gebhart/patrepeval huggingface dataset:
Waveguide for air-coupled ultrasonic phased-arrays with propagation time compensation and plug-in assembly (2021)

Waveguides allow grating lobe free beamforming for air-coupled ultrasonic phased-arrays by reducing the effective inter-element spacing to half wavelength. Since the sound waves propagate through the waveguide ducts, additional time delays are introduced. In this work, we present analytical, numerical, and experimental methods to estimate these time delays. Afterwards, two different waveguides are compared. The first one consists of equal-length ducts, requiring a time-consuming assembly process of the ultrasonic phased-array. In contrast, the second waveguide consists of Bézier-shaped ducts of unequal lengths but a planar input port allowing fast assembly. The analytical model is based on the geometric lengths of the waveguide ducts. The numerical model relies on a transient finite element analysis. All simulations are validated in an anechoic chamber using a calibrated microphone. The analytical (7.6% deviation) and numerical (3.2% deviation) propagation time models are in good agreement with the measurements. By using the analyzed propagation times for the compensation of the unequal waveguide duct lengths, we restored the beamforming capability without significant sound pressure level (SPL) loss. This work shows the possibility of reduced transducer assembly time for waveguided air-coupled phased-arrays without a reduced SPL.
P4‐351: Longitudinal volume changes of the hippocampus, parahippocampus and entorhinal cortex improve the prediction of conversion from MCI to Alzheimer's disease (2011)

Magnetic resonance imaging (MRI) data from the multi-centre Alzheimer's Disease Neuroimaging Initiative (ADNI) project was used to investigate the predictive power of longitudinal volumetric MRI measures in differentiating Mild Cognitive Impairment (MCI) patients converting to Alzheimer's disease (AD) (MCI-c) from those that remain stable (MCI-s). Longitudinal percentage volume changes (PVC) in hippocampal, parahippocampal and entorhinal cortex (ERC) and left/right asymmetry were compared to standard cross-sectional measures. Data on 58 MCI-c and 239 MCI-s subjects was acquired from the public ADNI consortium database. Multiple 1.5T scanners were used to obtain MP-RAGE scans at baseline, six-months and one-year. Hippocampal volume and parahippocampal/ERC thickness were measured using FreeSurfer and used to calculate PVC and asymmetry measures between baseline & six-months, six-months & one-year and baseline & one-year. A mixed-model logistic regression analyses using a generalised linear approach with random effects for centre and controlling for age and gender was used to examine the extent to which normalised volumes could predict group membership. Akaike information criterion (AIC) and Bayesian information criterion (BIC) were used to identify the best models which were then reported in terms of sensitivity, specificity and balanced accuracy. Cross-sectional volumes at one-year were found to be the best model (Sensitivity = 71%, Specificity = 69%, Accuracy = 70%) with both the left hippocampus (p <0.001) and right ERC (p = 0.05) significantly predicting conversion. The best longitudinal models from each group were PVCs between baseline and one-year (Sensitivity = 64%, Specificity = 67%, Accuracy = 66%) with the left ERC as the most accurate predictor (p = 0.001), and asymmetry changes between six-months and one-year (Sensitivity = 61%, Specificity = 64%, Accuracy = 62%). Combining cross-sectional volumes at baseline with PVC measures from baseline to six-months improved the ability to predict conversion (Sensitivity = 70%, Specificity = 72%, Accuracy = 71%). Longitudinal PVC and asymmetry measures were not as accurate at predicting group membership as cross-sectional volumes. However, the ability to predict conversion was improved by combining longitudinal measures with cross-sectional volumes. Consistent with previous findings, we confirm that the left hippocampus and right ERC are the most accurate cross-sectional predictors of conversion, but PVCs of the left ERC are a more important longitudinal marker of conversion.
Design and development of C-arm based cone-beam CT for image-guided interventions: initial results (2006)

X-ray cone-beam computed tomography (CBCT) is of importance in image-guided intervention (IGI) and image-guided radiation therapy (IGRT). In this paper, we present a cone-beam CT data acquisition system using a GE INNOVA 4100 (GE Healthcare Technologies, Waukesha, Wisconsin) clinical system. This new cone-beam data acquisition mode was developed for research purposes without interfering with any clinical function of the system. It provides us a basic imaging pipeline for more advanced cone-beam data acquisition methods. It also provides us a platform to study and overcome the limiting factors such as cone-beam artifacts and limiting low contrast resolution in current C-arm based cone-beam CT systems. A geometrical calibration method was developed to experimentally determine parameters of the scanning geometry to correct the image reconstruction for geometric non-idealities. Extensive phantom studies and some small animal studies have been conducted to evaluate the performance of our cone-beam CT data acquisition system.
Insight into the functional versatility of RNA through model-making with applications to data fitting (2007)

The RNA World hypothesis posits that life emerged from self-replicating RNA molecules. For any single biopolymer to be the basis for life, it must both store information and perform diverse functions. It is well known that RNA can store information. Advances in recent years have revealed that RNA can exhibit remarkable functional versatility as well. In an effort to judge the functional versatility of RNA and thereby the plausibility that RNA was at one point the basis for life, a statistical chemical approach is adopted. Essential biological functions are reduced to simple molecular models in a minimalist, biopolymer-independent fashion. The models dictate requisite states, populations of states, and physical and chemical changes occurring between the states. Next, equations are derived from the models, which lead to complex phenomenological constants such as observed and functional constants that are defined in terms of familiar elementary chemical descriptors: intrinsic rate constants, microscopic ligand equilibrium constants, secondary structure stability, and ligand concentration. Using these equations, simulations of functional behavior are performed. These functional models provide practical frameworks for fitting and organizing real data on functional RNAs such as ribozymes and riboswitches. At the same time, the models allow the suitability of RNA as a basis for life to be judged. We conclude that RNA, while inferior to extant proteins in most, but not all, functional respects, may be more versatile than proteins, performing a wider range of elementary biological functions at a tolerable level. Inspection of the functional models and various RNA structures uncovers several surprising ways in which the nucleobases can conspire to afford chemical catalysis and evolvability. These models support the plausibility that RNA, or a closely related informational biopolymer, could serve as the basis for a fairly simple form of life.
Architecture-compatible code boosting for performance enhancement of the IBM RS/6000 (2002)

Boosting, first introduced by M.D. Smith et al. (1990), is an instruction scheduling technique that increases the instruction-level parallelism by allowing the compiler to move instructions speculatively up past conditional branches and providing hardware support to delay committing the side effects of the boosted instructions until the conditional branches have been resolved. The paper proposes an enhanced compilation technique similar to boosting that provides performance improvements while maintaining instruction set architecture compatibility and eliminating the need for complex hardware support. The technique, called architecture-compatible (AC) boosting, has been implemented for the IBM RS/6000 architecture. Code scheduling and machine simulation tools have been implemented, and experiments have been performed to demonstrate the feasibility of AC boosting on the current as well as future implementations of the IBM RS/6000 architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sensor and instrumentation for progesterone detection (2012)

The reported research work uses a real time and noninvasive method to detect progesterone hormone concentration in purified water using Electrochemical Impedance Spectroscopy (E.I.S.) technique. Planar capacitive sensor, consisting of inter-digitated microelectrodes, is designed and fabricated on silicon substrate using thin-film Microelectromechanical system (MEMS) based semiconductor device fabrication technology. The sensor in conjunction with EIS is used to evaluate conductivity, permeability and dielectric properties of reproductive hormone progesterone and its concentration quantification in purified water. Impedance spectrums are obtained with various concentrations of the hormone in purified water by using an electric circuit in order to extract sample conductance. Relationship of sample conductance with progesterone concentration level is studied in this research work. The ability of E.I.S. to detect progesterone concentration is aimed to be used in dairy farming industry in order to obtain better reproductive performance of the dairy cattle.
From a Low-Cost Air Quality Sensor Network to Decision Support Services: Steps towards Data Calibration and Service Development (2021)

Air pollution is a widespread problem due to its impact on both humans and the environment. Providing decision makers with artificial intelligence based solutions requires to monitor the ambient air quality accurately and in a timely manner, as AI models highly depend on the underlying data used to justify the predictions. Unfortunately, in urban contexts, the hyper-locality of air quality, varying from street to street, makes it difficult to monitor using high-end sensors, as the cost of the amount of sensors needed for such local measurements is too high. In addition, development of pollution dispersion models is challenging. The deployment of a low-cost sensor network allows a more dense cover of a region but at the cost of noisier sensing. This paper describes the development and deployment of a low-cost sensor network, discussing its challenges and applications, and is highly motivated by talks with the local municipality and the exploration of new technologies to improve air quality related services. However, before using data from these sources, calibration procedures are needed to ensure that the quality of the data is at a good level. We describe our steps towards developing calibration models and how they benefit the applications identified as important in the talks with the municipality.
A novel ROC approach for performance evaluation of target detection algorithms (2007)

Receiver operator characteristic (ROC) analysis is an emerging automated target recognition system performance assessment tool. The ROC metric, area under the curve (AUC), is a universally accepted measure of classifying accuracy. In the presented approach, the detection algorithm output, i.e., a response plane (RP), must consist of grayscale values wherein a maximum value (e.g. 255) corresponds to highest probability of target locations. AUC computation involves the comparison of the RP and the ground truth to classify RP pixels as true positives (TP), true negatives (TN), false positives (FP), or false negatives (FN). Ideally, the background and all objects other than targets are TN. Historically, evaluation methods have excluded the background, and only a few spoof objects likely to be considered as a hit by detection algorithms were <i>a priori</i> demarcated as TN. This can potentially exaggerate the algorithm's performance. Here, a new ROC approach has been developed that divides the entire image into mutually exclusive target (TP) and background (TN) grid squares with adjustable size. Based on the overlap of the thresholded RP with the TP and TN grids, the FN and FP fractions are computed. Variation of the grid square size can bias the ROC results by artificially altering specificity, so an assessment of relative performance under a constant grid square size is adopted in our approach. A pilot study was performed to assess the method's ability to capture RP changes under three different detection algorithm parameter settings on ten images with different backgrounds and target orientations. An ANOVA-based comparison of the AUCs for the three settings showed a significant difference (p<0.001) at 95% confidence interval.
Simulation modeling within workflow technology (1995)

This paper presents an approach for integrating simulation modeling and analysis capabilities within the workflow management system (WFMS) being developed in the Large Scale Distributed Information Systems (LSDIS) Lab at the University of Georgia. Simulation modeling can be used for studying the efficiency of workflow designs as well as studying the general performance and reliability of WFMSs. We also discuss the importance of using sophisticated monitoring and animation capabilities, and the use of workflow management technology to advance simulation technology itself. Finally, we demonstrate a sample simulation where tasks and task managers are simulated.
Evolution of mobile location-based services (2003)

Utilizing user location as a key determinant of information requirement needs.
Bridging the Gap Between 2D and 3D Organ Segmentation with Volumetric Fusion Net (2018)

There has been a debate on whether to use 2D or 3D deep neural networks for volumetric organ segmentation. Both 2D and 3D models have their advantages and disadvantages. In this paper, we present an alternative framework, which trains 2D networks on different viewpoints for segmentation, and builds a 3D Volumetric Fusion Net (VFN) to fuse the 2D segmentation results. VFN is relatively shallow and contains much fewer parameters than most 3D networks, making our framework more efficient at integrating 3D information for segmentation. We train and test the segmentation and fusion modules individually, and propose a novel strategy, named cross-cross-augmentation, to make full use of the limited training data. We evaluate our framework on several challenging abdominal organs, and verify its superiority in segmentation accuracy and stability over existing 2D and 3D approaches.
Effects of thermal aging on moisture diffusion in insulation paper immersed with mineral oil (2018)

Thermal aging of insulation paper has obvious effects on its moisture absorption property. The presented studies aim to investigating the effects of aging on moisture diffusion in oil-immersed insulation paper. Based on the experimental designs and preparation of experimental materials, the transient moisture contents of insulation paper with different aging status were obtained at different conditions. Then, the experimental results were discussed. Furthermore, the diffusion factors and equilibrium time constants were extracted based on the model of moisture diffusion in oil-immersed insulation paper, which are applicable to our studies. Finally, the effects of thermal aging on the diffusion factor and equilibrium time constant were analyzed. The results show that: 1) With the aging of insulation paper, the rate of moisture absorption increases, and the equilibrium moisture content of insulation paper decreases at the same temperature. Besides, the equilibrium time constant decreases with aging at the same temperature. 2) Considering the effects of aging, thickness of insulation paper and temperature, the empirical expression of diffusion factor was obtained and verified.
Disentangling the lifespans of hepatitis C virus‐infected cells and intracellular vRNA replication‐complexes during direct‐acting anti‐viral therapy (2019)

The decay rate of hepatitis C virus (HCV)-infected cells during therapy has been used to determine the duration of treatment needed to attain a sustained virologic response, but with direct-acting anti-virals (DAA), this rate has been difficult to estimate. Here, we show that it is possible to estimate it, by simultaneously analysing the viral load and alanine aminotransferase (ALT) kinetics during combination DAA therapy. We modelled the HCV RNA and ALT serum kinetics in 26 patients with chronic HCV genotype 1b infection, under four different sofosbuvir-based combination treatments. In all patients, ALT decayed exponentially to a set point in the normal range by 1-3 weeks after initiation of therapy. The model indicates that the ALT decay rate during the first few weeks after initiation of therapy reflects the death rate of infected cells, with an estimated median half-life of 2.5 days in this patient population. This information allows independent estimation of the rate of loss of intracellular replication complexes during therapy. Our model also predicts that the final ALT set point is not related to the release of ALT by dying HCV-infected cells. Using ALT data, one can separately obtain information about the rate of 'cure' of HCV-infected cells versus their rate of death, something not possible when analysing only HCV RNA data. This information can be used to compare the effects of different DAA combinations and to rationally evaluate their anti-viral effects.
A novel human prostate-specific gene-1 (HPG-1): molecular cloning, sequencing, and its potential involvement in prostate carcinogenesis. (2003)

Prostate-specific genes that have a role in normal and abnormal prostate growth are needed for early and specific diagnosis and treatment of prostate cancer. In the present study, the differential display-PCR technique was used to obtain a prostate-specific approximately 339-bp cDNA fragment. On screening the human-prostate lambdagt10 library with this fragment, a full-length 1468-bp human prostate-specific gene (HPG-1) with an open reading frame of 127 amino acids (aa) was retrieved. Extensive database search revealed that the HPG-1 has novel nucleotide/aa sequences. It was localized on Homo sapiens 3q26 chromosomal locus, a region that has been shown to be involved in prostate carcinoma. The computer-generated translated protein has a calculated molecular mass of 14.8 kDa with several potential glycosylation and phosphorylation sites including two N-linked glycosylation, one tyrosine phosphorylation, and one N-myristoylation sites. The in vitro transcription and translation procedures using HPG-1 cDNA yielded a protein of similar molecular mass of approximately 15 kDa. Hydrophilicity analysis of the deduced aa sequence indicated that HPG-1 is a membrane-anchored/attached protein. Analysis for tissue specificity by using the Northern blot and reverse transcription-PCR-Southern blot procedures using 19 different human tissues revealed that HPG-1 is expressed specifically only in prostate tissue. To examine its involvement in prostate carcinogenesis, three prostate cancer epithelial cell lines, one androgen-responsive (LNCaP) and two androgen-nonresponsive (DU-145 and PC-3), were examined for the expression of HPG-1. Using the Northern blot and quantitative reverse transcription-PCR procedures it was found that LNCaP and DU-145 cells and not the PC-3 cells have HPG-1 expression, with LNCaP cells having approximately 2-3-fold higher levels of HPG-1 mRNA transcripts compared with DU-145 cells. In vitro culture of LNCaP cell with antisense and not the sense oligonucleotide decreased the HPG-1 mRNA levels and inhibited the cell growth in a concentration-dependent manner; at 72 h there was an 86% inhibition of cell growth. HPG-1 mRNA expression in LNCaP cells was found to be responsive to androgen. Thus, the novel androgen-responsive HPG-1, which has prostate-specific expression and seems to be involved in carcinogenesis, may have applications in the specific diagnosis and treatment of prostate cancer.
A new approach for estimating research impact: An application to French cancer research (2020)

Much attention has been paid to estimating the impact of investments in scientific research. Historically, those efforts have been largely ad hoc, burdensome, and error prone. In addition, the focus has been largely mechanical—drawing a direct line between funding and outputs—rather than focusing on the scientists that do the work. Here, we provide an illustrative application of a new approach that examines the impact of research funding on individuals and their scientific output in terms of publications, citations, collaborations, and international activity, controlling for both observed and unobserved factors. We argue that full engagement between scientific funders and the research community is needed if we are to expand the data infrastructure to enable a more scientific assessment of scientific investments.
NH Tautomerism in the Dimethyl Ester of Bonellin, a Natural Chlorin (1998)

The NH protons of the chlorins (17,18-dihydroporphyrins) and fully conjugated porphyrins can undergo tautomerization between the four central nitrogens. We have investigated the NH tautomerization process of bonellin dimethyl ester by NMR spectroscopy and molecular modeling. In this natural chlorin derivative, the tautomerization was observed to occur between the two degenerate N21−H, N23−H trans-tautomers. The dynamic 1H NMR measurements showed a coalescence temperature of 297 K for the total tautomeric exchange process (N21−Ha ⇌ N23−Hb). The free energy of activation ΔG297⧧ was calculated to be 14.4 kcal/mol on the basis of the Eyring equation. The two-dimensional 1H and 15N heteronuclear single quantum coherence (HSQC) and heteronuclear multiple bond correlation (HMBC) NMR techniques were used to assign the 15N and NH proton resonances at natural abundance. In addition to the strong 15N−1H one-bond correlations, the HSQC spectrum showed weak correlations between the diagonally opposite nitrogen and proton, thus providing clear evidence for the NH tautomeric exchange. These weak correlations arise from the exchange between the NH protons after the refocusing period of the HSQC pulse sequence. The semiempirical molecular modeling methods AM1 and PM3 were used to estimate the energies of the possible tautomers. The AM1 and PM3 methods with an unrestricted Hartree−Fock (UHF) spin-pairing option both favor strongly the chlorin tautomers in which an aromatic 18-atom 18 π-electron delocalization pathway is possible without delocalizing the lone-pair electrons of N24 in the reduced sub-ring. In the proposed tautomerization pathway, the fully aromatic N21−H, N22−H and N22−H, N23−H cis-tautomers were found to be energetically more advantageous than the less aromatic N21−H, N24−H and N23−H, N24−H cis-tautomers. The stepwise tautomerization mechanism is concluded for the proton transfer.