gebhart/patrepeval huggingface dataset:
Convolution-based estimation of organ dose in tube current modulated CT (2015)

Among the various metrics that quantify radiation dose in computed tomography (CT), organ dose is one of the most representative quantities reflecting patient-specific radiation burden.1 Accurate estimation of organ dose requires one to effectively model the patient anatomy and the irradiation field. As illustrated in previous studies, the patient anatomy factor can be modeled using a library of computational phantoms with representative body habitus.<sup>2</sup> However, the modeling of irradiation field can be practically challenging, especially for CT exams performed with tube current modulation. The central challenge is to effectively quantify the scatter irradiation field created by the dynamic change of tube current. In this study, we present a convolution-based technique to effectively quantify the primary and scatter irradiation field for TCM examinations. The organ dose for a given clinical patient can then be rapidly determined using the convolution-based method, a patient-matching technique, and a library of computational phantoms. 58 adult patients were included in this study (age range: 18–70 y.o., weight range: 60–180 kg). One computational phantom was created based on the clinical images of each patient. Each patient was optimally matched against one of the remaining 57 computational phantoms using a leave-one-out strategy. For each computational phantom, the organ dose coefficients (CTDI<sub>vol</sub>-normalized organ dose) under fixed tube current were simulated using a validated Monte Carlo simulation program. Such organ dose coefficients were multiplied by a scaling factor, (CTDI<sub>vol </sub>)<sub>organ, convolution</sub> that quantifies the regional irradiation field. The convolution-based organ dose was compared with the organ dose simulated from Monte Carlo program with TCM profiles explicitly modeled on the original phantom created based on patient images. The estimation error was within 10% across all organs and modulation profiles for abdominopelvic examination. This strategy enables prospective and retrospective patient-specific dose estimation without the need of Monte Carlo simulation.
Real-Time FO-SPR Monitoring of Solid-Phase DNAzyme Cleavage Activity for Cutting-Edge Biosensing (2019)

DNA nanotechnology has a great potential in biosensor design including nanostructuring of the biosensor surface through DNA origami, target recognition by means of aptamers, and DNA-based signal amplification strategies. In this paper, we use DNA nanotechnology to describe for the first time the concept of real-time solid-phase monitoring of DNAzyme cleavage activity for the detection of specific single-stranded DNA (ssDNA) with a fiber optic surface plasmon resonance (FO-SPR) biosensor. Hereto, we first developed a robust ligation strategy for the functionalization of the FO-SPR biosensing surface with ssDNA-tethered gold nanoparticles, serving as the substrate for the DNAzyme. Next, we established a relation between the SPR signal change, due to the cleavage activity of the 10-23 DNAzyme, and the concentration of the DNAzyme, showing faster cleavage kinetics for higher DNAzyme concentrations. Finally, we implemented this generic concept for biosensing of ssDNA target in solution. Hereto, we designed a DNAzyme-inhibitor complex, consisting of an internal loop structure complementary to the ssDNA target, that releases active DNAzyme molecules in a controlled way as a function of the target concentration. We demonstrated reproducible target detection with a theoretical limit of detection of 1.4 nM, proving that the presented ligation strategy is key to a universal DNAzyme-based FO-SPR biosensing concept with promising applications in the medical and agrofood sector.
Muscle-reflex control of robust swing leg placement (2013)

Swing leg placement is vital to dynamic stability in legged robots and animals. The most common approaches to generating swing leg motions in robotics use either position or impedance tracking of defined joint trajectories. While these approaches suffice in humanoids, they severely limit swing leg placement under large disturbances in prosthetic limbs, for which stabilizing reactions cannot be planned centrally. We previously identified a control for a conceptual double-pendulum swing leg that does not require predefined trajectories to robustly place the leg into target points on the ground in the presence of large disturbances. We here develop a more detailed neuromuscular model of the human swing leg and interpret the identified control with local muscle reflexes. The resulting reflex control robustly places the swing leg into a wide range of landing points observed in human walking and running, and it generates similar patterns of joint torques and muscle activations. While we plan to take advantage of the comparison between the neuromuscular model and humans to further improve robust swing leg placement, the current results suggest an alternative to existing swing leg controls in humanoid and rehabilitation robotics which does not require central processing.
A method of motion tracking during CT for motion correction (2011)

Patient motion is a significant problem in pediatric PET/CT, and motion correction techniques could potentially remove the need for anaesthesia or sedation that are normally required for very young patients. Effective methods exist for motion correction of neurological PET images, and although there is a scarcity of equivalent methods for CT, a potential method of correcting for rigid head motion during the CT scan has recently been proposed. In this study, we describe a motion tracking method for CT using an optical motion tracking system. Since pose is reported in tracker coordinates, and motion correction requires motion in CT scanner coordinates, a calibration is required to determine the transformation needed to convert between the coordinate systems. We describe such a calibration method, and evaluate it by acquiring two CT scans of a Hoffman 3D brain phantom, with a tracker target attached, in different poses. The applied motion between two scans was calculated from the change in target pose measured by the tracker, and converted to scanner coordinates. This motion was applied to one of the reconstructed image volumes, which was then compared with the other image volume. The mean registration error of the two volumes was estimated from landmark analysis to be less than 0.3 mm on average in all directions, which agreed well with a calculated maximum uncertainty of 0.7 mm. Errors of this magnitude could be acceptable if the CT scans were only used for attenuation correction, but may need to be further reduced for motion correction applications. We anticipate that this will be achievable with improvements to our technique, and intend in future work to use motion data to attempt motion correction in spiral CT studies.
Doppler ultrasound detection of shear waves remotely induced in tissue phantoms by focused ultrasound (2000)

Remote generation of shear waves in tissues by radiation force of focused ultrasound is the basis of shear wave elasticity imaging (SWEI), a new acoustic method of medical diagnostics. Feasibility of SWEI was previously demonstrated in the experiments with optical and NMR detection of ultrasonically induced shear waves [Sarvazyan et al., Ultrasound Med. Biol. 24, 1419 (1998)]. In the present study the SWEI system with ultrasonic pulsed Doppler detection of shear waves was designed and tested using a range of gelatin-based phantoms and muscle tissue. Radiation force was generated by a focusing transducer of 8 cm diameter and 7 cm focal length. The carrier frequency was 1 MHz with intensity 1.85 W/cm2 at the surface of the transducer. The Doppler detection transducer operating at 3.5 MHz was installed in the center of the pumping transducer. The developed procedures of tissue motion detection and Doppler signal-processing algorithms based on the autocorrelation method allowed estimation of the velocity with accuracy better than 0.2 mm/s. The waveforms of the shear wave at various distances from the pumping ultrasonic beam axis were measured and the shear wave velocities were evaluated. The oscillation character of relaxation process for some phantoms and muscle tissue was shown experimentally.
Dual-stage erbium-doped, erbium/ytterbium-codoped fiber amplifier with up to +26-dBm output power and a 17-nm flat spectrum (1996)

By concatenating an aluminum-codoped erbium-doped fiber with an efficient erbium/ytterbium-codoped fiber, we produce a gain spectrum that is f lat within 0.5 dB for 17 nm from 1544 to 1561 nm. By using energy transfer between erbium and ytterbium ions, we are able to pump the second stage with a high-power 1064-nm source to achieve an output power as high as +26 dBm. Using 980-nm pumping of the first stage, we produce an overall noise figure below 5 dB.
Biosynthesis of nocardicin A by Nocardia uniformis subsp. tsuyamanensis. I. Inco oration of 14C-amino acids into nocardicin A by growing cells. (1977)

The biosynthesis of nocardicin A by Nocardia uniformis subsp. tsuyamanensis was studied. L-Tyrosine, p-hydroxyphenylpyruvic acid, DL-p-hydroxymandelic acid and L-p-hydroxyphenylglycine have stimulatory effect on the production of nocardicin A. In feeding experiment with 14C-amino acids, L-tyrosine-U-14C, L-serine-U-14C, glycine-U-14C and L-homoserine-U-14C were incorporated into nocardicin A. Tyrosine was incorporated into the two aromatic rings of nocardicin A, serine into the β-lactam ring and homoserine into the 3-amino-3-carboxypropoxy moiety. Thus the precursors of nocardicin A are tyrosine, serine and homoserine.
Self-calibrating protocols enhance wearable EEG diagnostics and consumer applications (2015)

Advances in electroencephalography (EEG) sensors and embedded signal processing modules are driving interest in wearable EEG devices. EEG based Neurofeedback (NFB) works by reinforcing desired brainwave patterns and shows great promise for enhancing performance and treating mental disorders. Yet, both clinical and at-home efficacies remain low. We propose a novel Self-Calibrating Protocol (SCP) which can robustly classify brain states when coupled with five standard machine learning algorithms. Our results indicate that commercially available, wearable EEG sensors provide sufficient data fidelity at fast enough rates to differentiate between arbitrary, user-defined states in real time. We conclude that SCP allows for the first time to completely bypass the pitfalls of using "normed" neurophysiological states and leads off to individualized therapeutics and bespoke performance enhancement applications.
551. Enhancement of Gene Therapy Treatment for Sandhoff Disease Through Complimentary Drug Therapy (2016)

GM2 gangliosidoses is a group of neurodegenerative lysosomal storage disorders caused by deficiency in the β-hexosaminidase A (HexA) enzyme. HexA is a heterodimer composed of 2 subunits; α- (encoded by the HEXA gene) and β-hexosaminidase β (Encoded by the HEXB gene). Mutations in either gene may cause inactivity of HexA leading to either Tay-Sachs disease (TSD, HEXA mutation) or Sandhoff disease (SD, HEXB mutation) respectively. TSD and SD are clinically indistinguishable phenotypes principally affecting infants and young children that are fatal before the age of 4 years; there is currently no effective available treatment. A mouse model for SD has been developed and these mice reach a humane end point at 14-17 weeks of age. Gene therapy can be an important primary therapeutic strategy, but may fall short of a complete rescue. Neuroinflammation and neurodegeneration have been identified as hallmark pathological mechanisms in GM2 gangliosidosis and can be adjunctive therapeutic targets. Neuroanti-inflammatory/neuroprotective agents like non-steroidal anti-inflammatory drugs (NSAIDs), Histone deacetylase inhibitors and pharmacological chaperones have shown ameliorating effects in SD and similar disease models when used alone. Adeno associated virus (AAV) based expression of Hexosaminidase isoenzymes has been shown to increase survival of Sandhoff mice for long term. We tested the combined role of gene therapy and neuroanti-inflammatory/neuroprotective agents in SD mice. Our methods include injecting neonatal SD mice with a relatively low dose (2×1013 vg/kg) of a novel AAV9 vector expressing Hex A using both α and β subunits. A pilot study established the survival of these mice to be approximately 24 weeks, a 55% increase in life span over vehicle-injected controls. We observed a 47% increase in Hex A activity in the midbrain of treated mice as compared to the vehicle injected controls. Cohorts received treatment with neonatal gene therapy alone or in combination with indomethacin (a NSAID), pyrimethamine (a proven pharmacological chaperone for Hex A) and ITF2357 (a histone deactylase inhibitor) to elicit their combinational therapeutic potential. Each drug is administered daily via oral gavage starting the age of 6 weeks. All treatments have been completed and mice are being monitored for survival benefit and locomotor behaviour. Further analyses of enzyme activity, GM2 ganglioside levels and copy numbers will be done. The results of this study will establish a proof-of-concept for a novel combination gene therapy approach for treatment of GM2 gangliosidoses and similar disorders.
Conformational and biochemical analysis of the cyclic peptides which modulate serine protease activity (2004)

Prostate-specific antigen (PSA), a member of the kallikrein sub-group of the trypsin serine protease family, is a widely used marker for prostate cancer. Several sequences with specific binding to PSA have been identified by using phage display peptide libraries. The GST-fusion proteins of the characterized sequences have been shown to increase the enzyme activity of PSA to a synthetic substrate. The corresponding three cyclic synthetic analogues CVFTSNYAFC (A-1), CVFAHNYNYLVC (B-2) and CVAYCIEHHCWTC (C-4) have similar PSA promoting activity. Despite differences in the amino acid sequences, all three peptides bind to the same region of PSA. The conformation of the peptides was investigated by proton NMR spectroscopy. In addition, alanine replacement was used to characterize the prerequisites for binding. It is proposed that interactions with PSA are based on the aromatic and hydrophobic features of the amino acid side chains. Furthermore, it is suggested that peptides form beta-turn structures forced by cysteine bridges directing important aromatic side chains to the same side of the turn-structure.
Data-driven process decomposition for circuit synthesis (2002)

This paper presents a new method for decomposing a high-level program description of a circuit into a collection of small modules in the same program notation. The modules are simple enough to be immediately implemented as transistor networks. The method consists of two main steps: the description is first put into Dynamic Single Assignment form in which each variable is assigned at most once in each execution; secondly, the DSA program is projected on different sets of variables and channels to produce each module. The decomposed system is semantically equivalent to the original one under the assumption of slack elasticity: the communicating channels between the modules can have an arbitrary slack (buffer length). In some cases, the decomposition produces modules that are too small and have to be grouped together. Unlike all other methods for circuit synthesis from high-level programs, this method is not syntax-directed. Rather it is based on data dependency among the different variables and channels of the system. The method is general: it is not restricted to asynchronous implementation.
Organic Liquid Crystals as Single‐Ion Li<sup>+</sup> Conductors (2020)

The development of new materials for tomorrow's electrochemical energy storage technologies, based on thoroughly designed molecular architectures is at the forefront of materials research. In this line, we report herein the development of a new class of organic lithium-ion battery electrolytes, thermotropic liquid crystalline single-ion conductors, for which the single-ion charge transport is decoupled from the molecular dynamics (i. e., obeys Arrhenius-type conductivity) just like in inorganic (single-)ion conductors. Focusing on an in-depth understanding of the structure-to-transport interplay and the demonstration of the proof-of-concept, we provide also strategies for their further development, as illustrated by the introduction of additional ionic groups to increase the charge carrier density, which results in a substantially enhanced ionic conductivity especially at lower temperatures.
Large‐Scale Production and Properties of a Solvent‐Detergent‐Treated Factor IX Concentrate from Human Plasma (1988)

A human solvent-detergent (SD)-treated factor IX concentrate has been produced from cryoprecipitate-poor plasma using DEAE-Sepharose CL-6B and heparin-Sepharose CL-6B chromatography. The DEAE eluate was incubated with an SD mixture [0.3% tri(n-butyl) phosphate-1% Tween 80, 6-h at 24 degrees C] which was found to inactivate, in less than 1 h, more than 3.8 log10 of vesicular stomatitis virus and more than 4.8 log10 of Sindbis virus; the SD was removed by a subsequent heparin adsorption step. The specific activity of the concentrate was 10.9 +/- 1.3 IU factor IX: c/mg protein (n = 15). The factor IX coagulant to antigen ratio was 0.7 +/- 0.1. The concentrate was essentially free of factors II, VII and X, and protein C. The usual major contaminants of prothrombin complex concentrate (PCC) were absent: the concentrate contained about 94% alpha-1 proteins, and only 4 major proteins were resolved by SDS-PAGE (respective apparent molecular weight: 130, 86, 76 and 69 kilodaltons), and by crossed immunoelectrophoresis against an anti-PCC serum. The nonactivated partial thromboplastin time was equivalent to that of PCC; the product was devoid of factor IXa, of other activated procoagulant factors and of coagulant-active phospholipids (removed with SD in the heparin breakthrough fraction). Animal studies using the Wessler test and acute-toxicity test in rabbits revealed no adverse side effects. SD treatment could thus be used to inactivate viruses in factor IX concentrate and improve the safety of replacement therapy in hemophilia B.
Multiple Auditory Steady-State Responses (2002)

Steady-state responses are evoked potentials that maintain a stable frequency content over time. In the frequency domain, responses to rapidly presented stimuli show a spectrum with peaks at the rate of stimulation and its harmonics. Auditory steady-state responses can be reliably evoked by tones that have been amplitude-modulated at rates between 75 and 110 Hz. These responses show great promise for objective audiometry, because they can be readily recorded in infants and are unaffected by sleep. Responses to multiple tones presented simultaneously can be independently assessed if each tone is modulated at a different modulation frequency. This ability makes it possible to estimate thresholds at several audiometric frequencies in both ears at the same time. Because amplitude-modulated tones are not significantly distorted by free-field speakers or microphones, they can also be used to evaluate the performance of hearing aids. Responses to amplitude and frequency modulation may also become helpful in assessing suprathreshold auditory processes, such as those necessary for speech perception.
The CLU mobility management scheme for digital cellular systems (2002)

A digital cellular system is divided into location areas and the movement of mobile users is tracked only when they cross from one location area to another. The system pages over an entire location area when it needs to find a mobile to terminate an incoming call. Most cellular systems use this basic mobility management scheme to track mobile locations, and attempt to optimize the size of the location areas versus the number of pages needed to locate a mobile. In this paper, we present a new mobility management scheme called cell location update (CLU) which informs each site of mobiles present in its coverage area. Paging to locate a mobile is done over a much smaller set of sites rather than an entire location area. This new scheme significantly reduces paging related traffic: up to 70% reduction in the case of iDEN, and up to 50% in the case of GSM. The number of corresponding location area updates is also reduced by about 40%.
Personalized Keyphrase Detection using Speaker and Environment\n Information (2021)

In this paper, we introduce a streaming keyphrase detection system that can\nbe easily customized to accurately detect any phrase composed of words from a\nlarge vocabulary. The system is implemented with an end-to-end trained\nautomatic speech recognition (ASR) model and a text-independent speaker\nverification model. To address the challenge of detecting these keyphrases\nunder various noisy conditions, a speaker separation model is added to the\nfeature frontend of the speaker verification model, and an adaptive noise\ncancellation (ANC) algorithm is included to exploit cross-microphone noise\ncoherence. Our experiments show that the text-independent speaker verification\nmodel largely reduces the false triggering rate of the keyphrase detection,\nwhile the speaker separation model and adaptive noise cancellation largely\nreduce false rejections.\n
Estimation of Galileo Uncalibrated Hardware Delays for Ambiguity-fixed Precise Point Positioning (2014)

Ambiguity fixing in Precise Point Positioning (PPP) has been extensively studied in recent years. The provision of uncalibrated hardware delays (UHDs) to the PPP algorithm, on top of precise orbits and clocks, allows the recovery of the integer values of the carrier-phase ambiguities. Experimental results show that integer ambiguity resolution increases the accuracy in the position domain. Most of the research so far has been done on GPS, where the wide- and narrow-lane approach for ambiguity resolution has proven successful. In the context of multi-GNSS PPP, the aim of this study is to extend the method to Galileo. Initial results for UHD estimation for Galileo satellites are presented. The contribution of ambiguity-fixing to GPS+Galileo PPP is assessed.
Molecularly Imprinted Polymers (2002)

Abstract Molecular imprinting is a method with which materials containing highly specific recognition sites with high affinities for a wide range of organic compounds can be made. Since its inception, the number and types of monomers and templates that have been used successfully has increased dramatically. In addition, our understanding of the mechanisms through which the materials operate is increasing. Some areas of application have become well developed and commercial applications are on the horizon. The applications discussed in this article include separation technology, sensors, catalysis, and antibody and receptor site mimics.
Generation and detection of acoustic streaming to differentiate between solid and cystic breast lesions (1994)

Results from both a pilot clinical study and phantom studies performed to evaluate a new ultrasonic technique to distinguish cysts from solid lesions are presented. High intensity pulses are used to induce acoustic streaming in cyst fluid, and this motion is detected using existing flow detection techniques. Since acoustic streaming cannot be generated in solid lesions, its detection would indicate a cyst. In six of seven breast cysts streaming was generated and detected in vivo. In phantom studies, a direct relationship between streaming velocity and cyst size and an indirect relationship between streaming velocity and cyst fluid viscosity were demonstrated
OREXIN 1 AND 2 RECEPTOR INVOLVEMENT IN CO<sub>2</sub>-INDUCED PANIC-ASSOCIATED BEHAVIOR AND AUTONOMIC RESPONSES (2015)

SORA1s may represent a novel method of treating anxiety disorders, with no apparent sedative effects that were present with a benzodiazepine.