PL) containing high levels of GF might improve healing processes. Today platelet products are already applied in bone and maxillofacial surgery. In recent years, cosmetic surgery and facial rejuvenation procedures are growing steadily. New methods including platelet products aiming to induce non-surgical reduction of wrinkles upon topical injection and to minimize surgical risks in general are developed. Several point-of-care devices are already available on the market. However, the amount of PL obtained by these kits is far too high for certain applications in cosmetic surgery and they offer no possibility of storing the remaining material in a sterile manner. Therefore we developed a procedure for the sterile production of smaller amounts of PL in a closed system that can also be split into several products for repeated administration. The closed system was determined to be a bag system designed for an autologous blood donation of 100 ml whole blood. We set a special focus on the validation of the production procedure, mainly regarding sterility and platelet recovery. For validation 22 healthy volunteers were asked for a blood donation, which was centrifuged twice to obtain concentrated platelets (CP). A freeze-thaw cycle caused lysis of the CP to get approximately 8.48 ± 1.36 ml PL. We yielded satisfying results of 100% sterility and a platelet recovery of 36.92% ± 18.71%. We therefore conclude that the PL obtained is ready for studies comparing it with traditional treatments.
Development of an Intelligent Sprayer to Optimize Pesticide Applications in Nurseries and Orchards (2010)

Variable rate spray applications using intelligent control systems can greatly reduce pesticide use and off-target contamination of environment in nursery and orchard productions.The current equipment with variable rate functions for tree crops is limited to ultrasonic sensor based control systems that only detect tree occurrence to switch nozzles on or off and measure tree width in low accuracy to change spray application rates.However, the size and foliage density of canopies can vary greatly with trees even in the same orchard or nursery.The goal of this study was to develop an intelligently functioned sprayer prototype with utilization of a high precision laser scanner controlled system to deliver variable-rate spray outputs that match the canopy sectional structures in real time, in an effort to improve pesticide spray efficiency without reducing the level of crop protection expected from pesticides.A high speed laser scanner was used to acquire data on the geometry, density characteristics and occurrence of the canopy on-the-go.A fast algorithm was developed to calculate tree canopy characteristic parameters using the data from the laser sensor.The algorithm also performed automatic detection of the ground surface, the tree row centerline, and tree width, height, volume and foliage density.A flow rate control unit was designed with Pulse Width Modulation (PWM) signals to adjust the flow rate from each individual nozzle in accordance with the detected tree sectional canopy size and density in real time.A back pressure bypass device was assembled into the spraying
Understanding In-Context Learning via Supportive Pretraining Data (2023)

Xiaochuang Han, Daniel Simig, Todor Mihaylov, Yulia Tsvetkov, Asli Celikyilmaz, Tianlu Wang. Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2023.
Thermal and Microwave-Assisted Rapid Syntheses of Substituted Imidazo[1,2-a]pyridines Under Solvent- and Catalyst-Free Conditions (2011)

a y a p p a Ad i m u r t h y S y n t h e s i s 2 0 1 0 , 6 3 5 .
Oriented arrangement of simple monomers enabled by confinement: towards living supramolecular polymerization (2021)

The living supramolecular polymerization technique provides an exciting research avenue. However, in comparison with the thermodynamic spontaneous nucleation, using simple monomers to realize living supramolecular polymerization is hardly possible from an energy principle. This is because the activation barrier of kinetically trapped simple monomer (nucleation step) is insufficiently high to control the kinetics of subsequent elongation. Here, with the benefit of the confinement from the layered double hydroxide (LDH) nanomaterial, various simple monomers, (such as benzene, naphthalene and pyrene derivatives) successfully form living supramolecular polymer (LSP) with length control and narrow dispersity. The degree of polymerization can reach ~6000. Kinetics studies reveal LDH overcomes a huge energy barrier to inhibit undesired spontaneous nucleation of monomers and disassembly of metastable states. The universality of this strategy will usher exploration into other multifunctional molecules and promote the development of functional LSP.