gebhart/patrepeval huggingface dataset:
Model based restoration of the RF data for high resolution vascular ultrasound imaging (2013)

High resolution ultrasound imaging of vascular structures such as carotid artery is of major importance in evaluating cardiovascular diseases. However, due to the bandlimited nature of the interrogating pulse the resolution of B-scan images is often insufficient to show fine vascular details. Recently, a new class of deconvolution algorithms from the compressive sensing (CS) field has been used in ultrasound imaging for resolution improvement. Compared to the classical deconvolution methods, these CS methods (CSMs) robustly exploit the sparsity of tissue reflectivity (TR) and provide significant resolution gains. However, CSMs generally assume the ultrasound pulse is invariant throughout the propagation path which is not realistic due to frequency dependent absorption and scattering in biological tissues. As such, pulse variance severely compromises the performance of CSMs in recovering the TR with high fidelity. We propose a new technique that performs sparse deconvolution and accounts for pulse variance that occurs during wave propagation. Our method uses the Model-Based Estimation Pursuit (MBEP) to restore the RF signal in terms of Gaussian Chirplets whose delay and amplitude parameters are related to the location and strength of scatterers (i.e, TR) and its spectral parameters are sensitive to dispersion characteristics of the tissue. MBEP successively extracts GCs from RF data via partitioning, parameter estimation, and removal of the estimated echo. MBEP is highly adaptive to the varying pulses at the tissue-vessel interfaces. MBEP and a CSM (ℓ1-regularized Least Squares Deconvolution, ℓ1-LSD) were tested on ultrasound RF data acquired from a blood vessel tissue-mimicking phantom. Our analysis show that, compared to the ℓ1-LSD, MBEP offers a higher fidelity restoration of the TR as well as marked improvement in resolution gain and processing times.
Prospecting Lighting Applications with Ligand Field Tools and Density Functional Theory: A First-Principles Account of the 4f<sup>7</sup>–4f<sup>6</sup>5d<sup>1</sup> Luminescence of CsMgBr<sub>3</sub>:Eu<sup>2+</sup> (2015)

The most efficient way to provide domestic lighting nowadays is by light-emitting diodes (LEDs) technology combined with phosphors shifting the blue and UV emission toward a desirable sunlight spectrum. A route in the quest for warm-white light goes toward the discovery and tuning of the lanthanide-based phosphors, a difficult task, in experimental and technical respects. A proper theoretical approach, which is also complicated at the conceptual level and in computing efforts, is however a profitable complement, offering valuable structure-property rationale as a guideline in the search of the best materials. The Eu(2+)-based systems are the prototypes for ideal phosphors, exhibiting a wide range of visible light emission. Using the ligand field concepts in conjunction with density functional theory (DFT), conducted in nonroutine manner, we develop a nonempirical procedure to investigate the 4f(7)-4f(6)5d(1) luminescence of Eu(2+) in the environment of arbitrary ligands, applied here on the CsMgBr3:Eu(2+)-doped material. Providing a salient methodology for the extraction of the relevant ligand field and related parameters from DFT calculations and encompassing the bottleneck of handling large matrices in a model Hamiltonian based on the whole set of 33,462 states, we obtained an excellent match with the experimental spectrum, from first-principles, without any fit or adjustment. This proves that the ligand field density functional theory methodology can be used in the assessment of new materials and rational property design.
Regression Test Selection Technique For Multi-Programming Language (2010)

Regression testing is a maintenance activity applied to modified software to provide confidence that the changed parts are correct and that the unchanged parts have not been adversely affected by the modifications. Regression test selection techniques reduce the cost of regression testing, by selecting a subset of an existing test suite to use in retesting modified programs. This paper presents the first general regression-test-selection technique, which based on code and allows selecting test cases for any programs written in any programming language. Then it handles incomplete program. We also describe RTSDiff, a regression-test-selection system that implements the proposed technique. The results of the empirical studied that performed in four programming languages java, C#, Cµ and Visual basic show that the efficiency and effective in reducing the size of test suit.
A novel process configuration for anaerobic digestion of source‐sorted household waste using hyper‐thermophilic post‐treatment (2005)

A novel reactor configuration was investigated for anaerobic digestion (AD) of the organic fraction of municipal solid waste (OFMSW). An anaerobic hyper-thermophilic (68 degrees C) reactor R68 was implemented as a post-treatment step for the effluent of a thermophilic reactor R1 (55 degrees C) in order to enhance hydrolysis of recalcitrant organic matter, improve sanitation and ease the stripping of ammonia from the reactor. The efficiency of the combined system was studied in terms of methane yield, volatile solids (VS) reduction, and volatile fatty acid (VFA) production at different hydraulic retention times (HRT). A single-stage thermophilic (55 degrees C) reactor R2 was used as control. VS reduction and biogas yield of the combined system was 78-89% and 640-790 mL/g VS, respectively. While the VS reduction in the combined system was up to 7% higher than in the single-stage treatment, no increase in methane yield was observed. Shifting the HRT of the hyper-thermophilic reactor from 5 days to 3 days resulted in a drop in the methanogenic activity in the hydrolysis reactor to a minimum. Operation of R68 at HRTs of 24-48 h was sufficient to achieve high VS conversion into VFAs. Removal of pathogens was enhanced by the hyper-thermophilic post-treatment. 7% of the ammonia load was removed in the hyper-thermophilic reactor with a flow of headspace gas through the reactor equivalent to four times the biogas flow produced in reactor R1.
An effective kinetic representation of fluctuation-driven neuronal networks with application to simple and complex cells in visual cortex (2004)

A coarse-grained representation of neuronal network dynamics is developed in terms of kinetic equations, which are derived by a moment closure, directly from the original large-scale integrate-and-fire (I&F) network. This powerful kinetic theory captures the full dynamic range of neuronal networks, from the mean-driven limit (a limit such as the number of neurons N --> infinity, in which the fluctuations vanish) to the fluctuation-dominated limit (such as in small N networks). Comparison with full numerical simulations of the original I&F network establishes that the reduced dynamics is very accurate and numerically efficient over all dynamic ranges. Both analytical insights and scale-up of numerical representation can be achieved by this kinetic approach. Here, the theory is illustrated by a study of the dynamical properties of networks of various architectures, including excitatory and inhibitory neurons of both simple and complex type, which exhibit rich dynamic phenomena, such as, transitions to bistability and hysteresis, even in the presence of large fluctuations. The implication for possible connections between the structure of the bifurcations and the behavior of complex cells is discussed. Finally, I&F networks and kinetic theory are used to discuss orientation selectivity of complex cells for "ring-model" architectures that characterize changes in the response of neurons located from near "orientation pinwheel centers" to far from them.
Reversing the effect of formalin on the binding of propidium iodide to DNA (1994)

Formalin, an excellent preservative of cellular morphology, is a commonly used fixative for tissue specimens in hospital pathology laboratories. This preserved material is a potential source of tissue for diagnostic and retrospective research studies on DNA using flow cytometry. Unfortunately, formalin interferes with the binding of propidium iodide (PI) and other fluorescent dyes to DNA, thus altering the measurement of DNA content by flow cytometry or image analysis. This interference has been attributed to the cross-linking of histones by formalin. Since formalin alters the measurement of DNA content in formalin-fixed and formalin-fixed, paraffin-embedded tissues, this study was designed to explore the use of various physicochemical methods to reverse the effect of the formalin on the binding of PI to DNA. This study demonstrates that resuspending formalin-fixed cells in PBS and heating them at 75 degrees C for at least 1 h prior to staining with PI restores the staining of the DNA to approximately the same fluorescence intensity as that of fresh tissue.
Multiplication and Movement of<i>Xylella fastidiosa</i>Within Grapevine and Four Other Plants (1995)

Xylella fastidiosa, a xylem-limited bacterium that causes Pierce's disease of grapevine and other plant diseases, has numerous symptomless hosts. The multiplication and spread of X. fastidiosa within grapevine (Vitis vinifera) and four other reported plant hosts that were preferred plants for insect vectors (Himalayan blackberry, Rubus discolor ; California mugwort, Artemisia douglasiana ; watergrass, Echinochloa crusgalli; and Bermuda grass, Cynodon dactylon) were assessed after vector inoculation. The bacterium was detected by culture and enzyme-linked immunosorbent assay. The incubation times required before first detection in grape, blackberry, mugwort, and watergrass were 4, 32, 30, and 18 days, respectively. The maximum bacterial concentration (CFU per gram) and percentage of infection in these species were >10 8 (100%), 1 x 10 7 (58%), 2 x 10 6 (20%), and 4 x 10 5 (31%), respectively. Systemic movement of X. fastidiosa distal to the inoculation site was detected only in grapevine and blackberry. The bacterium was never detected in inoculated Bermuda grass. The wide range in the capacities of these hosts to support the bacterium's multiplication and spread suggests that the epidemiological importance of plant host species for the spread of Pierce's disease varies greatly.
Antimicrobial Susceptibility Patterns of<i>Pseudomonas aeruginosa</i>from Diabetes Patients with Foot Ulcers (2011)

Pseudomonas aeruginosa is an invasive organism that frequently causes severe tissue damage in diabetic foot ulcers. A major problem in P. aeruginosa infection may be that this pathogen exhibits a high degree of resistance to a broad spectrum of antibiotics. The study aimed to isolate and determine the antimicrobial susceptibility patterns of the P. aeruginosa population from diabetes patients with foot ulcers attending tertiary care hospitals in and around Coimbatore and their antimicrobial susceptibility pattern. The study was carried out at the Department of Microbiology, Dr. N.G.P. Arts and Science College, Coimbatore, for a period of one year (June 2006 to April 2007). The present study comprised 270 pus specimens collected from diabetic patients with foot ulcers. All pus samples were subjected to gram staining; bacterial culture and subsequently the antibiotic sensitivity to 15 different antibiotics for the confirmed P. aeruginosa were performed as per the standard procedures. Eighteen strains (14.28%) of P. aeruginosa from 270 diabetic foot ulcers were detected. Almost all the strains exhibited a varying degree of resistance to the antibiotics tested. Multidrug resistance for about 8 to 11 antibiotics was observed among the 55.5% of the isolates. Disk diffusion results show 100% resistance to ampicillin, cefoperazone, erythromycin, norfloxacin, and only cefotaxime, ciprofloxacin exhibited greater activity against Pseudomonas aeruginosa.
Effect of oxygen pressure on the structure and thermal stability of ultrathin Al2O3 films on Si(001) (2002)

Al 2 O 3 /Si(001) surfaces and interfaces were investigated using scanning reflection electron microscopy, reflection high-energy electron diffraction, x-ray photoelectron spectroscopy, and Auger electron spectroscopy. A uniform, stoichiometric and ultrathin Al2O3 film of about 0.6 nm was grown on an atomically flat Si(001)-2×1 surface, and the resulting Al2O3/Si(001) interface was atomically abrupt. An intentional reoxidation of the Al2O3/Si(001) system under low oxygen pressure (2×10−6, 5×10−6, and 2×10−5 Torr O2) showed that the ultrathin Al2O3 film stoichiometry and the interface abruptness were maintained with progress in reoxidation time. Furthermore, the film and the interface showed no degradation under low-pressure reoxidation at various temperatures (400–750 °C). A high-pressure reoxidation of the Al2O3/Si(001) system at 5×10−5 Torr O2 resulted in the formation of an interfacial SiO2 layer which grew in a layer-by-layer mode with atomic-scale uniformity and had an atomically abrupt interface with Si(001) substrate up to 700 °C. Additionally, a very weak temperature dependence of the growth of interfacial SiO2 was observed. A high-pressure reoxidation at 750 °C led to the formation of crystalline ultrathin Al2O3 film and also caused degradation of the film by formation of SiO2 in the near-surface region, where a slight decrease in the Al2O3 film thickness was observed. This was attributed to the formation of interstitial Si in the interfacial SiO2 layer and the subsequent mobility of Si and Al under this growth condition. Under low-pressure reoxidation, the Si and Al were immobile because of the absence of an interfacial SiO2 layer at the Al2O3/Si(001) interface. These results indicate that the oxygen pressure of the ambience plays an important role in the oxidation of the Al2O3/Si(001) interface, and the mobility, transport, and chemical reactions at various oxidation temperatures (400–750 °C).
Interpreting the Latent Space of GANs for Semantic Face Editing (2020)

Despite the recent advance of Generative Adversarial Networks (GANs) in high-fidelity image synthesis, there lacks enough understanding of how GANs are able to map a latent code sampled from a random distribution to a photo-realistic image. Previous work assumes the latent space learned by GANs follows a distributed representation but observes the vector arithmetic phenomenon. In this work, we propose a novel framework, called InterFaceGAN, for semantic face editing by interpreting the latent semantics learned by GANs. In this framework, we conduct a detailed study on how different semantics are encoded in the latent space of GANs for face synthesis. We find that the latent code of well-trained generative models actually learns a disentangled representation after linear transformations. We explore the disentanglement between various semantics and manage to decouple some entangled semantics with subspace projection, leading to more precise control of facial attributes. Besides manipulating gender, age, expression, and the presence of eyeglasses, we can even vary the face pose as well as fix the artifacts accidentally generated by GAN models. The proposed method is further applied to achieve real image manipulation when combined with GAN inversion methods or some encoder-involved models. Extensive results suggest that learning to synthesize faces spontaneously brings a disentangled and controllable facial attribute representation.
Generative Adversarial Networks for Electronic Health Records: A Framework for Exploring and Evaluating Methods for Predicting Drug-Induced Laboratory Test Trajectories (2017)

Generative Adversarial Networks (GANs) represent a promising class of generative networks that combine neural networks with game theory. From generating realistic images and videos to assisting musical creation, GANs are transforming many fields of arts and sciences. However, their application to healthcare has not been fully realized, more specifically in generating electronic health records (EHR) data. In this paper, we propose a framework for exploring the value of GANs in the context of continuous laboratory time series data. We devise an unsupervised evaluation method that measures the predictive power of synthetic laboratory test time series. Further, we show that when it comes to predicting the impact of drug exposure on laboratory test data, incorporating representation learning of the training cohorts prior to training GAN models is beneficial.
Improved Efficacy of Stem Cell Labeling for Magnetic Resonance Imaging Studies by the Use of Cationic Liposomes (2003)

Labeling stem cells with FDA-approved superparamagnetic iron oxide particles makes it possible to track cells in vivo with magnetic resonance imaging (MRI), but high intracellular levels of iron can cause free radical formation and cytotoxicity. We hypothesized that the use of cationic liposomes would increase labeling efficiency without toxic effects. Rabbit skeletal myoblasts were labeled with iron oxide by: 1) uptake of iron oxide incorporated into cationic transfection liposomes (group I) or 2) customary endocytosis (group II). In both groups, cell proliferation and differentiation were measured and toxicity was assayed using trypan blue and ratio fluorescence microscopy with BODIPY 581/591 C11. The effects of the intracellular iron oxide on magnetic resonance image intensities were assessed in vitro and in vivo. Both methods resulted in uptake of iron intracellularly, yielding contrast-inducing properties on MRI images. In group II, however, incubation with iron oxide at high concentrations required for endocytosis caused generation of free radicals, a decrease in proliferation, and cell death. Cytotoxic effects in the remaining cells were still visible 24 h after incubation. Conversely, in group I, sufficient intracellular uptake for detection in vivo by MRI could be achieved at 100-fold lower concentrations of iron oxide, which resulted in a high percentage of labeled cells, high retention of the label, and no cytotoxic effects even after stressing the cells with a hypoxia-reoxygenation insult. The use of cationic liposomes for iron oxide stem cell labeling increases labeling efficiency approximately 100-fold without toxic effects. This technique results in high-contrast-inducing properties on MRI images both in vitro and in vivo and could thus be a valuable tool for tracking stem cells noninvasively.
A cognitive trust-based approach for Web service discovery and selection (2005)

Provision of services within a virtual framework for resource sharing across institutional boundaries has become an active research area. Many such services encode access to computational and data resources, comprising single machines to computational clusters. Such services can also be informational, and integrate different resources within an institution. Consequently, we envision a service rich environment in the future, where service consumers are represented by intelligent agents. If interaction between agents is automated, it is necessary for these agents to be able to automatically discover services and choose between a set of equivalent (or similar) services. In such a scenario trust serves as a benchmark to differentiate between services. In this paper we introduce a novel framework for automated service discovery and selection of Web Services based on a user's trust policy. The framework is validated by a case study of data mining Web Services and is evaluated by an empirical experiment.
Orchestration of a large infrastructure of Remote Desktop Windows Servers (2017)

The CERN Windows Terminal Service infrastructure is an aggregation of multiple virtual servers running Remote Desktop Services, accessed by hundreds of users every day; it has two purposes: provide external access to the CERN network, and exercise access control to certain parts of the accelerator complex. Currently, the deployment and configuration of these servers and services requires some interaction by system administrators, although scripts and tools developed at CERN do contribute to alleviate the problem. Scaling up and down the infrastructure (i.e., adding or removing servers) is also an issue, since it’s done manually. However, recent changes in the infrastructure and the adoption of new software tools that automate software deployment and configuration open new possibilities to improve and orchestrate the current service. Automation and Orchestration will not only reduce the time and effort necessary to deploy new instances, but also simplify operations like patching, analysis and rebuilding of compromised nodes and will provide better performance in response to load increase. The goal of this CERN project, we’re now a part of, is to automate provisioning (and decommissioning) and scaling (up and down) of the infrastructure. Given the scope and magnitude of problems that must be solved, no single solution is capable of addressing all; therefore, multiple technologies are required. For deployment and configuration of Windows Server systems we resort to Puppet, while for orchestration tasks, Microsoft Service Management Automation will be used.
676. DNA Sequences Encoding shRNAs Can Replace Mutant ITR in scAAV Genome for Efficient Replication and Packaging and Transcribe shRNAs by pol III Promoter Activity of wt ITR for Efficient Gene Silencing (2015)

The two inverted terminal repeats (ITRs) at each end of recombinant adeno-associated virus (rAAV) genome are the only sequences inherited from wild type (Wt) viral genome. They contribute to rAAV genome replication, packaging, intracellular processing and stabilization, and integration into host genome. Previously we showed DNA sequences encoding shRNAs (shDNA) are the barriers in self-complementary AAV (scAAV) genome replication, resulting in vector genome truncations and heterogeneity. We now observe the same phenomena in the genome replication and packaging of single-stranded AAV vectors harboring shDNA. When detected on a denaturing gel, these truncated genomes were doubled in size as seen for scAAV, indicating they are intra-molecular double-stranded DNA molecules. We hypothesized DNA with hairpin structures could serve as the mutant ITR during rAAV genome replication and packaging. To test this, we replaced the mutant ITR in scAAV genome with the DNA encoding shRNA against Apob or Firefly luciferase gene. Southern blot of Hirt's DNAs revealed that vector genomes flanked with shDNA and wtITR, but not with shDNA and mutant ITR, were efficiently rescued and replicated when co-transfected with adeno-helper plasmid and Rep/Cap trans-plasmid into HEK293 cells. Large scale AAV production and analyses of CsCl gradient purified rAAV genomes in both native and denaturing gels further demonstrated that hybrid shDNA-wtITR vector genomes were efficiently packaged into AAV capsid as double-stranded genomes. To test their functionalities in vivo, we intravenously injected 2×1011 GCs of scAAV9 containing shApoB-wtITR genome with an EGFP gene into adult C57 mice and harvested liver tissues 3 weeks later. Compared to regular scAAVEGFP vector, the shApoB-wtITR AAV vectors achieved comparable EGFP transduction efficacy in the liver. Interestingly, without a H1 promoter the shApob produced abundant small antisense RNA and silenced mouse ApoB gene as efficienct as conventional scAAVshRNA vectors. Southern blots of mouse liver detected linear and circularized forms of AAV genomes, thus implying that wtITR in the circularized genome may serve as a strong pol III promoter to drive shRNA expression. Currently, we are in the process of replacing Wt ITR with an artificial chimeric ITR with only rep binding element, terminal resolution sites and D sequence of authentic ITR retained. In summary, hairpin structure sequences can function as an alternative mutant ITR for production of functional scAAV. Our findings may have significant impact on AAV biology and vectorology, potentially enabling us to create artificially intelligent and programmable vector genomes with improved packaging efficacy, expanded genome sizes, modulated tissue tropism and propensity of integration, regulatable in vivo persistence and potency, etc.