gebhart/patrepeval huggingface dataset:
GNSS Antenna Arrays Hardware requirements for algorithm implementation (2006)

GNSS antenna arrays and beam forming/nulling have long been studied from an algorithm perspective. However, the hardware and implementation design issues are not as well understood. A low cost data collection platform for continuous recording of eight simultaneous IF streams are presented with an analysis of its performance. Also, the requirements on front end components are examined, specifically their impact on array processing versus single antenna processing. Focus is exclusively on digital beam forming as that is the only feasible approach for advanced algorithm implementation, and differences between traditional receiver architectures and a software defined radio approach will be emphasized. It is found that simultaneous recording of multiple IF streams allows for great flexibility in the field of antenna array processing for GNSS. Also, commercial off the shelf components shows sufficient performance, although care must be taken regarding issues such as phase consistency and cross talk between front ends.
Identification of Off-Patent Drugs That Reverse Daunorubicin Efflux Mediated by ABCB1 in T-ALL Cells. (2006)

Abstract In acute leukemias, the overexpression of P-glycoprotein, encoded by the ATP Binding Cassette B1 (ABCB1) gene contributes to multidrug resistance (MDR), and is considered one of the major obstacles to successful cancer chemotherapy. The identification of small molecules that reverse ABCB1 efflux activity is critical for the successful treatment of cancers, including relapsed T-lineage acute lymphoblastic leukemia (T-ALL). However, the dose-limiting toxicities of many MDR reversal agents have restricted their use in clinical trials, and more effective and clinically applicable reversal agents remain to be identified. We have recently developed a T-ALL cell line that overexpresses ABCB1 and exhibits multiple drug resistance (MDR) to daunorubicin, prednisolone, and vincristine, but not L-asparaginase. The MDR can be reversed by suppression of ABCB1 expresssion with siRNA or 5 μM cyclosporine (CSA). Using this cell line, we developed a flow cytometry based, high-throughput screening assay that quantifies ABCB1 efflux using the fluorescent probe JC-1 (Swerts, et al Leuk Lymphoma 45:2221–8, 2004). We screened a library of 880 off-patent drugs for their ability to inhibit ABCB1 efflux at concentrations of 4 μM, and 19 compounds were identified, including CSA. Based on a published record of safe internal use in humans, 12 compounds were retained for further analysis (3 compounds were originally described as calcium channel blockers, 1 as sodium channel blocker, 1 as ACE inhibitor, 1 as dopamine uptake inhibitor, 1 as Topoisomerase II inhibitor, 2 as steroids, 2 as antifungal and 1 as immunosuppressant). We determined the 50% inhibitory concentration (IC50) of drug for ABCB1 efflux, the efflux reversal concentration of drug that rescued DNR-induced T-ALL cell death (ECrev50), and the corresponding in vitro toxic dose in 50% of treated T-ALL cells (TD50). Due to space limitations, detailed data could not be presented in the abstract. To our knowledge, 8 of the 12 compounds have not been previously described as ABCB1 inhibitors. These compounds may be useful as chemosensitizers or as lead compounds for development of improved ABCB1 inhibitors in T-ALL as well as other cancers.
Front Cover: Asymmetric Spirobiacridine‐based Delayed Fluorescence Emitters for High‐performance Organic Light‐Emitting Devices (Chem. Eur. J. 42/2021) (2021)

Horizontally oriented thermally activated delayed fluorescent (TADF) emitters realizing high-performance sky-blue organic light-emitting devices (OLEDs) are reported in this work. The cover image represents that triphenyltriazine-based TADF emitters maximize the potential of sky-blue TADF OLEDs. The small structural differences in acceptor units makes a significant differences to device performance. More information can be found in the Full Paper by H. Sasabe, J. Kido et al. (DOI: 10.1002/chem.20101188).
Video generation for high spatio-temporal resolution imaging (2009)

We propose a color video generation method for spatio-temporal high-resolution video imaging in dark conditions. The proposed method consists of two steps. First, RGB-separated video sequences with different spatio-temporal resolution sets are captured to increase the amount of captured light. Second, a high spatio-temporal resolution color video is reconstructed from those input video sequences in the regularization framework. We show the advantages of our method using a prototype camera system and simulation results.
Multiple-frequency phased array pattern synthesis for HIFU surgery (2011)

We present a simulation/experimental study to evaluate and optimize the focusing capabilities of a phased array prototype when excited by multiple-frequency components. A multiple-focus multiple-frequency pattern synthesis algorithm for phased arrays has been developed and tested using linear simulations in Matlab. The algorithm maintains the precise phase relationship between the frequency components at each focal spot to achieve a desirable therapeutic outcome. Preliminary simulations indicate that the focal region can be shaped based on the alignment and phase of multiple-frequency components. The pattern synthesis algorithm is experimentally validated with a 3.5 MHz, 64-element prototype designed for small-animal and superficial therapeutic HIFU applications (Imasonic, Inc) which has a 52% fractional bandwidth, allowing for therapeutic output in the frequency range of 2.7-4.6 MHz. Validation with hydrophone measurements at the focal locations showed that there is in increase in harmonic generation at the focal point with the frequency mixed patterns when compared to a conventional single frequency excitation pattern. This increased non-linearity, will allow for increased thermal absorption at the focal point, thus allowing for larger treatment volumes with the same total power or reduced treatment time per shot when compared to the single frequency case. Ex vivo experiments with fresh porcine liver were conducted to study the effect of multiple-frequency patterns when compared with conventional single frequency patterns during lesion formation. The lesion size was increased for the multiple-frequency patterns when compared the single frequency pattern at normalized power with respect to each other. In conclusion, wideband piezocomposite array transducers, together with multi-channel arbitrary waveform generators are enabling technologies which allow for complex, multiple-focus, multiple-frequency HIFU patterns. These patterns can enhanced the focal gain with proper phase alignment. Furthermore, multiple frequency patterns have been shown to be able to increase the harmonic generation at the focal spot, thus improving local absorption. Our early results with ex vivo porcine liver indicate that multiple frequency excitation can enhance the therapeutic gain at the focal points.
Numeric and Symbolic Programs (1993)

This paper describes a new technique for estimating and understanding the speed improvement that can result from executing a program on a parallel computer. The technique requires no additional programming and minimal effort by a program's author. The analysis begins by tracing a sequential program. A parallelism analyzer (pp) uses information from the trace to simulate parallel execution of the program. In addition to predicting parallel performance, pp measures many aspects of a program's dynamic behavior. This paper presents measurements of six substantial programs. These results indicate that the three symbolic (nonnumeric) programs differ substantially from the numeric programs and, as a consequence, cannot be automatically parallelized with the same compilation techniques.
Smart procurement of naturally generated energy (SPONGE) for PHEVs (2016)

In this paper, we propose a new engine management system for hybrid vehicles to enable energy providers and car manufacturers to provide new services. Energy forecasts are used to collaboratively orchestrate the behaviour of engine management systems of a fleet of plug-in hybrid electric vehicle (PHEVs) to absorb oncoming energy in a smart manner. Cooperative algorithms are suggested to manage the energy absorption in an optimal manner for a fleet of vehicles, and the mobility simulator SUMO (Simulation of Urban MObility) is used to demonstrate the efficacy of the proposed idea.
Effect of TxID signal on the performance of the legacy ATSC terrestrial DTV receivers (2011)

In this paper, the effect of the TxID signal on the performance of the legacy ATSC terrestrial DTV receivers is investigated not only with extensive computer simulation but also with laboratory and field tests. According to the various test results, the performance loss of the conventional DTV receiver due to the TxID signal is less than 0.2 dB in average when the TxID signal is injected 30 dB below the DTV signal.
Analyzing Web Search Behavior for Software Engineering Tasks (2019)

Web search plays an integral role in software engineering (SE) to help with various tasks such as finding documentation, debugging, installation, etc. In this work, we present the first large-scale analysis of web search behavior for SE tasks using the search query logs from Bing, a commercial web search engine. First, we use distant supervision techniques to build a machine learning classifier to extract the SE search queries with an F1 score of 93%. We then perform an analysis on one million search sessions to understand how software engineering related queries and sessions differ from other queries and sessions. Subsequently, we propose a taxonomy of intents to identify the various contexts in which web search is used in software engineering. Lastly, we analyze millions of SE queries to understand the distribution, search metrics and trends across these SE search intents. Our analysis shows that SE related queries form a significant portion of the overall web search traffic. Additionally, we found that there are six major intent categories for which web search is used in software engineering. The techniques and insights can not only help improve existing tools but can also inspire the development of new tools that aid in finding information for SE related tasks.
Modeling Pulmonary Cystic Fibrosis in a Human Lung Airway-on-a-chip (2021)

Abstract Background Cystic fibrosis (CF) is a genetic disease caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR), which results in impaired airway mucociliary clearance, inflammation, infection, and respiratory insufficiency. The development of new therapeutics for CF are limited by the lack of reliable preclinical models that recapitulate the structural, immunological, and bioelectrical features of human CF lungs. Methods We leveraged organ-on-a-chip technology to develop a microfluidic device lined by primary human CF bronchial epithelial cells grown under an air-liquid interface and interfaced with pulmonary microvascular endothelial cells (CF Airway Chip) exposed to fluid flow. The responses of CF and healthy Airway Chips were analyzed in the presence or absence of polymorphonuclear leukocytes (PMNs) and the bacterial pathogen, Pseudomonas aeruginosa . Results The CF Airway Chip faithfully recapitulated many features of the human CF airways, including enhanced mucus production, increased cilia density and a higher ciliary beating frequency compared to chips lined by healthy bronchial epithelial cells. The CF chips also secreted higher levels of IL-8, which was accompanied by enhanced PMN adhesion to the endothelium and transmigration into the airway compartment. In addition, CF Airway Chips provided a more favorable environment for Pseudomonas aeruginosa growth, which resulted in enhanced secretion of inflammatory cytokines and recruitment of PMNs to the airway. Conclusions The human CF Airway Chip may provide a valuable preclinical tool for pathophysiology studies as well as for drug testing and personalized medicine.
Appendix B. Location Determination (1990)

This is the completely revised and updated version of the popular and highly regarded textbook, Applied Geophysics. It describes the physical methods involved in exploration for hydrocarbons and minerals, which include gravity, magnetic, seismic, electrical, electromagnetic, radioactivity, and well-logging methods. All aspects of these methods are described, including basic theory, field equipment, techniques of data acquisition, data processing and interpretation, with the objective of locating commercial deposits of minerals, oil, and gas and determining their extent. In the fourteen years or so since the first edition of Applied Geophysics, many changes have taken place in this field, mainly as the result of new techniques, better instrumentation, and increased use of computers in the field and in the interpretation of data. The authors describe these changes in considerable detail, including improved methods of solving the inverse problem, specialized seismic methods, magnetotellurics as a practical exploration method, time-domain electromagnetic methods, increased use of gamma-ray spectrometers, and improved well-logging methods and interpretation.
Targetting of protein phosphatase 1 to the sarcoplasmic reticulum of rabbit skeletal muscle by a protein that is very similar or identical to the G subunit that directs the enzyme to glycogen (1990)

The amount of protein phosphatase 1 (PP1) activity in rabbit skeletal muscle associated with membranes (predominantly sarcoplasmic reticulum) is similar to that bound to glycogen-protein particles. Membrane-vesicle-associated (sarcovesicular) PP1 can be solubilised with 0.5% Triton X-100 (but not 0.5M NaCl) and is complexed to a protein that is structurally and functionally very similar or identical to the G subunit which targets PP1 to glycogen-protein particles. This conclusion is based on immunoblotting and immunotitration experiments using two different preparations of G-subunit-specific antibodies, binding of Triton-solubilised sarcovesicular enzyme to glycogen, stimulation of phosphorylase phosphatase activity by glycogen, phosphorylation of the same tryptic peptides by cyclic-AMP-dependent protein kinase (A-kinase) and release of catalytic subunit following phosphorylation by A-kinase. Membrane-association is not mediated via glycogen because sarcovesicular PP1 is (1) not released by digestion with alpha-amylase or at dilutions which fully dissociate the glycogen-bound enzyme, and (2) is solubilised by Triton X-100 (whereas glycogen-associated PP1 is not). These findings demonstrate that sarcovesicular PP1 is highly homologous to, or the same as, glycogen-associated PP1G and raises the possibility that a common targetting subunit may direct PP1 to different subcellular locations.
Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 2. Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives (2016)

Following the discovery of cell penetrant pyridine-4-carboxylate inhibitors of the KDM4 (JMJD2) and KDM5 (JARID1) families of histone lysine demethylases (e.g., 1), further optimization led to the identification of non-carboxylate inhibitors derived from pyrido[3,4-d]pyrimidin-4(3H)-one. A number of exemplars such as compound 41 possess interesting activity profiles in KDM4C and KDM5C biochemical and target-specific, cellular mechanistic assays.
Hard x-ray focusing optics for concealed object detection (2006)

In this paper, we discuss hard x-ray optics, in general, and lobster-eye focusing optics, in particular, for concealed object detection, at longer distances. The longer distance (~50m) scenario is important for Improvised Explosives Detection (IED), "seeing through walls," "seeing objects under ground," and related applications.
Direct Imaging of Intermolecular Bonds in Scanning Tunneling Microscopy (2010)

Local, noncovalent intermolecular interactions in organic monolayers have been directly imaged using scanning tunneling hydrogen microscopy (STHM). Unprecedented spatial resolution directly reveals the relation between the intermolecular interactions, the molecular chemical structure, and the ordering in the film.
Time series data analysis in multiple granularity levels (2009)

A single-pass method for analysing time series data and extracting time-correlations (time-delayed relationships) among multiple time series data streams is described. The proposed method can detect and report time-delayed relationships among multiple time series data streams without having to transform the original data into another domain. Each time-correlation rule explains how the changes in the values of one set of time series data streams influence the values in another set of time series data streams. Those rules can be stored digitally and fed into various data analysis tools for further analysis. Performance experiments showed that the described method is 95% accurate and has a linear running time with respect to the amount of input data for pair-wise time series correlations.
Resolution of aplanatic solid immersion lens based microscopy (2012)

We study the resolution of a subsurface microscopy system based on the use of an aplanatic solid immersion lens. Resolution limits under various criteria are calculated theoretically as well as numerically. Images of combinations of dipoles of various orientations are considered. Both lateral and longitudinal resolutions are studied. The theoretical criteria are compared against the visually resolvable simulated images of the dipoles. The observations are explained explicitly through a detailed analysis of the dyadic Green's function. A new resolution criterion is also proposed, which provides a very accurate estimate of the resolution limits.
ExpansionHunter Denovo: a suite of tools for detecting novel expansions of short tandem repeats (2020)

ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats. EHdn is intended for analysis of a collection of BAM/CRAM files containing alignments of short (100-200bp) reads.
Photosolvolysis of 2‐Allylated Anilines to 2‐Indanols (1986)

Abstract It is shown that 2‐allylated anilines ( cf. Schemes 2–4, 7 , and 8 ) on irradiation in protic solvents such as H 2 O. MeOH, and EtOH in the presence of H 2 SO 4 undergo a novel photosolvolysis reaction to yield specifically trans ‐2‐hydroxy‐ and trans ‐2‐alkoxy‐1‐methylindanes. Intermediates are presumably tricyclo[4.3.0.0 1,8 ]nona‐2,4‐dienes formed in an intramolecular [2 s + 2 s ] cycloaddition reaction ( cf. Scheme 7 ). On the other hand, N , N , N ‐trimethyl‐2‐(1′‐methylallyl)anilinium salts 18 ( Scheme 6 ) and 2‐(3′‐butenyl)‐ N , N ‐dimethylaniline ( 17 ) lose on irradiation in MeOH or H 2 SO 4 /MeOH the ammonium group reductively to yield (1‐methylallyl)benzene ( 19 ) and 1‐methylindane ( 20 ), respectively.
Analysis of T cell repertoire and function in mice transgenic for the human Vβ3 TCR (1993)

We have constructed mice containing the human V beta 3 TCR gene from the influenza virus haemagglutinin specific human CD4+ T cell clone HA1.7. Similar cell yields were obtained from transgenic and non-transgenic lymphoid tissue, with normal levels of T cells and with no unusual bias of the CD4 or CD8 subpopulations. Immunostaining and FACS analysis of transgenic thymocytes, spleen, and mesenteric lymph nodes revealed that the majority of T cells expressed the human V beta 3 TCR on the cell surface. Small numbers of cells expressing murine TCR beta chain were also detected. Polymerase chain reaction analysis revealed that an extensive V alpha TCR repertoire was used in the human V beta 3 transgenic mice. Lymphocytes from the spleen and mesenteric lymph nodes of transgenic mice were assessed for functional activity in vitro. Isolated cells were stimulated with mitogen or superantigen, as well as directly through the TCR-CD3 complex, and their ability to proliferate and secrete lymphokines analysed. Cells from transgenic mice responded well after stimulation with phytohaemagglutinin, concanavalin A, anti-CD3 antibody, anti-CD3 antibody with phorbol ester, and Staphylococcus aureus enterotoxin B, and also showed alloreactivity in a mixed lymphocyte reaction. Minimal levels of response were detected after stimulation with murine TCR beta antibody. Together, these data suggest that a human TCR beta chain is able to associate with a murine TCR alpha chain, to form a fully functional surface TCR-CD3 complex.
Serine-Selective Bioconjugation (2020)

The first general method for the rapid, chemoselective, and modular functionalization of serine residues in native polypeptides is reported. Using a reagent platform based on P(V) oxidation state, this redox-economic approach can be used to append nearly any kind of cargo onto serine generating a stable, benign, and hydrophilic phosphorothioate linkage. The method tolerates all other known nucleophilic functional groups of naturally occurring proteinogenic amino acids. A variety of applications can be envisaged enabled by this expansion of the toolbox of site-selective bioconjugation methods.
Criticality of assumptions in the study of performance degradation caused by mode-dependent loss in SDM systems (2014)

Mode dependent loss is expected to be a major cause of impairments in SDM systems. We show that the accurate characterization of its impact on system performance depends on the assumptions that are made on how the system is modeled and operated in a very subtle way which has eluded the majority of previous studies.
Mode-locked diode lasers for THz asynchronous optical sampling (2019)

Even though Terahertz Time Domain Spectroscopy (TDS) setups have been available for decades in laboratories worldwide and possible applications have been shown in many research papers, a breakthrough of applications actively used on an industrial scale is yet to come. Apart from the THz sources, such as photoconductive antennas (PCAs), a conventional TDS system consists of an ultrafast laser source, a mechanical delay line used for the sampling, and a data acquisition system. While the femtosecond laser makes up for the majority of the system cost, the mechanical delay is accountable for the long acquisition time. In order to push pulsed THz systems one step further towards industrial applications, this work addresses both: the optical source and the sampling mechanism. To overcome the necessity of the delay line an asynchronous optical sampling (ASOPS) approach is chosen. Here, the sampling mechanism is obtained by operating two femtosecond lasers with slightly different repetition rates &utri;f resulting in an inherent sampling of the THz transient. While this was shown with ultrafast solid state lasers such as Ti:Sapphire or fiber lasers, we use edge emitting mode locked semiconductor quantum well lasers operating in the 830nm wavelength regime. In a first step, two laser diodes operated in compact external cavity configurations are hybridly modelocked at repetition rates around 390MHz with a RF synthesizer each in order to obtain a stable pulse scanning. In a second step, we evaluate hybridly modelocked monolithic edge emitting laser diodes at 12:8 GHz for THz TDS ASOPS.