gebhart/patrepeval huggingface dataset:
Position-restricted approximate string matching with metric Hamming distance (2017)

Approximate string matching is an important problem in many applications such as computer security, bioinformatics, and time series analysis. This paper presents a simple data structure for the position-restricted approximate string matching problem under a metric distance measure. In the problem discussed in this paper, a query is given as a triplet of a pattern string of a fixed length, a threshold, and a searching interval, so all occurrences of the pattern in the interval on a preprocessed text allowing errors within the threshold should be reported. Our proposed method is a framework which combines metric data structures and succinct rank/select data structure, and allows to execute such position-restricted approximate string matching queries efficiently. We show the experimental results to demonstrate when and how our method outperforms other alternatives.
On the effect of phase noise and time-selective channel on OFDM transmission: SINR analysis (2012)

This paper studies the detrimental effect of phase noise on the performance of orthogonal frequency division multiplexing (OFDM) transmissions over time-selective channels. In the literature, most of existing papers analyze the performance of OFDM systems in the presence of either time-selective channels or phase noise. Unlike the existing studies, this paper formulates an approximate expression of signal-to-interference-plus-noise ratio (SINR) at an OFDM receiver in the presence of both phase noise and time-selective channel response. The formulated SINR expression can be used as guidelines in determining appropriate OFDM transmission settings under a given quality-of-service (QoS) requirement. To illustrate the tightness of the approximate SINR formulation, empirical and theoretical values of SINR under different OFDM system settings are presented in this paper.
The Magnitude and IgG Subclass of Antibodies Elicited by Targeted DNA Vaccines Are Influenced by Specificity for APC Surface Molecules (2018)

Upon APC-targeted DNA vaccination, transfected cells secrete fusion proteins with targeting units specific for surface molecules on APC. In this study, we have tested several different targeting units for their ability to influence the magnitude and subclass of Ab responses to hemagglutinin from influenza A virus. The experiments employed bivalent homodimeric Ig-based molecules (vaccibodies). The overall efficiency in BALB/c mice depended on the targeting units in the following order: αMHC class II > αCD11c > αCD40 > Xcl-1 = MIP-1α > FliC > GM-CSF > Flt-3L > αDEC205. GM-CSF induced mainly IgG1, whereas Xcl1, MIP-1α, αCD40, and αDEC205 induced predominantly IgG2a. A more balanced mixture of IgG1 and IgG2a was observed with αCD11c, αMHC class II, Flt-3L, and FliC. Similar results of IgG subclass-skewing were obtained in Th1-prone C57BL/6 mice with a more limited panel of vaccines. IgG1 responses in BALB/c occurred early after immunization but declined relatively rapidly over time. IgG2a responses appeared later but lasted longer (>252 d) than IgG1 responses. The most efficient targeting units elicited short- and long-term protection against PR8 influenza (H1N1) virus in BALB/c mice. The results suggest that targeting of Xcr1<sup>+</sup> conventional type 1 dendritic cells preferentially induces IgG2a responses, whereas simultaneous targeting of several dendritic cell subtypes also induces IgG1 responses. The induction of distinct subclass profiles by different surface molecules supports the APC-B cell synapse hypothesis. The results may contribute to generation of more potent DNA vaccines that elicit high levels of Abs with desired biologic effector functions.
Fabrication and evaluation of GaN negative and bifocal microlenses (2005)

Methods of fabricating negative and bifocal microlens arrays have been demonstrated in this paper. The technique of photoresist molding using a sapphire positive lens template was used for the patterning of negative microlenses, while the bifocal microlens arrays were fabricated using a two-step etch process. In both cases, the lenses were etched using inductively coupled plasma. Microlenses with diameters as small as 10μm have been demonstrated and were characterized using atomic force microscopy and confocal microscopy. The lens arrays were found to be smooth, uniform, and to have focal lengths consistent with their design and calculated values.
Selective Inhibitors of Dual Leucine Zipper Kinase (DLK, MAP3K12) with Activity in a Model of Alzheimer’s Disease (2017)

Significant data exists to suggest that dual leucine zipper kinase (DLK, MAP3K12) is a conserved regulator of neuronal degeneration following neuronal injury and in chronic neurodegenerative disease. Consequently, there is considerable interest in the identification of DLK inhibitors with a profile compatible with development for these indications. Herein, we use structure-based drug design combined with a focus on CNS drug-like properties to generate compounds with superior kinase selectivity and metabolic stability as compared to previously disclosed DLK inhibitors. These compounds, exemplified by inhibitor 14, retain excellent CNS penetration and are well tolerated following multiple days of dosing at concentrations that exceed those required for DLK inhibition in the brain.
A Novel Two-Section Tunable Discrete Mode Fabry-PÉrot Laser Exhibiting Nanosecond Wavelength Switching (2008)

A novel widely tunable laser diode is proposed and demonstrated. Mode selection occurs by etching perturbing slots into the laser ridge. A two-section device is realized with different slot patterns in each section allowing Vernier tuning. The laser operates at 1.3 mum and achieves a maximum output power of 10 mW. A discontinuous tuning range of 30 nm was achieved with a side mode suppression greater than 30 dB. Wavelength switching times of approximately 1.5 ns between a number of wavelength channels separated by 7 nm have been demonstrated.
Maternal and Early Postnatal Immune Activation Produce Dissociable Effects on Neurotransmission in mPFC–Amygdala Circuits (2018)

Inflammatory processes may be involved in the pathophysiology of neuropsychiatric illnesses including autism spectrum disorder (ASD). Evidence from studies in rodents indicates that immune activation during early development can produce core features of ASD (social interaction deficits, dysregulation of communication, increases in stereotyped behaviors, and anxiety), although the neural mechanisms of these effects are not thoroughly understood. We treated timed-pregnant mice with polyinosinic:polycytidylic acid (Poly I:C), which simulates a viral infection, or vehicle on gestational day 12.5 to produce maternal immune activation (MIA). Male offspring received either vehicle or lipopolysaccharide, which simulates a bacterial infection, on postnatal day 9 to produce postnatal immune activation (PIA). We then used optogenetics to address the possibility that early developmental immune activation causes persistent alterations in the flow of signals within the mPFC to basolateral amygdala (BLA) pathway, a circuit implicated in ASD. We found that our MIA regimen produced increases in synaptic strength in glutamatergic projections from the mPFC to the BLA. In contrast, our PIA regimen produced decreases in feedforward GABAergic inhibitory postsynaptic responses resulting from activation of local circuit interneurons in the BLA by mPFC-originating fibers. Both effects were seen together when the regimens were combined. Changes in the balance between excitation and inhibition were differentially translated into the modified spike output of BLA neurons. Our findings raise the possibility that prenatal and postnatal immune activation may affect different cellular targets within brain circuits that regulate some of the core behavioral signs of conditions such as ASD.<b>SIGNIFICANCE STATEMENT</b> Immune system activation during prenatal and early postnatal development may contribute to the development of autism spectrum disorder (ASD). Combining optogenetic approaches and behavioral assays that reflect core features of ASD (anxiety, decreased social interactions), we uncovered mechanisms by which the ASD-associated behavioral impairments induced by immune activation could be mediated at the level of interactions within brain circuits implicated in control of emotion and motivation (mPFC and BLA, specifically). Here, we present evidence that prenatal and postnatal immune activation can have different cellular targets in the brain, providing support to the notion that the etiology of ASD may be linked to the excitation/inhibition imbalance in the brain affecting the signal flow within relevant behavior-driving neural microcircuits.
Non-uniform random number generation through piecewise linear approximations (2007)

A hardware architecture for non-uniform random number generation, which allows the generator's distribution to be modified at run-time without reconfiguration is presented. The architecture is based on a piecewise linear approximation, using just one table lookup, one comparison and one subtract operation to map from a uniform source to an arbitrary non-uniform distribution, resulting in very low area utilisation and high speeds. Customisation of the distribution is fully automatic, requiring less than a second of CPU time to approximate a new distribution, and typically around 1000 cycles to switch distributions at run-time. Comparison with Gaussian-specific generators shows that the new architecture uses less than half the resources, provides a higher sample rate and retains statistical quality for up to 50 billion samples, but can also generate other distributions. When higher statistical quality is required and multiple samples are required per cycle, a two-level piecewise generator can be used, reducing the RAM required per generated sample while retaining the simplicity and speed of the basic technique.
Early Experience With Pay-for-Performance (2005)

Paying clinicians to reach a common, fixed performance target may produce little gain in quality for the money spent and will largely reward those with higher performance at baseline.
Electrodeposition of iron-chromium-nickel alloy (1987)

Un depot electrolytique d'alliage Fe-18%Cr-8%Ni a ete realise a partir d'un bain de sulfate contenant glycine et acide borique. On etudie l'influence de la glycine, des autres parametres de depot (densite de courant, pH, temperature) et des conditions hydrodynamiques sur la qualite et la composition des alliages deposes
COVID-19 Contact-tracing Apps: a Survey on the Global Deployment and Challenges (2020)

To address the massive spike in uncertainties triggered by the coronavirus disease (COVID-19), there is an ever-increasing number of national governments that are rolling out contact-tracing Apps to aid the containment of the virus. The first hugely contentious issue facing the Apps is the deployment framework, i.e. centralized or decentralized. Based on this, the debate branches out to the corresponding technologies that underpin these architectures, i.e. GPS, QR codes, and Bluetooth. This work conducts a pioneering review of the above scenarios and contributes a geolocation mapping of the current deployment. The Apps vulnerabilities and the directions of research are identified, with a special focus on the Bluetooth-inspired decentralized paradigm.
INTRODUCTION TO CLASSICAL AND MODERN OPTICS (1984)

REVIEWER'S ADDRESS: William F. Long School of Optometry University of Missouri-St. Louis St. Louis, Missouri 63121
Novel Inter-Mode Decision Algorithm Based on Macroblock (MB) Tracking for the P-Slice in H.264/AVC Video Coding (2008)

We propose a fast macroblock (MB) mode prediction and decision algorithm based on temporal correlation for P-slices in the H.264/AVC video standard. There are nine 4times4 and 8times8 modes, and four 16 times 16 modes in the intra-mode prediction and 8 block types including SKIP mode exist for the best coding gain based on rate-distortion (R-D) optimization. This scheme gives rise to exhaustive computations (search) in the coding procedure. To overcome this problem, a thresholding method for fast inter-mode decision using an MB tracking scheme to find the most correlated block and the R-D cost of that block, are suggested for early inter-mode determination. An inter-mode candidate selection method is first suggested through the statistical analysis. Then, an adaptive inter-mode search algorithm is applied by using the R-D cost of the most correlated MB. Through comparative analysis, a speed-up factor of up to 70.83 % was verified with a negligible bit increment and a minimal loss of image quality.
Analysis and design of full-bridge LC parallel resonant plasma driver with variable-inductor based phase control (2010)

This paper presents the analysis and design of the full-bridge (FB) LC parallel resonant plasma driver at the radio-frequency (RF) operation with variable-inductor based phase control scheme. Since the switching frequency of the RF plasma module is mainly fixed at 13.56MHz for EMC regulation, the variable-inductor control scheme can adjust the transconductance amplitude to enable load-current regulation. Additionally, in order to have minimal conduction loss on the switches, the design criterion of the required dead-time for ZVS condition with the minimal circulating current of the LC parallel resonant tank is required. Based on the equivalent circuit models of the RF plasma module described prior work, the analysis and design of the driver for the RF plasma module are presented. Finally, by using the SIMPLIS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> simulation software, the FB LC parallel resonant plasma driver with the variable-inductor based phase control is simulated to validate the achievement of required functions. Furthermore, the dead-times and lagging phases are obtained from the simulation results, which are compared with the calculated results to validate the feasibility of design criterion.
Tissue-Nonspecific Alkaline Phosphatase Acts Redundantly with PAP and NT5E to Generate Adenosine in the Dorsal Spinal Cord (2013)

Prostatic acid phosphatase (PAP) and ecto-5'-nucleotidase (NT5E) hydrolyze extracellular AMP to adenosine in dorsal root ganglia (DRG) neurons and in the dorsal spinal cord. Previously, we found that adenosine production was reduced, but not eliminated, in Pap⁻/⁻/Nt5e⁻/⁻ double knock-out (dKO) mice, suggesting that a third AMP ectonucleotidase was present in these tissues. Here, we found that tissue-nonspecific alkaline phosphatase (TNAP, encoded by the Alpl gene) is expressed and functional in DRG neurons and spinal neurons. Using a cell-based assay, we found that TNAP rapidly hydrolyzed extracellular AMP and activated adenosine receptors. This activity was eliminated by MLS-0038949, a selective pharmacological inhibitor of TNAP. In addition, MLS-0038949 eliminated AMP hydrolysis in DRG and spinal lamina II of dKO mice. Using fast-scan-cyclic voltammetry, we found that adenosine was rapidly produced from AMP in spinal cord slices from dKO mice, but virtually no adenosine was produced in spinal cord slices from dKO mice treated with MLS-0038949. Last, we found that AMP inhibited excitatory neurotransmission via adenosine A1 receptor activation in spinal cord slices from wild-type, Pap⁻/⁻, Nt5e⁻/⁻, and dKO mice, but failed to inhibit neurotransmission in slices from dKO mice treated with MLS-0038949. These data suggest that triple elimination of TNAP, PAP, and NT5E is required to block AMP hydrolysis to adenosine in DRG neurons and dorsal spinal cord. Moreover, our data reveal that TNAP, PAP, and NT5E are the main AMP ectonucleotidases in primary somatosensory neurons and regulate physiology by metabolizing extracellular purine nucleotides.
Antisense Oligonucleotide Treatment Enhances the Recovery of Acute Lung Injury through IL-10–Secreting M2-like Macrophage-Induced Expansion of CD4+ Regulatory T Cells (2013)

MicroRNAs (miRNAs) have been shown as an important regulator in the pathologies of acute lung injury (ALI). However, the potential effect of miRNA-based therapeutic studies in ALI remains poorly understood. We assessed the effect of antisense oligonucleotides (ASOs) against miR-155 on the development of ALI using a murine ALI model. We found that miR-155 ASO treatment could enhance the recovery of ALI as evidenced by accelerated body weight back, reduced level of bronchoalveolar lavage (BAL) protein and proinflammatory cytokines, and reduced number of BAL cells. Adoptive cell transfer assay in RAG1(-/-) mice showed that CD4(+)CD25(+) regulatory T cells (Tregs) mediated the enhanced recovery of ALI. Mechanistic evidence showed that enhanced expansion of Tregs in vivo, dominantly induced by IL-10-secreting M2-like macrophages, was critical for their elevated proportion in miR-155 ASO-treated ALI mice. Finally, we report that C/EBPβ, a target molecule of miR-155, was upregulated and associated with IL-10 secretion and M2-like phenotype of macrophages. These data provided a previously unknown mechanism for miRNA-based therapy against ALI, which could ultimately aid the understanding of recovery of ALI and the development of new therapeutic strategies against clinical inflammatory lung disease.
Developing templates for integrating quantitative geophysics and hydraulic fracture completions data: Part I ‐ Principles and theory (2011)

Unconventional resource plays require that geophysicists redefine the value seismic brings for economic development of these assets. A large part of developing resource plays comes from optimizing engineering practices. Understanding that seismic data contains information regarding resource potential, rock properties, in‐situ stress, reservoir pressure and fracture intensity/orientation allows for educated and optimized large scale development plans. The heuristic interpretation templates provided herein outline a method to interpret seismic data for estimated ultimate recovery (EUR) and the important physical properties for hydraulic fracturing all of which provide insight for optimizing completion efforts.
Sensor-Less Five-Level Packed U-Cell (PUC5) Inverter Operating in Stand-Alone and Grid-Connected Modes (2015)

In this paper, a new mode of operation has been introduced for packed U-cell (PUC) inverter. A sensor-less voltage control based on redundant switching states is designed for the five-level packed U-cell (PUC5) inverter, which is integrated into switching process. The sensor-less voltage control is in charge of fixing the dc capacitor voltage at half of the dc source value results in generating symmetric five-level voltage waveform at the output with low harmonic distortion. The sensor-less voltage regulator reduces the complexity of the control system, which makes the proposed converter appealing for industrial applications. An external current controller has been applied for grid-connected application of the introduced sensor-less PUC5 to inject active and reactive power from inverter to the grid with arbitrary power factor, while the PUC auxiliary dc bus is regulated only by sensor-less controller combined with new switching pattern. Experimental results obtained in stand-alone and grid-connected operating modes of proposed PUC5 inverter prove the fast response and good dynamic performance of the designed sensor-less voltage control in balancing the dc capacitor voltage at desired level.
Disaccharides Impact the Lateral Organization of Lipid Membranes (2014)

Disaccharides are well-known for their membrane protective ability. Interaction between sugars and multicomponent membranes, however, remains largely unexplored. Here, we combine molecular dynamics simulations and fluorescence microscopy to study the effect of mono- and disaccharides on membranes that phase separate into Lo and Ld domains. We find that nonreducing disaccharides, sucrose and trehalose, strongly destabilize the phase separation leading to uniformly mixed membranes as opposed to monosaccharides and reducing disaccharides. To unveil the driving force for this process, simulations were performed in which the sugar linkage was artificially modified. The availability of accessible interfacial binding sites that can accommodate the nonreducing disaccharides is key for their strong impact on lateral membrane organization. These exclusive interactions between the nonreducing sugars and the membranes may rationalize why organisms such as yeasts, tardigrades, nematodes, bacteria, and plants accumulate sucrose and trehalose, offering cell protection under anhydrobiotic conditions. The proposed mechanism might prove to be a more generic way by which surface bound agents could affect membranes.
An approach to the diagnosis and management of systemic vasculitis (2010)

The systemic vasculitides are a complex and often serious group of disorders which, while uncommon, require careful management in order to ensure optimal outcome. In most cases there is no known cause. Multi-system disease is likely to be fatal without judicious use of immunosuppression. A prompt diagnosis is necessary to preserve organ function. Comprehensive and repeated disease assessment is a necessary basis for planning therapy and modification of treatment protocols according to response. Therapies typically include glucocorticoids and, especially for small and medium vessel vasculitis, an effective immunosuppressive agent. Cyclophosphamide is currently the standard therapy for small vessel multi-system vasculitis, but other agents are now being evaluated in large randomized trials. Comorbidity is common in patients with vasculitis, including the cumulative effects of potentially toxic therapy. Long-term evaluation of patients is important in order to detect and manage relapses.
Critical evaluation of sampling techniques for residual glucose determination in carbon‐limited chemostat culture of <i>Saccharomyces cerevisiae</i> (2003)

In this paper, three sampling techniques for rapid quenching of cellular metabolism and subsequent separation of cells from fermentation broth are compared: (i) quick freezing of fermentation broth directly in liquid nitrogen; (ii) quenching metabolism by exposing the fermentation broth to stainless steel beads (4-mm diameter) in a filter syringe precooled to -18 degrees C; and (iii) withdrawal of the filtrate through a 0.45 microm filter attached to a syringe and a needle inserted directly into the fermentor. It was concluded that use of liquid nitrogen as a quenching method to rapidly arrest cellular metabolism, for quantitative analysis of extracellular glucose, is not a very reliable method and that the filter syringe steel beads work very well.
An adaptive scan generator for a scanning tunneling microscope (1994)

A novel scan generator for a scanning tunneling microscope (STM) has been developed. The instrument compares tunneling current with three thresholds values, to generate an x-scanner signal with a dynamically changeable step size for adaptation to sharp topographical changes. It has two advantages compared to conventional STM scan generators (i) a better protection from a tip crash and (ii) minimization of the image acquisition time. The implementation is made with a digital signal processor (DSP) DSP32C from AT&T, mounted on a commercially available PC AT-compatible plug-in card. Test images of extremely rough surfaces confirm the usefulness of our novel scan generator. The concept could also be used for different scanning probe microscopes.
Capillary flow control in nanochannels via hybrid surface (2015)

We report a simple and effective approach to control the speed of capillary flow in nanochannels in a quantitative manner.