gebhart/patrepeval huggingface dataset:
Salivary levels of anticonvulsants (1977)

Phenobarbital, phenytoin, carbamazepine, primidone, and ethosuximide were measured in saliva and plasma obtained simultaneously from 115 patients. A method to correct for the effect of salivary pH on phenobarbital concentration of saliva was developed. Salivary concentrations of these drugs were found to be equivalent to the plasma free drug and to correlate closely with the total plasma levels. Expressed as percent of total plasma drug, the salivary (S) and plasma free (P) concentrations were: phenytoin, S 11.1 ± 2.0 percent (mean ± SD), P 10.1 ± 2.4 percent (r = 0.97); carbamazepine, S 26.0 ± 2.4 percent, P 25.9 t 3.4 percent (r = 0.97); phenobarbital, S 43.1 ± 5.2 percent, P 40.8 ± 7.9 percent (r = 0.91); primidone, S 75.4 ± 24.9 percent, P 66.4 ± 8.8 percent (r = 0.76). Ethosuximide was not bound by plasma proteins, and its plasma and salivary levels were equal.
High-power broadband source tunable from 2.8 to 4 μm based on difference frequency generation (2017)

Summary form only given. Mid-infrared (MIR) frequency comb sources enable high-speed and accurate detection of various species, since many molecules possess their fingerprints in this wavelength range. Usually, broadband radiation in this spectral region is obtained from optical parametric oscillators (OPOs), which provide high output power and broad tuning capabilities [1]. However, OpO sources require locking of the cavity to the pumping oscillator, which increases the complexity. MIR sources based on difference frequency generation (DFG) are interesting alternatives to OPOs, due to their simplicity, single-pass configuration, broad tunability, and fully passive cancellation of the carrier-envelope offset in the generated idler pulses. However, the conversion efficiency of the DFG process is usually insufficient to reach the output power levels easily achieved in OPO systems. Here, we demonstrate a widely tunable DFG source based on a mode-locked Yb-doped fiber laser, with average MIR output power reaching 165 mW, which is more than in previous reports on similar DFG systems [2, 3].
Figure S7 from Preclinical Efficacy of the Antibody–Drug Conjugate CLDN6–23-ADC for the Treatment of CLDN6-Positive Solid Tumors (2023)

&lt;p&gt;Supplemental Figure S7. CLDN6 expression in ovarian and endometrial cancer tissue samples.&lt;/p&gt;
Topological Structure of the Configuration Space and the Separation of Spin and Spatial Variables for <i>N</i>-Electron Systems (1996)

The relationship between the topological structure of the multidimensional configuration space and the structure of the symmetrical permutation group SN is analyzed. This relationship permits to separate the spin and spatial variables during the solution of the spinless stationary Schrödinger equation. It is possible to simplify the construction of wave functions for N-electron systems and to expand the class of trial functions in the variation method. The relation of the suggested approach to the construction of wave functions by traditional methods is demonstrated by the example of three-electron systems.
Synergistic Upregulation of Target Genes by TET1 and VP64 in the dCas9–SunTag Platform (2020)

Overexpression of a gene of interest is a general approach used in both basic research and therapeutic applications. However, the conventional approach involving overexpression of exogenous genes has difficulty achieving complete genome coverage, and is also limited by the cloning capacity of viral vectors. Therefore, an alternative approach would be to drive the expression of an endogenous gene using an artificial transcriptional activator. Fusion proteins of dCas9 and a transcription activation domain, such as dCas9-VP64, are widely used for activation of endogenous genes. However, when using a single sgRNA, the activation range is low. Consequently, tiling of several sgRNAs is required for robust transcriptional activation. Here we describe the screening of factors that exhibit the best synergistic activation of gene expression with TET1 in the dCas9-SunTag format. All seven factors examined showed some synergy with TET1. Among them, VP64 gave the best results. Thus, simultaneous tethering of VP64 and TET1 to a target gene using an optimized dCas9-SunTag format synergistically activates gene expression using a single sgRNA.
Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony (2019)

Baboons (genus <i>Papio</i>) are broadly studied in the wild and in captivity. They are widely used as a nonhuman primate model for biomedical studies, and the Southwest National Primate Research Center (SNPRC) at Texas Biomedical Research Institute has maintained a large captive baboon colony for more than 50 yr. Unlike other model organisms, however, the genomic resources for baboons are severely lacking. This has hindered the progress of studies using baboons as a model for basic biology or human disease. Here, we describe a data set of 100 high-coverage whole-genome sequences obtained from the mixed colony of olive (<i>P. anubis</i>) and yellow (<i>P. cynocephalus</i>) baboons housed at the SNPRC. These data provide a comprehensive catalog of common genetic variation in baboons, as well as a fine-scale genetic map. We show how the data can be used to learn about ancestry and admixture and to correct errors in the colony records. Finally, we investigated the consequences of inbreeding within the SNPRC colony and found clear evidence for increased rates of infant mortality and increased homozygosity of putatively deleterious alleles in inbred individuals.
On the Role of Deterministic Fine-Grain Data Synchronization for Scientific Applications: A Revisit in the Emerging Many-Core Era (2007)

The design of microprocessor chip for high-end computing systems is moving towards many-core architectures with 10s or 100+ processing units. An important class of the target applications for such architectures are scientific numerical computations, many of which are intrinsically deterministic - that is for a given input a fixed output (result) should be produced no matter how the program is parallelized. It is critical that the read-after-write data dependencies in such programs should be implemented correctly and efficiently via fine-grain data synchronization. In this paper, we investigate the parallelization of three representative scientific computation kernels using fine-grain data synchronization supported by an recently proposed architectural mechanism for many-core chips, called synchronization state buffer (SSB). Using detailed simulation on a simulator for the IBM 160-core Cyclops-64 chip architecture with the SSB extension, our experiments demonstrate significant performance advantage of using fine-grain data synchronization based parallelization schemes for scientific workloads.
Matrice de micro électrodes à haute résolution spatiale pour la mesure du potentiel extracellulaire des cellules nerveuses (2009)

Une nouvelle approche basée sur des électrodes en 3D a été développée afin d’accroître le couplage électrique entre les cellules nerveuses et les capteurs d’une matrice de micro électrodes (MEA). Cette amélioration du couplage électrique obtenue par des matrices d’électrodes en 3D par rapport à des électrodes planaires standards a été confirmée par simulation. Des MEAs 3D ayant une meilleure résolution spatiale ont été fabriquées sur des plaquettes de Silicium.
Phlegmatization of TATP and HMTD with Activated Charcoal as Training Aid for Explosive Detection Dogs (2021)

Abstract Both TATP and HMTD could be phlegmatized by coprecipitation with active charcoal resulting in mixtures with a nominal content of 40 wt‐% (d40‐TATP) and 10 wt‐% (d10‐HMTD), respectively. In terms of impact and friction sensitivity for both peroxides a content of 40 wt‐% resulted in &gt;30 Nm impact sensitivity and &gt;360 N friction sensitivity. Both phlegmatized peroxides passed the Koenen Tube and Thermal Stability Test according to the UN recommendation on the transport of dangerous goods test manual. Investigations with a process mass spectrometer indicate that d40‐TATP can produce a saturated TATP headspace at least in the same time as the same amount of pure TATP. Measurements with the transpiration method demonstrated that the vapor pressure at 298.15 K of d40‐TATP (2.3 Pa) and d32.7‐TATP (0.9 Pa) is lower than that of pure TATP (6.7 Pa). Headspace SPME‐GC/MS measurements revealed that the active charcoal does not contribute to the vapor profile of the training aid. Both d40‐TATP and d10‐HMTD were tested as training aids for explosive detection dog teams (EDD). In both differentiation track and realistic environment scenarios a detection rate of 100 % could be achieved by German Federal Police EDD with a false positive rate of solely 3 %.
New octagonal shape double-clad Thulium-Ytterbium Co- doped fiber for generation of multi-wavelength and Q- switched lasers in 2 micron region (2014)

We demonstrate a simple, compact and low cost multi-wavelength and Q-switched fiber lasers based on newly developed octagonal shape double-clad Thulium-Ytterbium co-doped fiber (TYDF). The fiber is fabricated using the modified chemical vapor deposition (MCVD) process in conjunction with the solution doping technique. At 5 m long of TYDF, the laser produces three lines at 1914.5 nm, 1934.7 nm and 1953.6 nm with peak powers of 6.3 dBm, -1.6 dBm and 1.7 dBm, respectively due to the nonlinear polarization rotation effect in the laser ring cavity. The Q-switched TYDF laser operating at 1983.4 nm is also successfully demonstrated by exploiting a multi-walled carbon nanotubes (MWCNTs) polymer composite based saturable absorber. The composite is prepared by mixing the MWCNTs homogeneous solution into a dilute polyvinyl alcohol polymer solution before it is left to dry at room temperature to produce thin film. Then the film is sandwiched between two FC/PC fiber connectors and integrated into the laser cavity for Q-switching pulse generation. By varying the 905 nm multimode pump power from 1570 to 1606 mW, the pulse repetition rate increases from 27.4 to 37.8 kHz and the pulse width fluctuates within 4.9 mu s to 3.8 mu s. The maximum pulse energy of 10.6 nJ is obatined at pump power of 1570 mW.
Instrumented gait analysis: a measure of gait improvement by a wheeled walker in hospitalized geriatric patients (2017)

The impact of a WW can be quantified objectively by instrumented gait assessment. Thus, objective gait parameters may serve as surrogate markers for the use of walking aids in patients with gait and balance impairments.
Blood Glucose Prediction in Type 1 Diabetes Using Deep Learning on the Edge (2021)

Real-time blood glucose (BG) prediction can enhance decision support systems for insulin dosing such as bolus calculators and closed-loop systems for insulin delivery. Deep learning has been proven to achieve state-of-the-art performance in BG prediction. However, it is usually seen as a very computationally expensive approach, hence difficult to implement in wearable medical devices such as transmitters in continuous glucose monitoring (CGM) systems. In this work, we introduce a novel deep learning framework to predict BG levels with the edge inference on a microcontroller unit embedded in a low- power system. By using glucose measurements from a CGM sensor and a recurrent neural network that builds on long-short term memory, the personalized models achieves state-of-the-art performance on a clinical data set obtained from 12 subjects with T1D. In particular, the proposed method achieves an average root mean square error of 19.10 ± 2.04 for a 30-minute prediction horizon (PH) and 32.61 ± 3.45 for a 60-minute PH with high clinical accuracy. Notably, the framework has been optimized to achieve a minimum use of hardware resources (34KB FLASH and 1KB SRAM) as well as an execution time of 22 ms for low power operations (8 μW). The presented system has the potential to be implemented in wearable medical devices for diabetes care (CGM and insulin pumps) and to be integrated within an Internet of Things platform.
Simple Performance Modeling of a Radio-Frequency Ion Thruster (2007)

A simple performance model is developed for an inductively-coupled plasma (ICP) discharge, radio-frequency (RF) ion thruster. Methods of particle and energy balance are utilized for modeling the ICP discharge. A lumped-element circuit analysis, a transformer model, and a transmission line model are incorporated in the equations of energy balance for estimating the absorbed power by the plasma. In the transformer model, the short solenoid is treated as a two-turn primary coil and the plasma as a one-turn secondary air coil. The primary and mutual inductance are approximated by theories of single-layer coils. The ICP discharge model is successful in predicting the resonant frequency of the system with accuracy within 0.01 MHz. The reflected power of the system is predicted with accuracy within 30% and its trend is also validated. The anode current of the thruster is estimated by a simple one-dimensional ion extraction model, which yields accuracy within 10% of the measured values.
80 Gbit/s OTDM using electroabsorption modulators (1997)

An 80Gbit/s OTDM system constructed entirely with electroabsorption modulators (EAM) is presented. Tandem EAMs with dual frequency drive generate 4.5ps pulses. A low polarisation sensitivity EAM demultiplexer enables error free operation with a sensitivity of -21.5dBm.
Improved depth resolution in video-rate line-scanning multiphoton microscopy using temporal focusing (2005)

By introducing spatiotemporal pulse shaping techniques to multiphoton microscopy it is possible to obtain video-rate images with depth resolution similar to point-by-point scanning multiphoton microscopy while mechanically scanning in only one dimension. This is achieved by temporal focusing of the illumination pulse: The pulsed excitation field is compressed as it propagates through the sample, reaching its shortest duration (and highest peak intensity) at the focal plane before stretching again beyond it. This method is applied to produce, in a simple and scalable setup, video-rate two-photon excitation fluorescence images of Drosophila egg chambers with nearly 100,000 effective pixels and 1.5 microm depth resolution.
Logic and databases: a critique (1987)

article Free Access Share on Logic and databases: a critique Author: D Harel Dept.of Applied Mathematics and Computer Science, The Weizmann Institute of Science, Rehovot,Israel 76100 Dept.of Applied Mathematics and Computer Science, The Weizmann Institute of Science, Rehovot,Israel 76100View Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 22Issue 3March 1987 pp 14–20https://doi.org/10.1145/24697.24698Online:01 March 1987Publication History 2citation127DownloadsMetricsTotal Citations2Total Downloads127Last 12 Months2Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Relaxation processes of the triplet state of self-trapped excitons in alkali-halide crystals (1980)

The spin lattice relaxation, radiative and microwave excitation processes of the triplet self-trapped exciton have been studied in alkali chlorides and bromides by measuring the transient response of the X-ray excited luminescence to resonant pulse microwave. The model is applied to magnetic circular polarization data. The symmetry of dominant exciton-phonon coupling are discussed.
Genetic Variants of Methyl Metabolizing Enzymes and Epigenetic Regulators: Associations with Promoter CpG Island Hypermethylation in Colorectal Cancer (2009)

Aberrant DNA methylation affects carcinogenesis of colorectal cancer. Folate metabolizing enzymes may influence the bioavailability of methyl groups, whereas DNA and histone methyltransferases are involved in epigenetic regulation of gene expression. We studied associations of genetic variants of folate metabolizing enzymes (MTHFR, MTR, and MTRR), DNA methyltransferase DNMT3b, and histone methyltransferases (EHMT1, EHMT2, and PRDM2), with colorectal cancers, with or without the CpG island methylator phenotype (CIMP), MLH1 hypermethylation, or microsatellite instability. Incidence rate ratios were calculated in case-cohort analyses, with common homozygotes as reference, among 659 cases and 1,736 subcohort members of the Netherlands Cohort Study on diet and cancer (n = 120,852). Men with the MTHFR 677TT genotype were at decreased colorectal cancer risk (incidence rate ratio, 0.49; P = 0.01), but the T allele was associated with increased risk in women (incidence rate ratio, 1.39; P = 0.02). The MTR 2756GG genotype was associated with increased colorectal cancer risk (incidence rate ratio, 1.58; P = 0.04), and inverse associations were observed among women carrying DNMT3b C-->T (rs406193; incidence rate ratio, 0.72; P = 0.04) or EHMT2 G-->A (rs535586; incidence rate ratio, 0.76; P = 0.05) polymorphisms. Although significantly correlated (P < 0.001), only 41.5% and 33.3% of CIMP tumors harbored MLH1 hypermethylation or microsatellite instability, respectively. We observed inverse associations between MTR A2756G and CIMP among men (incidence rate ratio, 0.58; P = 0.04), and between MTRR A66G and MLH1 hypermethylation among women (incidence rate ratio, 0.55; P = 0.02). In conclusion, MTHFR, MTR, DNMT3b, and EHMT2 polymorphisms are associated with colorectal cancer, and rare variants of MTR and MTRR may reduce promoter hypermethylation. The incomplete overlap between CIMP, MLH1 hypermethylation, and microsatellite instability indicates that these related "methylation phenotypes" may not be similar and should be investigated separately.
Hardware‐accelerated protein identification for mass spectrometry (2005)

Abstract An ongoing issue in mass spectrometry is the time it takes to search DNA sequences with MS/MS peptide fragments (see, e.g., Choudary et al. , Proteomics 2001; 1: 651–667.) Search times are far longer than spectra acquisition time, and parallelization of search software on clusters requires doubling the size of a conventional computing cluster to cut the search time in half. Field programmable gate arrays (FPGAs) are used to create hardware‐accelerated algorithms that reduce operating costs and improve search speed compared to large clusters. We present a novel hardware design that takes full spectra and computes 6‐frame translation word searches on DNA databases at a rate of approximately 3 billion base pairs per second, with queries of up to 10 amino acids in length and arbitrary wildcard positions. Hardware post‐processing identifies in silico tryptic peptides and scores them using a variety of techniques including mass frequency expected values. With faster FPGAs protein identifications from the human genome can be achieved in less than a second, and this makes it an ideal solution for a number of proteome‐scale applications. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Modifications of the electronic structure of GaSb surface by chalcogen atoms: S, Se, and Te (2004)

Modifications to the electronic properties and chemical structures of the GaSb surface using the chalcogen atoms S, Se, and Te were investigated theoretically and experimentally. A self-consistent density-functional theory study indicates that an adsorption of a full monolayer coverage of chalcogen atoms on a Ga-terminated surface reduces the density of gap region states significantly. A greater photoluminescence enhancement was observed from GaSb samples treated by chalcogenide (Na2S, Na2Se, or Na2Te) in a nonaqueous than in an aqueous passivation medium. X-ray photoelectron spectroscopy reveals a Ga-rich surface after a nonaqueous passivation, with sulfidization providing a higher concentration of Ga(Sb)-chalcogen bonds than does a passivation with Na2Se or Na2Te. The uptake of chalcogen during the passivation is accompanied by the loss of surface antimony. The formation of Sb-X(X=S, Se, or Te) bonds competes with X displacing surface Sb, which dominates Se or Te incorporation in the GaSb surface lattice. The passivation kinetics was analyzed on basis of a single precursor-mediated coverage-dependent chemisorption proces.
Supplementary Table 7 from Copy Number Losses Define Subgroups of Dedifferentiated Liposarcoma with Poor Prognosis and Genomic Instability (2023)

&lt;p&gt;PDF file - 73K, Multivariate analysis of chromosome 19q loss and clinical factors in local recurrence.&lt;/p&gt;
Time course of effects of venlafaxine on migraine and generalized pruritus in a patient with depression (2021)

Venlafaxine has potential as a therapeutic option for patients with depressive disorder, migraine, and pruritus unresponsive to antihistamines.
On the Convergence and Robustness of Training GANs with Regularized Optimal Transport (2018)

Generative Adversarial Networks (GANs) are one of the most practical methods for learning data distributions. A popular GAN formulation is based on the use of Wasserstein distance as a metric between probability distributions. Unfortunately, minimizing the Wasserstein distance between the data distribution and the generative model distribution is a computationally challenging problem as its objective is non-convex, non-smooth, and even hard to compute. In this work, we show that obtaining gradient information of the smoothed Wasserstein GAN formulation, which is based on regularized Optimal Transport (OT), is computationally effortless and hence one can apply first order optimization methods to minimize this objective. Consequently, we establish theoretical convergence guarantee to stationarity for a proposed class of GAN optimization algorithms. Unlike the original non-smooth formulation, our algorithm only requires solving the discriminator to approximate optimality. We apply our method to learning MNIST digits as well as CIFAR-10images. Our experiments show that our method is computationally efficient and generates images comparable to the state of the art algorithms given the same architecture and computational power.
Transfer Functions for the DAMA Experiments (2013)

We examine what can and what cannot be revealed by the available DAMA dataset by computing the relevant amplitude transfer function (the ratio of the amplitude of the detected signal to that of an input signal) and the corresponding power transfer function. We find that the transfer functions are small except in the neighborhood of 1 cycle per year.