gebhart/patrepeval huggingface dataset:
Parametric imaging for characterizing focal liver lesions in contrast-enhanced ultrasound (2010)

The differentiation between benign and malignant focal liver lesions plays an important role in diagnosis of liver disease and therapeutic planning of local or general disease. This differentiation, based on characterization, relies on the observation of the dynamic vascular patterns (DVP) of lesions with respect to adjacent parenchyma, and may be assessed during contrast-enhanced ultrasound imaging after a bolus injection. For instance, hemangiomas (i.e., benign lesions) exhibit hyper-enhanced signatures over time, whereas metastases (i.e., malignant lesions) frequently present hyperenhanced foci during the arterial phase and always become hypo-enhanced afterwards. The objective of this work was to develop a new parametric imaging technique, aimed at mapping the DVP signatures into a single image called a DVP parametric image, conceived as a diagnostic aid tool for characterizing lesion types. The methodology consisted in processing a time sequence of images (DICOM video data) using four consecutive steps: (1) pre-processing combining image motion correction and linearization to derive an echo-power signal, in each pixel, proportional to local contrast agent concentration over time; (2) signal modeling, by means of a curve-fitting optimization, to compute a difference signal in each pixel, as the subtraction of adjacent parenchyma kinetic from the echopower signal; (3) classification of difference signals; and (4) parametric image rendering to represent classified pixels as a support for diagnosis. DVP parametric imaging was the object of a clinical assessment on a total of 146 lesions, imaged using different medical ultrasound systems. The resulting sensitivity and specificity were 97% and 91%, respectively, which compare favorably with scores of 81 to 95% and 80 to 95% reported in medical literature for sensitivity and specificity, respectively.
The effect of Dicer knockout on RNA interference using various Dicer substrate interfering RNA structures (2020)

Abstract Dicer-substrate siRNA (DsiRNA) was a useful tool for sequence-specific gene silencing. DsiRNA was proposed to have increased efficacy via RNAi gene silencing, but the molecular mechanism underlying the increased efficacy is not precise. We designed the tetra-looped DsiRNA as the tetra-looped RNAs have been reported more stable structure and increased binding efficiency with RNA and protein. To gain a deeper understanding of the Dicer function of DsiRNA, we knocked out Dicer in the HCT116 cell line and analyzed the efficacy of various Dicer substrates on RNAi gene silencing activity. Tetra-looped DsiRNA demonstrated increased efficacy of gene silencing Dicer expressing cells with activity favoring the guide strand. The gene silencing activity of all DsiRNAs was reduced in Dicer knockout cells. Thus, this study allows us to understand the Dicer function of key RNAi silencing and provides valuable resources for RNAi research and applications.
Nasopharyngeal Exposure to <i>Streptococcus pneumoniae</i> Induces Extended Age-Dependent Protection against Pulmonary Infection Mediated by Antibodies and CD138+ Cells (2018)

<i>Streptococcus pneumoniae</i> commonly resides asymptomatically in the nasopharyngeal (NP) cavity of healthy individuals but can cause life-threatening pulmonary and systemic infections, particularly in the elderly. NP colonization results in a robust immune response that protects against invasive infections. However, the duration, mechanism, and cellular component of such responses are poorly understood. In this study, we found that repeated NP exposure of mice to <i>S. pneumoniae</i> TIGR4 strain results in pneumococcal-specific Ab responses that protect against lethal lung challenge. Abs were necessary and sufficient for protection because Ab-deficient μMT mice did not develop postexposure protection, only becoming resistant to lung infection after transfer of immune sera from NP-exposed mice. T cells contributed to immunity at the time of NP exposure, but neither CD4<sup>+</sup> nor CD8<sup>+</sup> T cells were required. The protective activity was detectable 20 wk after exposure and was maintained in irradiated mice, suggesting involvement of long-lived Ab-secreting cells (ASC), which are radioresistant and secrete Abs for extended periods of time in the absence of T cells or persistent Ag. CD138<sup>+</sup> bone marrow cells, likely corresponding to long-lived ASC, were sufficient to confer protection. NP exposure of aged mice failed to protect against subsequent lung infection despite eliciting a robust Ab response. Furthermore, transfer of CD138<sup>+</sup> bone marrow cells or sera from NP-exposed old mice failed to protect naive young mice. These findings suggest that NP exposure elicits extended protection against pneumococcal lung infection by generating long-lived CD138<sup>+</sup> ASC and that the protective efficacy of these responses declines with age.
Severe thickness variation of sub-3 nm gate oxide due to Si surface faceting, poly-Si intrusion, and corner stress (1999)

In the fabrication of CMOS devices with sub-3 nm gate oxides, we have observed severe variation of the oxide thickness (t/sub ox/). For devices with 2.5 nm t/sub ox/ at the center of the channel, the physical t/sub ox/ ranges from 1.8 nm to 4.2 nm at various channel positions. This is caused by different oxide growth rates determined by the orientation and stress conditions of the local Si surface, especially at the rounded corners of the shallow-trench isolation (STI). In addition, poly-Si intrusion from the gate electrode also causes local t/sub ox/ thinning. Such severe variation of t/sub ox/ becomes the challenge of STI engineering, gate-oxide scaling and qualification.
Understanding Angiography-Based Aneurysm Flow Fields through Comparison with Computational Fluid Dynamics (2017)

Several factors affect the reconstruction of 2D flow fields from dynamic angiography sequences. The most important factors are the 3-dimensionality of the intrasaccular flow patterns and inflow jets, the alignment of the main vortex structure with the line of sight, the overlapping of surrounding vessels, and possibly frame rate undersampling. Flow visualization with DSA from >1 projection is required for understanding of the 3D intrasaccular flow patterns. Although these DSA-based flow quantification techniques do not capture swirling or secondary flows in the parent artery, they still provide a good representation of the mean axial flow and the corresponding flow rate.
Catalytic Asymmetric Amination of N‐Nonsubstituted α‐Alkoxycarbonyl Amides: Concise Enantioselective Synthesis of Mycestericin F and G (2011)

In an attempt to explore the synthetic utility of a ternary asymmetric catalyst comprising La(NO(3))(3)·6H(2)O, amide-based ligand (R)-L1, and D-valine tert-butyl ester H-D-Val-OtBu, we investigated a catalytic, asymmetric amination of functionalized N-nonsubstituted α-alkoxycarbonyl amides using di-tert-butyl azodicarboxylate as an electrophilic aminating reagent. A highly functionalized, cyclic N-nonsubstituted α-alkoxycarbonyl amide delivered the desired amination product in up to 96% enantiometric excess, with the requisite functionalities of the polar heads of sphingosines with the appropriate stereochemical arrangement. The rapid asymmetric assembly of these functional groups allowed a concise enantioselective synthetic route to sphingosines to be established with a broad flexibility towards derivative synthesis. These studies have culminated in an efficient catalytic enantioselective total synthesis of immunosuppressive fungal metabolites mycestericin F (3a) and G (3b).
T<sub>2</sub> and T quantification using optimal B<sub>1</sub> image reconstruction for multicoil arrays (2008)

This work demonstrates improvements to the accuracy of T(2) and T(2)* measurements obtained when OBR is used compared to RSS, particularly in the case of low SNR.
Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis (2013)

DNA methylation in mammals is highly dynamic during germ cell and preimplantation development but is relatively static during the development of somatic tissues. 5-hydroxymethylcytosine (5hmC), created by oxidation of 5-methylcytosine (5mC) by Tet proteins and most abundant in the brain, is thought to be an intermediary toward 5mC demethylation. We investigated patterns of 5mC and 5hmC during neurogenesis in the embryonic mouse brain. 5hmC levels increase during neuronal differentiation. In neuronal cells, 5hmC is not enriched at enhancers but associates preferentially with gene bodies of activated neuronal function-related genes. Within these genes, gain of 5hmC is often accompanied by loss of H3K27me3. Enrichment of 5hmC is not associated with substantial DNA demethylation, suggesting that 5hmC is a stable epigenetic mark. Functional perturbation of the H3K27 methyltransferase Ezh2 or of Tet2 and Tet3 leads to defects in neuronal differentiation, suggesting that formation of 5hmC and loss of H3K27me3 cooperate to promote brain development.
Integrating Parallel and Distributed Computing in Early Computing Classes (2022)

Parallel and distributed computing (PDC) has become pervasive in all aspects of computing, and thus it is essential that students include parallelism and distribution in the computational thinking that they apply to problem solving, from the very beginning. Computer science education is still teaching to a 20th century model of algorithmic problem solving. Sequence, branch, and loop are taught in our early courses as the only organizing principles needed for algorithms, and we invest considerable time in showing how best to sequentially process large volumes of data. All computing devices that students use currently have multiple cores as well as a GPU in many cases. Most of their favorite applications use multiple cores and numbers of distributed processors. Often concurrency offers simpler solutions than sequential approaches. Industry is desperate for software engineers who think naturally in terms of exploiting these capabilities, rather than seeing them as an exotic upper-level topic that gets layered over a sequential solution. However, we are still teaching students to solve problems using sequential thinking. In this workshop we overview key PDC concepts and provide examples of how they may naturally be incorporated in early computing classes. We will introduce plugged and unplugged curriculum modules that have been successfully integrated in existing computing classes at multiple institutions. We will highlight the upcoming summer training workshop, for which we have funding to support attendance, as well as other CDER (Center for Parallel and Distributed Computing Curriculum Development and Educational Resources) activities.
Impact of Perturbation Back-propagation on Carrier Phase Recovery in 224 Gb/s DP-16QAM Transmission (2013)

We experimentally investigate the impact of nonlinearity on cycle slip probability and demonstrate its reduction by perturbation back-propagation algorithm in 224 Gb/s DP-16QAM transmission with 50 and 37.5 GHz-grid over large-Aeff pure silica core fiber.
Underpinning and Retention (1992)

Various underpinning methods exist, and choosing a particular method or selection of methods is the job of the engineer. Consistent with the underpinning procedure is the need to retain the affected structure plus the surrounding ground and/or buildings. This book will offer advice on how to chose the correct procedure.
Engineering Properties of Overburden Materials for the Means Project (1982)

A geotechnical investigation was performed to determine the physical properties (classification) and engineering properties of the overburden material from a proposed oil shale mining site in Montgomery County (Means Project). Three overburden materials were received in sealed meal drums and were labeled Nancy Member, Borden Formation; Clay City Bed, Farmers Member, Borden Formation; and Henley bed, Farmers Member, Borden Formation. Hereafter, they will be referred to as the Nancy, Clay City and Henley, respectively. the various types of geotechnical laboratory tests performed on these materials are listed in Table 1.
T cell receptor excision circle (TREC) content following maximum HIV suppression is equivalent in HIV-infected and HIV-uninfected individuals (2001)

The finding that TREC expression was equivalent between HIV-positive patients after therapy and HIV-negative donors suggests that there is no reduction in thymic output among HIV-positive individuals after therapy. Given that TREC is inversely correlated with HLA-DR/CD38 expression, its analysis in studies of thymopoiesis should be evaluated in the context of maximum viral suppression to reduce HIV-mediated immune activation and/or by normalizing for cell turnover.
Contact Pressure in the Wrist During Computer Mouse Work (2012)

This study investigated the relationship between computer mouse work and contact pressure around the pisiform. Commonly performed mouse work was simulated using 3 different-shaped mice with 3 forearm positions. When typical mouse work was performed, the contact pressure on the pisiform area was evaluated using a digital pressure sensor and compared with that of the thenar area. Six mouse tasks were simulated. Results indicate that mouse users should avoid wrist-snap dragging and resting their wrist on the edge of the desk to minimize the pressure concentration on the pisiform area.
Extending the unambiguous velocity range using multiple carrier frequencies (2005)

Typically, velocity estimators based on the estimation of the Doppler shift will suffer from a limited unambiguous velocity range. Proposed are two novel multiple carrier based velocity estimators extending the velocity range above the Nyquist velocity limit. Numerical simulations indicate that the proposed estimators offer improved estimation performance compared to other existing techniques.
Monitoring live human mesenchymal stromal cell differentiation and subsequent selection using fluorescent RNA-based probes (2016)

Investigating mesenchymal stromal cell differentiation requires time and multiple samples due to destructive endpoint assays. Osteogenesis of human bone marrow derived mesenchymal stromal cells (hBMSCs) has been widely studied for bone tissue engineering. Recent studies show that the osteogenic differentiation of hBMSCs can be assessed by quantifying the ratio of two important transcription factors (Runx2/Sox9). We demonstrate a method to observe mRNA expression of two genes in individual live cells using fluorescent probes specific for Runx2 and Sox9 mRNA. The changes of mRNA expression in cells can be observed in a non-destructive manner. In addition, the osteogenic hBMSCs can be prospectively identified and obtained based on the relative intracellular fluorescence of Sox9 in relation to Runx2 using fluorescence activated cell sorting. Relatively homogeneous cell populations with high osteogenic potential can be isolated from the original heterogeneous osteogenically induced hBMSCs within the first week of induction. This offers a more detailed analysis of the effectiveness of new therapeutics both at the individual cell level and the response of the population as a whole. By identifying and isolating differentiating cells at early time points, prospective analysis of differentiation is also possible, which will lead to a greater understanding of MSC differentiation.
Regulatory T Cells Control Uveoretinitis Induced by Pathogenic Th1 Cells Reacting to a Specific Retinal Neoantigen (2006)

In many clinical cases, uveitis develops secondary to an infection. This could result from peripheral activation followed by ocular penetration and reactivation of T cells specific for microbial Ags expressed in the retina. To gain insights into the pathophysiology of uveitis, we developed a new mouse model based on stable retinal expression of influenza virus hemagglutinin (HA) neoantigen by adeno-associated virus-mediated gene transfer. One month thereafter, we adoptively transferred HA-specific T cells, which were activated in vitro or in vivo. Intraocular inflammation was clinically and histologically observed in all animals within 15 days. The ocular infiltrate was composed mostly of macrophages and HA-specific T cells with a proinflammatory cytokine profile. Depletion of CD4(+)CD25(+) regulatory T cells exacerbated the disease, whereas HA-specific CD4(+)CD25(+) T cells given i.v. controlled the disease. This novel model should allow to better study the pathophysiology and therapeutic of uveitis.
Patient-specific scatter correction for flat-panel detector-based cone-beam CT imaging (2015)

A patient-specific scatter correction algorithm is proposed to mitigate scatter artefacts in cone-beam CT (CBCT). The approach belongs to the category of convolution-based methods in which a scatter potential function is convolved with a convolution kernel to estimate the scatter profile. A key step in this method is to determine the free parameters introduced in both scatter potential and convolution kernel using a so-called calibration process, which is to seek for the optimal parameters such that the models for both scatter potential and convolution kernel is able to optimally fit the previously known coarse estimates of scatter profiles of the image object. Both direct measurements and Monte Carlo (MC) simulations have been proposed by other investigators to achieve the aforementioned rough estimates. In the present paper, a novel method has been proposed and validated to generate the needed coarse scatter profile for parameter calibration in the convolution method. The method is based upon an image segmentation of the scatter contaminated CBCT image volume, followed by a reprojection of the segmented image volume using a given x-ray spectrum. The reprojected data is subtracted from the scatter contaminated projection data to generate a coarse estimate of the needed scatter profile used in parameter calibration. The method was qualitatively and quantitatively evaluated using numerical simulations and experimental CBCT data acquired on a clinical CBCT imaging system. Results show that the proposed algorithm can significantly reduce scatter artefacts and recover the correct CT number. Numerical simulation results show the method is patient specific, can accurately estimate the scatter, and is robust with respect to segmentation procedure. For experimental and in vivo human data, the results show the CT number can be successfully recovered and anatomical structure visibility can be significantly improved.
Recycling nonlocality in quantum star networks (2023)

The nonlocality of an entangled qubit pair can be recycled for several Bell experiments. Here, we go beyond standard Bell scenarios and investigate the recycling of nonlocal resources in a quantum network. First, we show that the ability to recycle nonlocality can be independent of the size of the network. Then, we realize a photonic quantum three-branch star network in which three sources of entangled pairs independently connect three outer parties with a central node. After measuring, each outer party respectively relays their system to an independent secondary measuring party. We experimentally demonstrate that the outer parties can perform unsharp measurements that are strong enough to violate a network Bell inequality with the central party, but weak enough to maintain sufficient entanglement in the network to allow the three secondary parties to do the same. Moreover, the violations are strong enough to exclude any model based on standard projective measurements on the Einstein-Podolsky-Rosen pairs emitted in the network. Our experiment brings together the research program of recycling quantum resources with that of Bell nonlocality in networks.
Automatische Programmierung von Verarbeitungsmaschinen (2016)

Im Beitrag wird ein Konzept zur Automatisierung der Programmierung von Verarbeitungsmaschinen vorgestellt. Ziel ist die Verkürzung des Engineeringprozesses, wozu bereits auch heute vorhandene Steuerungsarchitekturen verwendet werden können. Der Schwerpunkt der Ausführungen liegt auf den digitalen Modellen der Verarbeitungsprozesse und -güter sowie auf der übergreifenden Methodik. Der Ansatz eignet sich für speicherprogrammierbare Steuerungen (SPS) sowie für Robotersteuerungen und setzt für die Modellierung auf den Standard AutomationML in Kombination mit Eclipse Vorto.
Meeting of the MINDS (2007)

Since its inception in the late 1950s, the field of Information Retrieval (IR) has developed tools that help people find, organize, and analyze information. The key early influences on the field are well-known. Among them are H. P. Luhn's pioneering work, the development of the vector space retrieval model by Salton and his students, Cleverdon's development of the Cranfield experimental methodology, Spärck Jones' development of idf , and a series of probabilistic retrieval models by Robertson and Croft. Until the development of the WorldWideWeb (Web), IR was of greatest interest to professional information analysts such as librarians, intelligence analysts, the legal community, and the pharmaceutical industry.
Diode‐Clamped Multilevel Inverters (2016)

The diode-clamped multilevel inverter employs clamping diodes and cascaded DC capacitors to produce AC voltage waveforms with multiple levels. This chapter discusses various aspects of the three-level (3L) neutral-point clamped (NPC) inverter, including the inverter topology, operating principle, and device commutation. It also discusses a conventional space vector modulation (SVM) scheme for the NPC inverter. The DC input voltage of the inverter is normally split by two cascaded DC capacitors, providing a floating neutral point. The chapter elaborates control of the neutral-point voltage deviation and introduces the operation of four- and five-level diode-clamped inverters with carrier-based modulation techniques. The neutral-point voltage can be controlled by adjusting the time distribution between the p- and n-type states of a small voltage vector. There always exists a small voltage vector in each switching sequence, whose dwell time is divided into two sub-periods, one for its p-type and the other for its n-type switching state.
Heat and Electricity Production from Poultry Litter Waste: Downdraft Gasification of Biowaste based on Validated Computational Simulations (2021)

Underutilised fuel sources such as wastes, and by-products are currently being investigated for their potential to displace fossil fuels in multiple industries. The Northern Irish poultry industry has the potential to benefit from using the waste generated on-site as a fuel source, significantly reducing the amount of CO2 produced annually. The results can be achieved through downdraft gasification of poultry-litter, that can be converted into a producer gas for running a combined heat and power or organic Rankine cycle unit. The study was carried out through feedstock analysis, modelling of the process using ECLIPSE simulation software, and experimental analysis of materials in a pilot scale fixed-bed downdraft gasifier. Anaerobic digestate and miscanthus were also investigated for comparing the gasification potential of poultry litter. Models validated through experimental analysis were then applied to a case study based of a typical rural poultry farm in Northern Ireland. Results show that enough poultry waste is generated on site to produce the required heat and electricity for each shed. The choice of using an internal combustion engine or an organic Rankine cycle unit depends on the electricity demand of the farm. A techno-economic analysis of the system was also carried out to understand potential payback period for the system. Downdraft gasification coupled with CHP could have a payback of 10 years given the correct conditions, while downdraft ORC would be around 11 years.