gebhart/patrepeval huggingface dataset:
Penalized PET Reconstruction using CNN Prior (2017)

Inspired by great performance of convolutional neural network (CNN), we propose an iterative positron emission tomography (PET) reconstruction using a CNN prior. We used the denoising CNN (DnCNN) method and trained the network using regular dose images as groundtruth and low dose images as input. Poisson thinning method is used for generating the low dose data by downsampling counts. Due to the DnCNN is trained at a certain noise level, the noise level change in each iteration is one of major problems. To address this issue, we propose a local linear fitting (LLF) function incorporated with DnCNN to improve the image quality by preventing unwanted bias. By using LLF function, we demonstrate that the proposed method is robust to noise level changes in iterations. In bias and variance studies in simulations, the proposed method outperforms the conventional iterative methods. We confirm that the proposed method improves the reconstructed image both quantitatively and qualitatively.
Interaction of antigenic peptides with MHC class I molecules on living cells studied by photoaffinity labeling (1992)

Using a direct binding assay based on photoaffinity labeling, we have studied the interaction of antigenic peptides with murine MHC class I molecules on living cells. Photoreactive derivatives were prepared by N-terminal amidation with iodo, 4-azido salicylic acid of the Kd restricted Plasmodium berghei circumsporozoite (P.b. CS) peptide 253-260 (YIPSAEKI) and the Db-restricted Adenovirus 5 early region 1A (Ad5 E1A) peptide 234-243 (SGPSNTPPEI). As assessed in functional competition experiments, both peptide derivatives retained the specific binding activity of the parental peptides for Kd or Dd, respectively. The P.b. CS photoprobe specifically labeled Kd molecules on P815 (H-2d) cells, but failed to label RMA (H-2b) cells. Conversely, the Ad5 E1A photoprobe specifically labeled Db molecules on RMA cells, but failed to label P815 cells. When the two photoprobes were tested on a panel of Con A-activated spleen cells expressing 10 different H-2 haplotypes, significant photoaffinity labeling was observed only on H-2d cells with the P.b. CS photoprobe and on H-2b cells with the Ad5 E1A photoprobe. Labeling of cell-associated Kd or Db molecules with the photoprobes was specifically inhibited by antigenic peptides known to be presented by the same class I molecule. Photoaffinity labeling of Kd with the P.b. CS photoprobe was used to study the dynamics of peptide binding on living P815 cells. Binding increased steadily with the incubation period (up to 8 h) at 37 degrees C and at ambient temperature, but was greatly reduced (greater than 95%) at 0 to 4 degrees C or in the presence of ATP synthesis inhibitors. The magnitude of the labeling was twofold higher at room temperature than at 37 degrees C. In contrast, binding to isolated Kd molecules in solution rapidly reached maximal binding, particularly at 37 degrees C. Dissociation of the photoprobe from either cell-associated or soluble Kd molecules was similar, with a half time of approximately 1 h at 37 degrees C, whereas the complexes were long-lived at 4 degrees C in both instances.
Scalable web-embedded volume rendering (2017)

In this paper, we develop a method to encapsulate and embed interactive 3D volume rendering into the standard web Document Object Model (DOM). The package we implemented for this work is called Tapestry. Using Tapestry, data-intensive and interactive volume rendering can be easily incorporated into web pages. For example, we can enhance a Wikipedia page on supernova to contain several interactive 3D volume renderings of supernova volume data. There is no noticeable slowdown during the page load by the web browser. A user can choose to interact with any of the volume renderings of supernova at will. We refer to each embedded 3D visualization as a hyperimage. Hyperimages depend on scalable server-side support where volume rendering jobs are performed and managed elastically. We show the minimal code change required to embed hyperimages into previously static web pages. We also demonstrate the supporting Tapestry server's scalability along several dimensions: web page complexity, rendering complexity, frequency of rendering requests, and number of concurrent sessions. Using solely standard open-source components, this work proves that it is now feasible to make volume rendering a scalable web service that supports a diverse audience with varying use cases.
Label-Free 3D Visualization of Cellular and Tissue Structures in Intact Muscle with Second and Third Harmonic Generation Microscopy (2011)

Second and Third Harmonic Generation (SHG and THG) microscopy is based on optical effects which are induced by specific inherent physical properties of a specimen. As a multi-photon laser scanning approach which is not based on fluorescence it combines the advantages of a label-free technique with restriction of signal generation to the focal plane, thus allowing high resolution 3D reconstruction of image volumes without out-of-focus background several hundred micrometers deep into the tissue. While in mammalian soft tissues SHG is mostly restricted to collagen fibers and striated muscle myosin, THG is induced at a large variety of structures, since it is generated at interfaces such as refraction index changes within the focal volume of the excitation laser. Besides, colorants such as hemoglobin can cause resonance enhancement, leading to intense THG signals. We applied SHG and THG microscopy to murine (Mus musculus) muscles, an established model system for physiological research, to investigate their potential for label-free tissue imaging. In addition to collagen fibers and muscle fiber substructure, THG allowed us to visualize blood vessel walls and erythrocytes as well as white blood cells adhering to vessel walls, residing in or moving through the extravascular tissue. Moreover peripheral nerve fibers could be clearly identified. Structure down to the nuclear chromatin distribution was visualized in 3D and with more detail than obtainable by bright field microscopy. To our knowledge, most of these objects have not been visualized previously by THG or any label-free 3D approach. THG allows label-free microscopy with inherent optical sectioning and therefore may offer similar improvements compared to bright field microscopy as does confocal laser scanning microscopy compared to conventional fluorescence microscopy.
Semiconductor Manufacturers' Efforts to Improve Trust in the Electronic Part Supply Chain (2007)

One of the major problem areas in the electronic part supply chain is the issue of counterfeit electronic parts and the risks associated with them. Guidelines are needed for detecting, avoiding, and preventing the use of counterfeits in order to mitigate the risks associated with such parts. As part of this effort, we have identified the role of part manufacturers in building trust in the supply chain. Part manufacturers, as the brand owners and trademark holders, play a critical role in enhancing trust in the electronic part supply chain.
High-Throughput Screening of a Collection of Known Pharmacologically Active Small Compounds for Identification of Candida albicans Biofilm Inhibitors (2013)

Candida albicans is the most common etiologic agent of systemic fungal infections with unacceptably high mortality rates. The existing arsenal of antifungal drugs is very limited and is particularly ineffective against C. albicans biofilms. To address the unmet need for novel antifungals, particularly those active against biofilms, we have screened a small molecule library consisting of 1,200 off-patent drugs already approved by the Food and Drug Administration (FDA), the Prestwick Chemical Library, to identify inhibitors of C. albicans biofilm formation. According to their pharmacological applications that are currently known, we classified these bioactive compounds as antifungal drugs, as antimicrobials/antiseptics, or as miscellaneous drugs, which we considered to be drugs with no previously characterized antifungal activity. Using a 96-well microtiter plate-based high-content screening assay, we identified 38 pharmacologically active agents that inhibit C. albicans biofilm formation. These drugs were subsequently tested for their potency and efficacy against preformed biofilms, and we identified three drugs with novel antifungal activity. Thus, repurposing FDA-approved drugs opens up a valuable new avenue for identification and potentially rapid development of antifungal agents, which are urgently needed.
THE INSULIN RESISTANCE SYNDROME: Definition and Dietary Approaches to Treatment (2005)

The ability of insulin to stimulate glucose disposal varies at least sixfold in apparently healthy individuals, and approximately one-third of the population that is most resistant to this action of insulin is at greatly increased risk to develop a number of adverse clinical outcomes. Type 2 diabetes occurs when insulin resistant individuals are unable to secrete enough insulin to compensate for the defect in insulin action, and this was the first clinical syndrome identified as being related to insulin resistance. Although the majority of insulin-resistant individuals are able to maintain the level of compensatory hyperinsulinemia needed to prevent the development of a significant degree of hyperglycemia, the combination of insulin resistance and hyperinsulinemia greatly increases the likelihood of developing a cluster of closely related abnormalities and the resultant clinical diagnoses that can be considered to make up the insulin resistance syndrome (IRS). Since being overweight/obese and sedentary decreases insulin sensitivity, it is not surprising that the prevalence of the manifestations of the IRS is increasing at a rapid rate. From a dietary standpoint, there are two approaches to attenuating the manifestations of the IRS: (a) weight loss to enhance insulin sensitivity in those overweight/obese individuals who are insulin resistant/hyperinsulinemic; and (b) changes in macronutrient content of diets to avoid the adverse effects of the compensatory hyperinsulinemia. This chapter will focus on defining the abnormalities and clinical syndromes that compose the IRS and evaluating the dietary changes that can ameliorate its adverse consequences.
Microemulsion Rheology: Newtonian and Non-Newtonian Regimes (1981)

ABSTRACT Viscosity measurements are reported for micro-emulsions formed with pure and commercial surfactants. Approximate viscosities were measured with the multiphase rolling ball viscometer. Viscosities as functions of shear rate were measured on a cone-and-plate rheometer with an environmental chamber designed to control both temperature and evaporation. At a fixed shear rate or shear stress, microemulsion viscosity often goes through two maxima as the salinity of the mixing brine increases and the microemulsion passes from a water-continuous to an oil-continuous phase. Microemulsions near these maxima were found in the present study to exhibit non-Newtonian behavior: under shear their viscosity decreases by as much as a factor of six. Away from the maxima, microemulsion appeared to be substantially Newtonian. Shear-history effects were observed for several microemulsions even though temperature, environment and experimental procedure were carefully controlled.
The Akt inhibitor triciribine sensitizes prostate carcinoma cells to TRAIL‐induced apoptosis (2009)

Aberrant PI3K/Akt signaling has been implicated in many human cancers, including prostate carcinomas. Currently different therapeutic strategies target the inhibition of this survival pathway. The nucleoside analog triciribine (TCN), which was initially described as a DNA synthesis inhibitor, has recently been shown to function as an inhibitor of Akt. Here, we demonstrate that TCN inhibits Akt phosphorylation at Thr308 and Ser473 and Akt activity in the human prostate cancer cell line PC-3. In addition, TCN sensitized PC-3 cells to TRAIL- and anti-CD95-induced apoptosis, whereas the cells remained resistant to DNA damaging chemotherapeutics. The observed sensitization essentially depended on the phosphorylation status of Akt. Thus, prostate cancer cell lines displaying constitutively active Akt, e.g. PC-3 or LNCaP, were sensitized to death receptor-induced apoptosis. Most importantly with respect to therapeutic application, derivatives of both TCN and TRAIL are already tested in current clinical trials. Therefore, this combinatorial treatment might open a promising therapeutic approach for the elimination of hormone-refractory prostate cancers, which are largely resistant to conventional DNA damaging anticancer drugs or irradiation.
Distributed Bilayer Photovoltaics Based on Nematic Liquid Crystal Polymer Networks (2007)

We discuss a liquid crystal composite approach to provide a distributed interface to vertically separate electron-donating and electron-accepting films in an organic photovoltaic device. Two different methods are used to prepare a nematic liquid crystal polymer network with a porous surface and electron-donating properties. This is infilled with an electron-accepting organic semiconductor to form a bilayer device. The interface is diffuse rather than localized so that more photogenerated excitons can reach it to generate charge before they recombine. Photoinduced absorption of a blend of the donor and acceptor materials confirms that excitons dissociate at the heterointerface. The spatial features of the diffuse interface are examined by Fourier analysis of topographic images. We find a correlation between the in-plane spatial frequencies of the interface and photovoltaic device performance. The device performance is investigated as a function of input irradiance. Any charge combination is monomolecular rather than bimolecular, and the monochromatic power conversion efficiency varies between 0.8% and 0.3% with input irradiance. Equivalent circuit analysis shows that this is limited by a high series resistance, a blocking contact, and nonoptimized spatial features of the porous interface.
Stellung der Kodifikation im Rechtssystem (1995)

Bevor die Normierung des Leasingrechts im einzelnen untersucht wird, sollen zunächst die Entstehungsgeschichte und der Hintergrund der Kodifikation beleuchtet werden.
Introduction of nerve growth factor (NGF) receptors into a medulloblastoma cell line results in expression of high- and low-affinity NGF receptors but not NGF-mediated differentiation. (1990)

Expression of the cloned human nerve growth factor receptor (NGFR) cDNA in cell lines can generate both high- and low-affinity binding sites. Since the inability to respond appropriately to differentiation factors such as NGF may contribute to determining the malignant phenotype of neuroblastomas, we sought to determine whether the same is true of medulloblastomas. To generate a human central nervous system neuronal cell line that would respond to NGF, we infected the medulloblastoma cell line D283 MED with a defective retrovirus carrying the cDNA coding for the human NGFR. The resultant cells (MED-NGFR) expressed abundant low- and high-affinity NGFRs, and NGF treatment induced a rapid transient increase of c-fos mRNA in the NGFR-expressing cells but not in the parent line or in cells infected with virus lacking the cDNA insert. However, the MED-NGFR cells did not internalize the NGFR at high efficiency, nor did they differentiate in response to NGF. Three important conclusions emerge from this study: (i) internalization of NGFRs is not necessary for some early rapid transcriptional effects of NGF; (ii) an unknown factor(s) that cooperates with the cloned NGFR in allowing high-affinity NGF binding is found in a primitive central nervous system cell line; and (iii) NGFRs introduced into and expressed by D283 MED (i.e., MED-NGFR) cells are partially functional but are unable to induce differentiation in these primitive neuron-like tumor cells, implying that high-efficiency receptor-mediated endocytosis of NGF and its receptor may be a necessary step in the cascade of events leading to NGF-mediated differentiation.
Inactivation of <i>Bacillus</i> spores by gaseous ozone (1986)

The sporicidal activity of ozone in the gas phase was investigated. Spores of six strains of Bacillus species deposited on filter paper or glass fibre filter were conditioned at different relative humidities (r.h.), and then exposed to ozone ranging in concentration from 0.5 to 3.0 mg/l at different r.h. There was a lag phase in the initial stage of exposure followed by an exponential decrease in the number of survivors with time, although no lag phase was observed with one strain. Inactivation rates increased with increasing exposure r.h. while no significant inactivation was attained at a r.h. of 50% or below. The conditioning r.h. influenced the duration of the lag phase. The D-values (decimal reduction time) in the logarithmic phase varied roughly in inverse proportion to the ozone concentration.
Investigation of Polymer Flood Performance in High Salinity Oil Reservoirs (2011)

Abstract The application of Enhanced Oil Recovery (EOR) techniques is encouraged by the growing demand for oil. Optimizing oil production from current resources is becoming the main strategy for many oil producing companies around the world. Among EOR processes, polymer flooding is an attractive option in many reservoirs. The objective of polymer flooding is to control water mobility inside the reservoir to favor higher oil recovery. Several design parameters are critical for the success or failure of polymer flooding applications. The salinity of formation water is one of the parameters which impose a limitation on polymer flood applicability. In Kuwait, most of oil reservoirs are high water salinity reservoirs. Therefore, improving the performance of polymer floods under high water salinity conditions may unlock these resources which can have enormous positive effects on oil reserves. One way for this improvement is to condition the reservoir under polymer flood applications by injecting a slug of water (preflush), ahead of polymer, with specific characteristics. In this work, lab experiments are conducted in which the effects of several design parameters of polymer flooding are investigated under high water salinity conditions. Design parameters include preflush salinity, preflush viscosity and preflush slug size. The results suggest these parameters correlate differently with oil recovery factor.
Detrimental Effects of Apolipoprotein E4: Potential Therapeutic Targets in Alzheimers Disease (2007)

As the major genetic risk factor for Alzheimer's disease, the apolipoprotein (apo) E4 isoform is a promising therapeutic target. ApoE4 likely contributes to Alzheimer's disease pathology by interacting with multiple factors through various pathways. Interactions with the amyloid beta peptide and the amyloid cascade, for example, may lead to cognitive decline and neurodegeneration. Alternatively, apoE4 might act independently of the amyloid beta peptide. Our working hypothesis is that apoE has isoform-specific effects on neuronal repair and remodeling. One or more injurious agents could result in neuronal damage, requiring neuronal repair or remodeling. The injurious agents (or "second hits") may be genetic, metabolic, or environmental. Potential therapeutic strategies include changing the structure of apoE4 to be more apoE3-like, inhibiting the protease that cleaves apoE4 into toxic fragments, and protecting mitochondria from apoE4 toxicity. Structural features that distinguish apoE4 and apoE3 determine their functional differences and hold the key to understanding how apoE4 is involved in Alzheimer's disease.
Ischemic Stroke in Young due to Combined Protein C and S Deficiency (2013)

WHO defines stroke as an event caused by the interruption of the blood supply to the brain, usually because a blood vessel bursts or is blocked by a clot. This cuts off the supply of oxygen and nutrients, causing damage to the brain tissue Globally, stroke is the third commonest cause of mortality [2] and the fourth leading cause of disease burden Ischemic stroke is the most common cerebrovascular disease, most often due to atherothrombotic diseases and uncommonly by disorders of hypercoagulation. Disorders of coagulation leading to thrombotic disorders are approximately 1% of all ischemic strokes and 4-8% of young strokes. Similarly combined deficiency of protein C and S can lead to hypercoagulable state and rarely present as cerebrovascular accident. We describe here a rare case of 27 year old male who presented with right middle cerebral artery territory infarct due to combined protein C and S deficiency.
Photoresist film analysis to investigate LWR generation mechanism (2013)

In order to understand the mechanism of line width roughness (LWR) generation and to find control knobs for improving photoresist design, we established PAG activity analysis methods by utilizing Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) and Transmission Electron Microscopy (TEM). TOF-SIMS depth profiling using Gas Cluster Ion Beam (GCIB) allowed the ability to clearly identify photoresist ingredient distribution in the photoresist films from the surface to the bottom of the resist films. TEM provided distribution information of photoresist ingredients in nanometer scale. As a result, PAG function and polymer reaction mechanism can be monitored by these methods. The TOFSIMS outputs during coating, exposure, and post-exposure bake (PEB) steps provide indications of distribution change of PAGs, quenching reaction derivatives, and remaining protecting group, which correspond to acid generation distribution, acid diffusion, and diffusion of deprotection reaction in photoresist film respectively during each consecutive lithographic patterning step. The difference in activity of PAGs can also be observed. These novel analytical methods can provide remarkably helpful information about identifying proper control knobs for lithographic performance of photoresist and for next generation lithography (NGL), especially extreme ultra violet lithography (EUVL) materials, where exposure tool time is very limited.
No convincing arguments for undergraduate LLB (1997)

The four-year LLB is due to be implemented at most South African universities in 1998. There was a concern expressed by some academics that new curricula would not be ready in time. Those who felt that the plan was ill-conceived feared that we would indeed be ready; after all, all that had to be done was to decide what to leave out.