gebhart/patrepeval huggingface dataset:
Prediction of pregnancy-induced hypertension using coherence analysis (2004)

The paper presents a novel method to predict hypertensive disorders in pregnancy using coherence analysis. Previous studies suggest that there is inadequate secondary trophoblast invasion in hypertensive pregnancies implying that there are differences in the functional relationships between the maternal and fetal circulations. Magnitude squared coherence (MSC) is a function with values between 0 and 1 that indicates how well two waveforms correspond to each other in the frequency domain. The results presented using the MSC of maternal and fetal blood flow velocity waveforms indicate that in complicated hypertensive pregnancies its value is lower than in non-hypertensive controls. With additional validation, this method has the potential to provide an early test for hypertensive obstetric complications.
Modeling dose distributions from portal dose images using the convolution/superposition method (1996)

Post-treatment dose verification refers to the process of reconstructing delivered dose distributions internal to a patient from information obtained during the treatment. The exit dose is commonly used to describe the dose beyond the exit surface of the patient from a megavoltage photon beam. Portal imaging provides a method of determining the dose in a plane distal to a patient from a megavoltage therapeutic beam. This exit dose enables reconstruction of the dose distribution from external beam radiation throughout the patient utilizing the convolution/superposition method and an extended phantom. An iterative convolution/superposition algorithm has been created to reconstruct dose distributions in patients from exit dose measurements during a radiotherapy treatment. The method is based on an extended phantom that includes the patient CT representation and an electronic portal imaging device (EPID). The convolution/superposition method computes the dose throughout the extended phantom, which allows the portal dose image to be predicted in the EPID. The process is then reversed to take the portal dose measurement and infer what the dose distribution must have been to produce the measured portal dose. The dose distribution is modeled without knowledge of the incident intensity distribution, and includes the effects of scatter in the computation. The iterative method begins by assuming that the primary energy fluence (PEF) at the portal image plane is equal to the portal dose image, the PEF is then back-projected through the extended phantom and convolved with the dose deposition kernel to determine a new prediction of the portal dose image. The image of the ratio of the computed PEF to the computed portal dose is then multiplied by the measured portal dose image to produce a better representation of the PEF. Successive iterations of this process then converge to the exiting PEF image that would produce the measured portal dose image. Once convergence is established, the dose distribution is determined by back-projecting the PEF and convolving with the dose deposition kernel. The method is accurate, provided the patient representation during treatment is known. The method was used on three phantoms with a photon energy of 6 MV to verify convergence and accuracy of the algorithm. The reconstructed dose volumes agree to within 3% of the forward computation dose volumes. Furthermore, this technique assumes no prior knowledge of the incident fluence and therefore may better represent the dose actually delivered.
Biomimetic biphasic 3‐D nanocomposite scaffold for osteochondral regeneration (2013)

Scaffold‐based interfacial tissue engineering aims to not only provide the structural and mechanical framework for cellular growth and tissue regeneration, but also direct cell behavior. Due to the disparity in composition of the osteochondral (cartilage and bone) interface, this work has developed a novel biomimetic biphasic nanocomposite scaffold integrating two biocompatible polymers containing tissue‐specific growth factor‐encapsulated core–shell nanospheres. Specifically, a poly(caprolactone) (PCL)‐based bone layer was successfully integrated with a poly(ethylene glycol) (PEG) hydrogel cartilage layer. In addition, a novel nanosphere fabrication technique for efficient growth factor encapsulation and sustained delivery via a wet coaxial electrospray technique was developed. Human bone marrow mesenchymal stem cell (hMSC) adhesion, osteogenic, and chondrogenic differentiation were evaluated. Our in vitro results showed significantly improved hMSC adhesion and differentiation in bone and cartilage layers, respectively. Studies have demonstrated promising results with novel biphasic nanocomposite scaffold for osteochondral tissue regeneration, thus, warranting further studies. © 2013 American Institute of Chemical Engineers AIChE J 60: 432–442, 2014
Simulation of all-optical XOR, AND, and OR gates in single format by using semiconductor optical amplifiers (2006)

Using the cross-gain modulation (XGM) characteristics of semiconductor optical amplifiers (SOAs), multi-functional all-optical logic gates including XOR, AND, and OR gates are successfully demonstrated at 10 Gbps by using VPI component makerTM simulation tool. Multi-quantum well (MQW) SOA is used for the simulation of all-optical logic system. Our suggested system is composed of four MQW SOAs, SOA-1 and SOA-2 for XOR logic operation and SOA- 3 and SOA-4 for AND logic operation. By the addition of two output signals XOR and AND, all-optical OR logic can be obtained.
Role of Tyrosine Kinase and Membrane-Spanning Domains in Signal Transduction by the Platelet-Derived Growth Factor Receptor (1988)

Three types of mutations were introduced into the platelet-derived growth factor (PDGF) receptor to cause a loss of PDGF-stimulated tyrosine kinase activity: (i) a point mutation of the ATP-binding site, (ii) a deletion of the carboxyl-terminal region, and (iii) replacement of the membrane-spanning sequences by analogous transmembrane sequences of other receptors. Transfectants expressing mutated receptors bind, 125I-labeled PDGF with a high affinity but had no PDGF-sensitive tyrosine kinase activity, phosphatidylinositol turnover, increase in the intracellular calcium concentration, change in cellular pH, or stimulation of DNA synthesis. However, PDGF-induced receptor down regulation was normal in the mutant cells. These results indicate that the transmembrane sequence has a specific signal-transducing function other than merely serving as a membrane anchor and that the receptor kinase activity is necessary for most responses to PDGF but is not required for receptor down regulation.
TH‐EF‐BRA‐06: A Novel Retrospective 3D K‐Space Sorting 4D‐MRI Technique Using a Radial K‐Space Acquisition MRI Sequence (2016)

Purpose: Current retrospective 4D‐MRI provides superior tumor‐to‐tissue contrast and accurate respiratory motion information for radiotherapy motion management. The developed 4D‐MRI techniques based on 2D‐MRI image sorting require a high frame‐rate of the MR sequences. However, several MRI sequences provide excellent image quality but have low frame‐rate. This study aims at developing a novel retrospective 3D k‐space sorting 4D‐MRI technique using radial k‐space acquisition MRI sequences to improve 4D‐MRI image quality and temporal‐resolution for imaging irregular organ/tumor respiratory motion. Methods: The method is based on a RF‐spoiled, steady‐state, gradient‐recalled sequence with minimal echo time. A 3D radial k‐space data acquisition trajectory was used for sampling the datasets. Each radial spoke readout data line starts from the 3D center of Field‐of‐View. Respiratory signal can be extracted from the k‐space center data point of each spoke. The spoke data was sorted based on its self‐synchronized respiratory signal using phase sorting. Subsequently, 3D reconstruction was conducted to generate the time‐resolved 4D‐MRI images. As a feasibility study, this technique was implemented on a digital human phantom XCAT. The respiratory motion was controlled by an irregular motion profile. To validate using k‐space center data as a respiratory surrogate, we compared it with the XCAT input controlling breathing profile. Tumor motion trajectories measured on reconstructed 4D‐MRI were compared to the average input trajectory. The mean absolute amplitude difference (D) was calculated. Results: The signal extracted from k‐space center data matches well with the input controlling respiratory profile of XCAT. The relative amplitude error was 8.6% and the relative phase error was 3.5%. XCAT 4D‐MRI demonstrated a clear motion pattern with little serrated artifacts. D of tumor trajectories was 0.21mm, 0.23mm and 0.23mm in SI, AP and ML directions, respectively. Conclusion: A novel retrospective 3D k‐space sorting 4D‐MRI technique has been developed and evaluated on human digital phantom. NIH (1R21CA165384‐01A1)
Novel Biomarker Proteins in Chronic Lymphocytic Leukemia: Impact on Diagnosis, Prognosis and Treatment (2016)

In many cancers, cells undergo re-programming of metabolism, cell survival and anti-apoptotic defense strategies, with the proteins mediating this reprogramming representing potential biomarkers. Here, we searched for novel biomarker proteins in chronic lymphocytic leukemia (CLL) that can impact diagnosis, treatment and prognosis by comparing the protein expression profiles of peripheral blood mononuclear cells from CLL patients and healthy donors using specific antibodies, mass spectrometry and binary logistic regression analyses and other bioinformatics tools. Mass spectrometry (LC-HR-MS/MS) analysis identified 1,360 proteins whose expression levels were modified in CLL-derived lymphocytes. Some of these proteins were previously connected to different cancer types, including CLL, while four other highly expressed proteins were not previously reported to be associated with cancer, and here, for the first time, DDX46 and AK3 are linked to CLL. Down-regulation expression of two of these proteins resulted in cell growth inhibition. High DDX46 expression levels were associated with shorter survival of CLL patients and thus can serve as a prognosis marker. The proteins with modified expression include proteins involved in RNA splicing and translation and particularly mitochondrial proteins involved in apoptosis and metabolism. Thus, we focused on several metabolism- and apoptosis-modulating proteins, particularly on the voltage-dependent anion channel 1 (VDAC1), regulating both metabolism and apoptosis. Expression levels of Bcl-2, VDAC1, MAVS, AIF and SMAC/Diablo were markedly increased in CLL-derived lymphocytes. VDAC1 levels were highly correlated with the amount of CLL-cancerous CD19+/CD5+ cells and with the levels of all other apoptosis-modulating proteins tested. Binary logistic regression analysis demonstrated the ability to predict probability of disease with over 90% accuracy. Finally, based on the changes in the levels of several proteins in CLL patients, as revealed from LC-HR-MS/MS, we could distinguish between patients in a stable disease state and those who would be later transferred to anti-cancer treatments. The over-expressed proteins can thus serve as potential biomarkers for early diagnosis, prognosis, new targets for CLL therapy, and treatment guidance of CLL, forming the basis for personalized therapy.
Passive Altimeter Study Using GPS Flight Data (2003)

Software GPS receiver results are presented for an over-land, passive altimeter application utilizing GPS signals. The flight data were collected using a DC-3 aircraft operated by Ohio University. The flight took place over southeast Ohio, where the terrain is hilly and forested. The GPS receiver on board the aircraft contains two channels. One channel has a right-hand-circular-polarized antenna facing upward, and the second has a left-hand-circular-polarized antenna facing downward. The upward antenna primarily receives the GPS direct signals, while the downward antenna primarily receives the ground-reflected GPS signals. Software radio GPS algorithms are used to process the data received from the upward channel. The information obtained after processing includes receiver position data, visible satellites, C/A code delay, Doppler frequency and navigation data bits as functions of time. This information is used to generate a reference signal to correlate the data received from the downward channel. Since the Doppler shift can be different between the reference and the reflected signals, the length of the coherent integration time is limited. Furthermore, the Doppler shift of the reflected signal can change rapidly as a function of the terrain. Therefore, a combination of coherent and noncoherent integration is used to enhance the signal-to-noise ratio of the reflected signals. The correlation result shows a C/A code delay corresponding to the path length difference between the direct and reflected signals. From the known locations of the receiver and the satellites, the height above ground of the receiver can be calculated. The flight data cover heights ranging from 0 to 3000 meters above the terrain.
Di-branched di-anchoring organic dyes for dye-sensitized solar cells (2009)

The first examples of di-branched di-anchoring organic sensitizers were synthesized and used in dye-sensitized solar cells leading to red-shifted IPCE maxima and increased photocurrent when compared to the corresponding mono-branched mono-anchoring dye, yielding power conversion efficiency of 5.7% (4.9% with ionic liquid electrolyte) with enhanced stability under 1 sun conditions from the di-anchoring groups.
Repeatability of magnetic resonance fingerprinting T<sub>1</sub> and T<sub>2</sub> estimates assessed using the ISMRM/NIST MRI system phantom (2016)

MRF measurements of T<sub>1</sub> and T<sub>2</sub> are highly repeatable over time and across wide ranges of T<sub>1</sub> and T<sub>2</sub> values. Magn Reson Med 78:1452-1457, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Miniature objective lens with variable focus for confocal endomicroscopy (2014)

Spectrally encoded confocal microscopy (SECM) is a reflectance confocal microscopy technology that can rapidly image large areas of luminal organs at microscopic resolution. One of the main challenges for large-area SECM imaging in vivo is maintaining the same imaging depth within the tissue when patient motion and tissue surface irregularity are present. In this paper, we report the development of a miniature vari-focal objective lens that can be used in an SECM endoscopic probe to conduct adaptive focusing and to maintain the same imaging depth during in vivo imaging. The vari-focal objective lens is composed of an aspheric singlet with an NA of 0.5, a miniature water chamber, and a thin elastic membrane. The water volume within the chamber was changed to control curvature of the elastic membrane, which subsequently altered the position of the SECM focus. The vari-focal objective lens has a diameter of 5 mm and thickness of 4 mm. A vari-focal range of 240 μm was achieved while maintaining lateral resolution better than 2.6 μm and axial resolution better than 26 μm. Volumetric SECM images of swine esophageal tissues were obtained over the vari-focal range of 260 μm. SECM images clearly visualized cellular features of the swine esophagus at all focal depths, including basal cell nuclei, papillae, and lamina propria.
A Soft Input Decoding Algorithm for Generalized Concatenated Codes (2016)

This paper proposes a soft input decoding algorithm and a decoder architecture for generalized concatenated (GC) codes. The GC codes are constructed from inner nested binary Bose-Chaudhuri-Hocquenghem (BCH) codes and outer Reed-Solomon codes. In order to enable soft input decoding for the inner BCH block codes, a sequential stack decoding algorithm is used. Ordinary stack decoding of binary block codes requires the complete trellis of the code. In this paper, a representation of the block codes based on the trellises of supercodes is proposed in order to reduce the memory requirements for the representation of the BCH codes. This enables an efficient hardware implementation. The results for the decoding performance of the overall GC code are presented. Furthermore, a hardware architecture of the GC decoder is proposed. The proposed decoder is well suited for applications that require very low residual error rates.
Processing moving queries over moving objects using motion-adaptive indexes (2006)

This paper describes a motion-adaptive indexing scheme for efficient evaluation of moving continual queries (MCQs) over moving objects. It uses the concept of motion-sensitive bounding boxes (MSBs) to model moving objects and moving queries. These bounding boxes automatically adapt their sizes to the dynamic motion behaviors of individual objects. Instead of indexing frequently changing object positions, we index less frequently changing object and query MSBs, where updates to the bounding boxes are needed only when objects and queries move across the boundaries of their boxes. This helps decrease the number of updates to the indexes. More importantly, we use predictive query results to optimistically precalculate query results, decreasing the number of searches on the indexes. Motion-sensitive bounding boxes are used to incrementally update the predictive query results. Furthermore, we introduce the concepts of guaranteed safe radius and optimistic safe radius to extend our motion-adaptive indexing scheme to evaluating moving continual k-nearest neighbor (kNN) queries. Our experiments show that the proposed motion-adaptive indexing scheme is efficient for the evaluation of both moving continual range queries and moving continual kNN queries.
OPTIMIZING CONTROL OF DIESEL INJECTION TIMING (1983)

A closed-loop digital system for the control of diesel engine timing has been investigated both experimentally and theoretically. The optimizing control system continuously searches for maximum brake torque (MBT) fuel injection timing, or a timing advanced or retarded a pre-determined amount from MBT. It utilizes peak seeking logic in which the injection timing is continuously dithered (alternately advanced and retarded by small amounts) and corrected in accordance with engine speed changes resulting from the dithering. Two types of optimizing control are discussed: time-based and crankangle-based. The time-based control operates at fixed dither frequency. The system used in the experimental tests was a time-based control system. With the crankangle-based control, dithering is synchronized to engine rotation. Thus, the dither frequency varies with engine speed.
Designing, optimizing, and assessing modular functional near-infrared brain imaging probes using an automated software workflow (2021)

Abstract Significance The exponential growth of research utilizing functional near-infrared spectroscopy (fNIRS) systems has led to the emergence of modular fNIRS systems composed of repeating optical source/detector modules. Compared to conventional fNIRS systems, modular fNIRS systems are more compact and flexible, making wearable and long-time monitoring possible. However, the large number of design parameters makes designing a modular probe a daunting task. Aim We aim to create a systematic software platform to facilitate the design, characterization, and comparison of modular fNIRS probes. Approach Our algorithm automatically tessellates any region-of-interest using user-specified module design parameters and outputs performance metrics such as spatial channel distributions, average brain sensitivity, and sampling rate estimates of the resulting probe. Automated algorithms for spatial coverage, orientation, and routing of repeated modules are also developed. Results We developed a software platform to help explore a wide range of modular probe features and quantify their performances. We compare full-head probes using three different module shapes and highlight the trade-offs resulting from various module settings. Additionally, we show that one can apply this workflow to improve existing modular probes without needing to re-design or re-manufacture them. Conclusion Our flexible modular probe design platform shows promise in optimizing existing modular probes and investigating future modular designs.
Vaccine-Induced Serum Immunoglobin Contributes to Protection from Herpes Simplex Virus Type 2 Genital Infection in the Presence of Immune T Cells (2001)

Herpes simplex type virus 2 (HSV-2) is a sexually transmitted pathogen that causes genital lesions and spreads to the nervous system to establish acute and latent infections. Systemic but not mucosal cellular and humoral immune responses are elicited by immunization of mice with a replication-defective mutant of HSV-2, yet the mice are protected against disease caused by subsequent challenge of the genital mucosa with virulent HSV-2. In this study, we investigated the role of immune serum antibody generated by immunization with a replication-defective HSV-2 vaccine prototype strain in protection of the genital mucosa and the nervous system from HSV-2 infection. Passive transfer of replication-defective virus-immune serum at physiologic concentrations to SCID or B-cell-deficient mice had no effect on replication of challenge virus in the genital mucosa but did significantly reduce the incidence and severity of genital and neurologic disease. In contrast, B-cell-deficient mice immunized with replication-defective HSV-2 were able to control replication of challenge virus in the genital mucosa, but not until 3 days postchallenge, and were not completely protected against genital and neurologic disease. Passive transfer of physiologic amounts of immune serum to immunized, B-cell-deficient mice completely restored their capacity to limit replication of challenge virus in the genital mucosa and prevented signs of genital and systemic disease. In addition, the numbers of viral genomes in the lumbosacral dorsal root ganglia of immunized, B-cell-deficient mice were dramatically reduced by transfer of immune serum prior to challenge. These results suggest that there is an apparent synergism between immune serum antibody and immune T cells in achieving protection and that serum antibody induced by vaccination with replication-defective virus aids in reducing establishment of latent infection after genital infection with HSV-2.
An lower ISM band frequency synthesizer and GMSK data modulator (1997)

In this paper a high resolution fractional-N RF frequency synthesizer is presented which is controlled by a fourth-order digital sigma-delta modulator allowing the synthesizer to be digitally modulated directly at RF. For data transmission a simplified digital filter which makes use of sigma-delta quantized tap coefficients is included which provides built in GMSK pulse shaping. The synthesizer makes use of two custom chips, with only a simple off chip loop filter and VCO required. The synthesizer operates from a single three volt supply and the two chips consume a total of 32 mW.