gebhart/patrepeval huggingface dataset:
Quantitative analysis of 3D stent reconstruction from a limited number of views in cardiac rotational angiography (2007)

Percutaneous coronary angioplasty consists in conducting a guidewire carrying a balloon and a stent through the lesion and deploying the stent by balloon inflation. A stent is a small 3D complex mesh hardly visible in X-ray images : the control of stent deployment is difficult although it is important to avoid post intervention complications. In a previous work, we proposed a method to reconstruct 3D stent images from a set of 2D cone-beam projections acquired in rotational acquisition mode. The process involves a motion compensation procedure based on the position of two markers located on the guidewire in the 2D radiographic sequence. Under the hypothesis that the stent and markers motions are identical, the method was shown to generate a negligible error. If this hypothesis is not fulfilled, a solution could be to use only the images where motion is weakest, at the detriment of having a limiter number of views. In this paper, we propose a simulation based study of the impact of a limited number of views in our context. The chain image involved in the acquisition of X-ray sequences is first modeled to simulate realistic noisy projections of stent animated by a motion close to cardiac motion. Then, the 3D stent images are reconstructed using the proposed motion compensation method from gated projections. Two gating strategies are examined to select projection in the sequences. A quantitative analysis is carried out to assess reconstruction quality as a function of noise and acquisition strategy.
Identification of potent water-soluble DNA-dependent protein kinase (DNA-PK) inhibitors using a small-molecule library approach [abstract] (2008)

4156 The clinical response to DNA-damaging anticancer therapies may be compromised by cellular DNA repair processes, and agents that impede DNA repair are thus of potential therapeutic interest as chemo- and radio-sensitising agents in the treatment of cancer. The phosphatidylinositol-3-kinase related kinase (PIKK) family member DNA-dependent protein kinase (DNA-PK) is a key player in the non-homologous end-joining pathway of DNA double-strand break (DSB) repair. Identification of the lead benzo[h]chromen-4-one DNA-PK inhibitor NU7026 (IC50 = 0.23 μM), guided the subsequent development of the potent and selective ATP-competitive chromenone NU7441 (DNA-PK IC50 = 13 nM). Although proof-of-principle studies with NU7441 confirmed promising activity in vitro as a chemo- and radio-potentiator in a range of human tumour cell lines, further biological studies were hampered by sub-optimal pharmaceutical properties.  Structure-activity relationship studies for DNA-PK inhibition by chromenone-derivatives were conducted in conjunction with homology modelling. This approach predicted the 1-, 8-, and 9-positions on the pendant dibenzothiophen-4-yl substituent of NU7441 as tolerant to substitution without detriment to DNA-PK inhibitory activity. The introduction of suitable functionality (e.g. OH, NH2 CO2H) at these positions provided a platform for the synthesis of focussed libraries of compounds bearing water-solubilising amine substituents. This could be achieved directly at the dibenzothiophene 1-position through nitration and subsequent functional group modification. By contrast, functionalisation of the dibenzothiophene 8- and 9-positions of NU7441 entailed incorporation of the required substituent into a synthetic precursor, prior to construction of the dibenzothiophene ring and coupling to the chromenone scaffold. Interestingly, substitution with a methyl or allyl group at the 3-position of the dibenzothiophen-4-yl ring enabled the separation by chiral hplc of atropisomers, as a consequence of restricted rotation about the dibenzothiophene-chromenone bond, albeit with a marked loss of potency (R = 3-Me, IC50 = 2.5 μM).  Library synthesis was undertaken employing a solution multiple-parallel approach, by O-alkylation (dibromoethane or methyl bromoacetate) or N-acylation (chloroacetyl chloride or 2-bromopropionyl chloride) of the appropriately substituted NU7441 derivatives, respectively, followed by reaction with a range of amines to afford the target compounds. These studies resulted in the identification of compounds that combined potent DNA-PK inhibition with excellent aqueous solubility (20-40 mg/mL as acid salts), without compromising cellular activity. Prominent amongst these derivatives is KU-0060648 (DNA-PK IC50 = 8.6 nM), which exhibits 20-1000 fold selectivity for DNA-PK over related PIKK enzymes and PI3K family members.
High-Resolution Analysis of the Efficiency, Heritability, and Editing Outcomes of CRISPR/Cas9-Induced Modifications of NCED4 in Lettuce (Lactuca sativa) (2018)

CRISPR/Cas9 is a transformative tool for making targeted genetic alterations. In plants, high mutation efficiencies have been reported in primary transformants. However, many of the mutations analyzed were somatic and therefore not heritable. To provide more insights into the efficiency of creating stable homozygous mutants using CRISPR/Cas9, we targeted <i>LsNCED4</i> (<i>9-cis-EPOXYCAROTENOID DIOXYGENASE4)</i>, a gene conditioning thermoinhibition of seed germination in lettuce. Three constructs, each capable of expressing Cas9 and a single gRNA targeting different sites in <i>LsNCED4</i>, were stably transformed into lettuce (Lactuca sativa) cvs. Salinas and Cobham Green. Analysis of 47 primary transformants (T<sub>1</sub>) and 368 T<sub>2</sub> plants by deep amplicon sequencing revealed that 57% of T<sub>1</sub> plants contained events at the target site: 28% of plants had germline mutations in one allele indicative of an early editing event (mono-allelic), 8% of plants had germline mutations in both alleles indicative of two early editing events (bi-allelic), and the remaining 21% of plants had multiple low frequency mutations indicative of late events (chimeric plants). Editing efficiency was similar in both genotypes, while the different gRNAs varied in efficiency. Amplicon sequencing of 20 T<sub>1</sub> and more than 100 T<sub>2</sub> plants for each of the three gRNAs showed that repair outcomes were not random, but reproducible and characteristic for each gRNA. Knockouts of <i>NCED4</i> resulted in large increases in the maximum temperature for seed germination, with seeds of both cultivars capable of germinating >70% at 37°. Knockouts of <i>NCED4</i> provide a whole-plant selectable phenotype that has minimal pleiotropic consequences. Targeting <i>NCED4</i> in a co-editing strategy could therefore be used to enrich for germline-edited events simply by germinating seeds at high temperature.
Effect of Ammonia on Pt, Ru, Rh, and Ni Cathodes During the Alkaline Hydrogen Evolution Reaction (2013)

The effects of ammonia on the hydrogen evolution reaction (HER) with Pt, Rh, Ru, and Ni have been investigated using electrochemical methods. The activity of the catalysts for HER, in the presence of ammonia follows the trend Rh > Pt > Ru > Ni. Pt and Ru exhibit a decrease in the activity toward HER. Cyclic voltammetric (CV) studies show that the presence of ammonia results in weaker metal–hydrogen underpotential deposition (M–Hupd) bonds. In addition, the activity of HER on Pt and Ru is retarded in the presence of ammonia, supporting the theory that the activity for HER is higher on the metal surface with Hupd than on the bare metal. On the contrary, the activity for HER on Rh surface in the presence of ammonia is enhanced, suggesting the M–Hupd bond is a barrier to the HER. CV for Ni in the presence of ammonia shows a Ni(OH)2 reduction peak. However, the overpotentials for HER on Ni are very high such that no significant difference is observed in the activity of HER.
AVR (2018)

Autonomous vehicle prototypes today come with line-of-sight depth perception sensors like 3D cameras. These 3D sensors are used for improving vehicular safety in autonomous driving, but have fundamentally limited visibility due to occlusions, sensing range, and extreme weather and lighting conditions. To improve visibility and performance, not just for autonomous vehicles but for other Advanced Driving Assistance Systems (ADAS), we explore a capability called Augmented Vehicular Reality (AVR). AVR broadens the vehicle's visual horizon by enabling it to wirelessly share visual information with other nearby vehicles, but requires the design of novel relative positioning techniques, new perspective transformation methods, approaches to isolate and predict the motion of dynamic objects in order to hide latency, and adaptive transmission strategies to cope with wireless bandwidth variability. We show that AVR is feasible using off-the-shelf wireless technologies, and it can qualitatively change the decisions made by autonomous vehicle path planning algorithms. Our AVR prototype achieves positioning accuracies that are within a few percent of car lengths and lane widths, and is optimized to process frames at 30fps.
The Acute Encephalopathy Induced by Intake of Sugihiratake Mushroom in the Patients with Renal Damage Might Be Associated with the Intoxication of Cyanide and Thiocyanate (2015)

A novel type of encephalopathy associated with the ingestion of Sugihiratake mushroom (Pleurocybella porrigens) occurred in patients with chronic renal failure treated on hemodialysis in fall, 2004 in Japan. To clarify the mechanism of encephalopathy onset, we, for the first time, purified the cyanogen glycoside fraction (CG) from Sugihiratake mushroom using reversed phase high-performance liquid chromatography and hydrophilic interaction chromatography. Furthermore, we investigated single dose toxicity of the CG in an adenine-induced rat model of chronic renal damage (CRD). Pathological examination of kidneys indicates the development of CRD. Oral administration of the CG induces the accumulation of thiocyanate in the hemolyzed blood and brain in CRD rats, although no morphological changes were found in the brain. No further enhancement of kidney damage is observed after the oral administration of the CG in CRD rats. This is the first experimental report to suggest that acute encephalopathy, induced by Sugihiratake mushroom intake in the patients with chronic renal failure, is associated with intoxication of cyanide and thiocyanate, presumably produced metabolically produced after the ingestion of Sugihiratake mushroom.
Home Location Identification of Twitter Users (2014)

We present a new algorithm for inferring the home location of Twitter users at different granularities, including city, state, time zone, or geographic region, using the content of users’ tweets and their tweeting behavior. Unlike existing approaches, our algorithm uses an ensemble of statistical and heuristic classifiers to predict locations and makes use of a geographic gazetteer dictionary to identify place-name entities. We find that a hierarchical classification approach, where time zone, state, or geographic region is predicted first and city is predicted next, can improve prediction accuracy. We have also analyzed movement variations of Twitter users, built a classifier to predict whether a user was travelling in a certain period of time, and use that to further improve the location detection accuracy. Experimental evidence suggests that our algorithm works well in practice and outperforms the best existing algorithms for predicting the home location of Twitter users.
Genetic characterization of Bordetella pertussis filamentous haemagglutinin: a protein processed from an unusually large precursor (1990)

The nucleotide sequence of the structural gene for filamentous haemagglutinin (FHA), fhaB, a crucial adherence factor for Bordetella pertussis, has been determined. Its 10774 nucleotides are far more than necessary to encode the 220 kD biologically active, mature polypeptide product, suggesting a role for co- or post-translational processing. Fusion proteins derived from various portions of the fhaB open reading frame (ORF) were used to generate polyclonal antisera. Western immunoblot analysis of purified FHA and Bordetella sp. whole cell extracts with these antisera indicated that the 220 kD product is encoded by the 5' portion of the ORF and that the smaller polypeptide species are breakdown products of this polypeptide. These data, as well as N-terminal amino acid sequencing of the major polypeptide species, suggest a scheme for the proteolytic processing of an FHA precursor polypeptide.
Functional lateralization for auditory temporal processing in male and female rats. (1993)

In 3 studies adult male rats showed significantly better discrimination of tone sequences with the right ear than with the left ear. This result parallels similar findings of left-hemisphere specialization for auditory temporal processing in humans and nonhuman primates. Furthermore, because clinical evidence supports a link between specialization of the left hemisphere for auditory temporal processing and for speech processing, these results may reflect evolutionary precursors to left-hemisphere language specialization. Because male rats showed a stronger ear advantage than female rats, the findings may relate to evidence of a stronger right ear advantage in men than in women. Finally, results suggest that neonatal handling enhances lateralization for auditory temporal processing in both sexes. Combined results implicate neuroendocrine mechanisms as important factors in the development of lateralization for auditory temporal processing.
Optical imaging and electrophysiology of rat barrel cortex. I. Responses to small single-vibrissa deflections (1998)

A study was undertaken to investigate the response of the rodent somatosensory barrel cortex to single-whisker, near-threshold vibrissal stimuli. Cortical responses to controlled whisker deflections were recorded by (i) conventional multi-unit extracellular recording within the cytochrome oxidase rich barrels centers and the interbarrel septa, and (ii) intrinsic signal optical imaging, a technique that provides a spatial view of cortical activation thought to be related to the deoxygenation of hemoglobin in activated areas. Barrel cortex neurons responded weakly to whisker deflections of 0.04 degrees. Their response to a series of small stimuli of increasing amplitude was well-fitted by a logarithmic function. Responses to larger stimuli declined monotonically with distance from the center of the barrel column, and were characterized by greater onset and offset firing rates, by greater post-excitatory reduction of firing to below spontaneous levels, and by shorter response latency. In comparison to measurements taken previously from primary vibrissal afferent fibers, we conclude that cortical cells can respond to activity in a very small fraction of first-order sensory neurons.
ChemInform Abstract: THE SYNTHESIS OF NETILMICIN VIA COMPLEXING OF VICINAL AND NON‐VICINAL AMINO‐HYDROXY GROUP PAIRS WITH DIVALENT TRANSITION‐METAL CATIONS (1984)

Abstract Die selektive Acetylierung von Sisomycin (I) führt zu dem Triacetat (II), dessen Struktur durch Hydrolyse zum Garamin‐Derivat (III) gesichert wird.
DNA-Compatible [3 + 2] Nitrone–Olefin Cycloaddition Suitable for DEL Syntheses (2019)

The limited scope of DNA-compatible chemistry restricts the types of chemical features that can be incorporated into DNA-encoded libraries (DELs). Here, a method to synthesize DNA-conjugated polycyclic isoxazolidines via a [3 + 2] nitrone-olefin cycloaddition is described. The reaction is compatible with many olefin-containing substrates and diverse N-alkylhydroxylamines. The ability to perform subsequent DNA ligation and PCR amplification was also confirmed. This methodology facilitates the synthesis of DELs containing topographically complex compounds with underexplored chemical features.
Route Mapping and Biometric Attendance System in School Buses (2020)

Many students are reported to be left behind in school buses unwittingly due to several reasons. Locked-in students might face adverse health issues and might even die due to the suffocation and extreme climate conditions. Hence, tracking a student's entry and exit to a school bus helps avoid the problem. This paper illustrates an attendance approach using biometrics. The system comprises of the smart tablet, a microcontroller-based fingerprint sensor, an automated gate and a developed android application. When integrated in school buses, a student can only board/exit the school bus when his/her fingerprint is recognized. Once students are to be dropped off back home, the system generates a route based on the attended students and furthermore detects and alerts the bus driver if an attended student has not boarded/exited the bus.
Peering into Batteries: Electrochemical Insight through in Situ and Operando Methods over Multiple Length Scales (2021)

In order to overcome the limitations of static and destructive characterizations of Li-ion battery materials and components, comprehensive investigation peering into batteries over various length and time scales is essential. In this regard, emerging in situ and operando characterization methodologies focusing on multiple size domains become a powerful approach to resolve current challenges and navigate future directions. This perspective provides a series of illustrative examples of in situ and operando characterizations over atomic, crystallite/particle, electrode, and battery system length scales with a focus on two electrode material classes: insertion and conversion materials. The operating principles, features, analysis methods, and information gained from each characterization method are discussed. Herein, we present the necessity and opportunity for in situ and operando characterization of electrochemical energy storage materials and systems. Further, we suggest future directions to gain the insight needed to tackle currently intractable issues on Li-ion battery application, failure, and emerging design concepts.
An empirical investigation into a large-scale Java open source code repository (2010)

Getting insight into different aspects of source code artifacts is increasingly important -- yet there is little empirical research using large bodies of source code, and subsequently there are not much statistically significant evidence of common patterns and facts of how programmers write source code. We pose 32 research questions, explain rationale behind them, and obtain facts from 2,080 randomly chosen Java applications from Sourceforge. Among these facts we find that most methods have one or zero arguments or they do not return any values, few methods are overridden, most inheritance hierarchies have the depth of one, close to 50% of classes are not explicitly inherited from any classes, and the number of methods is strongly correlated with the number of fields in a class.
Integrated data conversion for the electron beam exposure system EX-7 (1988)

Because pattern data operations for electron beam (EB) lithography requires the knowledge of shape-to-shape correlation with adjacent patterns, the hierarchical structure embedded with the input data is usually expanded. Consequently, drastic increase in both the processing time and data amount has resulted. To overcome this problem a novel data conversion technique has been developed. It can exploit the hierarchical structure and repetitiveness originally incorporated into large-scale integrated designs to efficiently generate EB pattern data. The conversion technique was implemented on a large-scale computer to make pattern data for the EX-7 EB exposure system. As a result, the highest density levels of 1- and 4-Mbit direct random access memories (DRAMS), scaled down to 0.5 μm, were converted within 0.5 h of central processing unit (cpu) time, achieving an average data compaction of (1)/(20) . Overlap elimination and tone reversal were performed at a speed of 108 primitive shapes per hour. The data amount increased to 40 from 17 Mbytes of uncorrected data, when the proximity effect correction was performed on the shrinked 4-Mbit DRAM pattern using this conversion technique.
Regularization of the improved proportionate affine projection algorithm (2012)

In sparse adaptive filters, the adaptation gain is “proportionately” redistributed among all the coefficients, emphasizing the large ones in order to speed up their convergence. The improved proportionate affine projection algorithm (IPAPA) is a very attractive choice for echo cancellation, since it combines the good convergence features of the affine projection algorithm (APA) and the gain factors of the improved proportionate normalized least-mean-square (IPNLMS) algorithm. Similar to the APA, a matrix inversion is required within the IPAPA. For practical reasons, the matrix needs to be regularized before inversion, i.e., a positive constant is added to the elements of its main diagonal. In this paper, we propose a formula for choosing the regularization parameter of the IPAPA, aiming at attenuating the effects of the noise in the adaptive filter estimate. Simulation results indicate the validity of this approach in both network and acoustic echo cancellation scenarios.
Mobile Code: The Future of the Internet (1999)

Use of the Internet has exploded in recent years with the appearance of the World-Wide Web. In this paper, we show how current technological trends necessarily lead to a system based substantially on mobile code, and in many cases, mobile agents. We discuss several technical and non-technical hurdles along the path to that eventuality. Finally, we predict that, within five years, nearly all major Internet sites will be capable of hosting and willing to host some form of mobile agents.
Signal space and its implementation for microwave nonlinear-network analysis (1998)

Today, harmonic balance is the most useful approach for microwave nonlinear-network analysis. Fast Fourier transform (FFT) is usually used to convert the nonlinear element time waveforms into the frequency domain as part of the harmonic-balance process. This approach is straightforward for a single-frequency excitation, but is quite complicated and time consuming for the multifrequency-excitation case. In this paper, we propose a mathematical model termed "signal space", which enables (for a given nonlinearity) a direct calculation of the current spectrum (given the voltage spectrum) and is suited for implementation for harmonic balance. Under describing-function criteria, we use the signal-space approach to get expressions for oscillator parameters such as oscillation frequency, stability condition, and injection-locking bandwidth. There is a good, agreement between our results and Kurakawa's expressions.
Low-Cost Self-Assembled Oxide Separator for Rechargeable Batteries (2019)

Rechargeable battery cells having a liquid electrolyte require a separator permeable to the electrolyte between the two electrodes. The volume changes of the electrodes during charge and discharge have previously limited porous separators to polymers with an electronic energy gap E g large enough for the Fermi levels of the two electrodes to be within it. We demonstrate that the plasticity of a costly polymer membrane is not needed for the separator in a liquid electrolyte. SiO 2 is an insulator with the required large energy gap, and SiO 2 particles are easy to prepare, cheap, and environmentally friendly. We demonstrate that removal of adsorbed species from the surface of a film of SiO 2 nanoparticles leads to weak bonding between the particles to give a self-assembled, porous layer that has the needed plasticity for a liquid-electrolyte separator that is wet by an alkali-metal anode.