gebhart/patrepeval huggingface dataset:
Identifying Active Progeny Virus Particles in Formalin-Fixed, Paraffin-Embedded Sections Using Correlative Light and Scanning Electron Microscopy (2023)

Immunohistochemical analysis of formalin-fixed paraffin-embedded (FFPE) tissue blocks is routinely used to identify virus-infected cells. However, detecting virus particles in FFPE sections using light microscopy is difficult because of the light diffraction resolution limitations of an optical microscope. In this study, light microscopy and field emission scanning electron microscopy were performed to observe 3-dimensional virus particles in FFPE sections in a nondestructive manner using NanoSuit or osmium conductive treatment methods. The virus particles in FFPE sections were immunostained with specific antibodies against the surface antigens of the viral particles and stained with 3,3'-diaminobenzidine. A metal solution (0.2% gold chloride or 2% osmium tetroxide) was applied to enhance the 3,3'-diaminobenzidine-stained area. This procedure is nondestructive for FFPE sections and is a simpler method than transmission electron microscopy. To validate the applicability of this technique, we performed 3-dimensional imaging of the virus particles of different sizes, such as human papillomavirus, cytomegalovirus, and varicella-zoster virus. Furthermore, ultrathin sections from the FFPE sections that were observed to harbor viral particles using field emission scanning electron microscopy were prepared and assessed using transmission electron microscopy. In the correlative areas, transmission electron microscopy confirmed the presence of large numbers of virus particles. These results indicated that the combination of marking viral particles with 3,3'-diaminobenzidine/metal staining and conductive treatment can identify active progeny virus particles in FFPE sections using scanning electron microscopy. This easy correlative imaging of field emission scanning electron microscopy of the identical area of FFPE in light microscopy may help elucidate new pathological mechanisms of virus-related diseases.
Syndiotactic-Specific Polymerization of Propene with Nickel-Based Catalysts. 2. Regiochemistry and Stereochemistry of the Initiation Steps (1996)

A homogeneous catalytic system based on a suitable Ni(II) diimine derivative and methylaluminoxane affords predominantly syndiotactic polypropylene at subambient temperatures. The polymer microstructure is that expected for a “chain-end” mechanism of steric control. NMR analysis of polymer samples carrying selectively 13C-enriched end groups indicates a largely prevailing 1,2 regiochemistry for the insertion of propene into Ni−13CH3 bonds in the initiation step and a syndiotactic steric control already effective in the second propagation step.
Saturation spectroscopy with laser optical pumping in atomic barium (1980)

The magnitude and sign of laser saturation resonances induced in atomic transitions with level degeneracy can be dramatically altered by the presence of optical pumping. This paper presents a detailed theoretical treatment of optical-pumping Lamb dips and crossover resonances, and their experimental observation in the 553-nm barium resonance transition. The physical principles underlying the laser optical-pumping saturation effect are also discussed.
Inversion type InP metal oxide semiconductor field effect transistor using novel atomic layer deposited BeO gate dielectric (2011)

We present results on n-channel inversion-type indium phosphide (InP) metal-oxide-semiconductor field-effect transistors (MOSFETs) with atomic layer deposited (ALD) beryllium oxide (BeO) gate dielectric using the gate-last process. InP MOSFETs with the BeO gate stack were realized with high performance including the improved drive current, subthreshold swing, and a peak effective electron mobility. The transmission electron microscopy and x-ray photoemission spectroscopy measurements demonstrate an interface between BeO and InP substrates with high quality and efficient thermal stability. The use of ALD BeO as a gate dielectric may be a potential solution for future III-V MOS device fabrication.
Myosin light chain kinase colocalizes with nonmuscle myosin IIB in myofibril precursors and sarcomeric Z-lines of cardiomyocytes (2006)

Myosin light chain kinase (MLCK) is a key regulator of various forms of cell motility involving actin and myosin II. MLCK is widely present in vertebrate tissues including the myocardium. However, the role of MLCK in cardiomyocyte function is not known. Previous attempts to gain insight into possible roles and identify potential molecular partners were disappointing and equivocal due to cross reactivity of early antibodies with striated muscle MLCK, which has a different genetic locus and a divergent amino acid sequence from the above mentioned enzyme. Using an immunofluorescence approach and a panel of antibodies directed against MLCK, cytoskeletal, and sarcomeric proteins, we localized MLCK to myofibril precursors and Z-lines of sarcomeres in embryonic and adult cardiomyocytes. The same structures contained nonmuscle myosin IIB implicating this protein as a possible target of MLCK. Our results suggest a role for MLCK in cardiomyocyte differentiation and contraction through regulation of nonmuscle myosin IIB.
Multi-GPU Accelerated Admittance Method for High-Resolution Human Exposure Evaluation (2015)

The high efficiency achieved makes it practical to investigate human exposure involving a large number of cases with a high resolution that meets the requirements of international dosimetry guidelines.
Femtosecond Laser Written Fiber Bragg Grating Sensors for Combustion Environments (2018)

Femtosecond laser written fiber Bragg gratings are useful for extreme sensing, including combustor applications for energy and aerospace. This paper reviews our fabrication and deployment of such sensors, for monitoring temperature gradients within such environments.
High-gain single-layer radial line slot array designed for V-band applications (2016)

A general design of a high-gain wideband single-layer radial line slot array antenna is discussed for V-band applications with a 6GHz gain bandwidth, to be compared with that of planar Fabry-Perot cavity antennas that is in general narrower. The antenna is based on a simple laminated single layer and a planar integrated feeding structure is proposed as a preliminary choice to excite such design.
Hydrogen Recovery from a H<sub>2</sub>−H<sub>2</sub>O−HBr Mixture Utilizing Silica-Based Membranes at Elevated Temperatures. 1. Preparation of H<sub>2</sub>O- and H<sub>2</sub>-Selective Membranes (1998)

Amorphous silica-based membranes were prepared for use in recovering hydrogen at elevated temperatures from a H2−H2O−HBr mixture produced by a thermochemical water decomposition process (the UT-3 process). The silica-based membranes, which were formed on porous tubes by chemical vapor deposition of tetraethoxysilane at 650 °C with a forced cross-flow through the porous wall, exhibited a H2 or H2O selectivity, which was related to the preparation and posttreatment conditions. The microporous silica membrane formed on a macroporous α-alumina tube and heat-treated at 900 °C in an inert atmosphere showed a H2 permeance of (3−4) × 10-7 mol m-2 s-1 Pa-1 and a H2/H2O selectivity of 7−15 at permeation temperatures of 200−400 °C. The microporous silica membrane which was formed on a mesoporous γ-alumina layer coated on the α-alumina tube and then calcined in air showed a H2O permeance of the order of 10-6 mol m-2 s-1 Pa-1 and a H2O/H2 selectivity of 12−25 at 200−400 °C. This membrane rejected HBr at a H2O/HBr selectivity of 300−1000.
Assessing Tumor Microenvironment of Metastasis Doorway-Mediated Vascular Permeability Associated with Cancer Cell Dissemination using Intravital Imaging and Fixed Tissue Analysis (2019)

The most common cause of cancer related mortality is metastasis, a process that requires dissemination of cancer cells from the primary tumor to secondary sites. Recently, we established that cancer cell dissemination in primary breast cancer and at metastatic sites in the lung occurs only at doorways called Tumor MicroEnvironment of Metastasis (TMEM). TMEM doorway number is prognostic for distant recurrence of metastatic disease in breast cancer patients. TMEM doorways are composed of a cancer cell which over-expresses the actin regulatory protein Mena in direct contact with a perivascular, proangiogenic macrophage which expresses high levels of TIE2 and VEGF, where both of these cells are tightly bound to a blood vessel endothelial cell. Cancer cells can intravasate through TMEM doorways due to transient vascular permeability orchestrated by the joint activity of the TMEM-associated macrophage and the TMEM-associated Mena-expressing cancer cell. In this manuscript, we describe two methods for assessment of TMEM-mediated transient vascular permeability: intravital imaging and fixed tissue immunofluorescence. Although both methods have their advantages and disadvantages, combining the two may provide the most complete analyses of TMEM-mediated vascular permeability as well as microenvironmental prerequisites for TMEM function. Since the metastatic process in breast cancer, and possibly other types of cancer, involves cancer cell dissemination via TMEM doorways, it is essential to employ well established methods for the analysis of the TMEM doorway activity. The two methods described here provide a comprehensive approach to the analysis of TMEM doorway activity, either in naïve or pharmacologically treated animals, which is of paramount importance for pre-clinical trials of agents that prevent cancer cell dissemination via TMEM.
Large-Scale Plasma Analysis Revealed New Mechanisms and Molecules Associated with the Host Response to SARS-CoV-2 (2020)

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every continent, registering over 1,250,000 deaths worldwide. The effects of SARS-CoV-2 on host targets remains largely limited, hampering our understanding of Coronavirus Disease 2019 (COVID-19) pathogenesis and the development of therapeutic strategies. The present study used a comprehensive untargeted metabolomic and lipidomic approach to capture the host response to SARS-CoV-2 infection. We found that several circulating lipids acted as potential biomarkers, such as phosphatidylcholine 14:0_22:6 (area under the curve (AUC) = 0.96), phosphatidylcholine 16:1_22:6 (AUC = 0.97), and phosphatidylethanolamine 18:1_20:4 (AUC = 0.94). Furthermore, triglycerides and free fatty acids, especially arachidonic acid (AUC = 0.99) and oleic acid (AUC = 0.98), were well correlated to the severity of the disease. An untargeted analysis of non-critical COVID-19 patients identified a strong alteration of lipids and a perturbation of phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, aminoacyl-tRNA degradation, arachidonic acid metabolism, and the tricarboxylic acid (TCA) cycle. The severity of the disease was characterized by the activation of gluconeogenesis and the metabolism of porphyrins, which play a crucial role in the progress of the infection. In addition, our study provided further evidence for considering phospholipase A2 (PLA2) activity as a potential key factor in the pathogenesis of COVID-19 and a possible therapeutic target. To date, the present study provides the largest untargeted metabolomics and lipidomics analysis of plasma from COVID-19 patients and control groups, identifying new mechanisms associated with the host response to COVID-19, potential plasma biomarkers, and therapeutic targets.
Områdessökning i geografiskt associerad data (2008)

This thesis considers the problems associated with searches in insufficiently geographically tagged data. The thesis was carried out at Booli Search Technologies AB, a company developing a search engine for the Swedish real estate market. The aim of the thesis is to identify some areas of possible improvements of the company’s existing technical platform, perform a benchmarking among similar services, suggest possible solutions and lastly, build a prototype from one of the suggested solutions. The thesis starts out with defining the problems that the search engine faces: some areas are not possible to perform searches on, the users are not presented with the full search result that they expect, some results are placed incorrectly on the map associated with the search results and results are also not described with enough geographical information. These problems are due to the fact that the data retrieved at the indexing stage in the company’s information retrieval process are insufficient and incomplete. As a result of a benchmarking process and after discussing the results, severalinteresting solutions were identified. A prototype was built on one solution, where polygons are defined and tied to areas, and by looking in which of those polygons a certain real estate object is positioned the geographical data was complemented. The prototype solved the problems stated in the beginning of the thesis, but the solution had some disadvantages, among them the need to define polygons for every area where the search result is to be improved.
Using H.264/AVC-based Scalable Video Coding (SVC) for Real Time Streaming in Wireless IP Networks (2007)

A streaming system based on the scalable video coding (SVC) extension of H.264/AVC is shown. SVC allows for data rate adaptation without re-encoding just by dropping packets of the bit stream. By that, it enables for instance multicast services to clients of heterogeneous capabilities at the same time, while consuming less bit rate compared to simulcasting the services. Additionally, the robustness of a streaming connection against packet losses can be significantly increased if the different layers of the coded video stream are unequally protected by a forward error correction scheme. In this case, users will experience graceful degradation of image quality rather than visible errors or interruptions. The introduction of new services using SVC can also take advantage of a backward-compatible base layer. Different use cases for SVC streaming in wireless IP networks and selected simulation results of the improved error robustness for a DVB-H wireless transmission are presented.
Fatal cytomegalovirus (CMV) colitis in a patient receiving low dose prednisolone therapy (1991)

Cytomegalovirus (CMV) colitis is uncommon in patients who are not gravely immunodepressed. We report a case of fatal CMV colitis in a 54-year-old woman on low dose steroid therapy. She was admitted to hospital after sudden onset of abdominal pain and hemorrhagic watery diarrhea. After 25 days in the hospital, treatment with high dosage of methylprednisolone was started for presumed ulcerative colitis. Her condition worsened and she died 52 days after admission. It is important to recognize CMV colitis as differential diagnosis to inflammatory bowel disease, particularly when the colitis is refractory to immunosuppressive treatment.
Cystic fibrosis growth retardation is not correlated with loss of Cftr in the intestinal epithelium (2011)

Maldigestion due to exocrine pancreatic insufficiency leads to intestinal malabsorption and consequent malnutrition, a mechanism proposed to cause growth retardation associated with cystic fibrosis (CF). However, although enzyme replacement therapy combined with increased caloric intake improves weight gain, the effect on stature is not significant, suggesting that growth retardation has a more complex etiology. Mouse models of CF support this, since these animals do not experience exocrine pancreatic insufficiency yet are growth impaired. Cftr absence from the intestinal epithelium has been suggested as a primary source of growth retardation in CF mice, a concept we directly tested by generating mouse models with Cftr selectively inactivated or restored in intestinal epithelium. The relationship between growth and functional characteristics of the intestines, including transepithelial electrophysiology, incidence of intestinal obstruction, and histopathology, were assessed. Absence of Cftr exclusively from intestinal epithelium resulted in loss of cAMP-stimulated short-circuit current, goblet cell hyperplasia, and occurrence of intestinal obstructions but only slight and transient impaired growth. In contrast, specifically restoring Cftr to the intestinal epithelium resulted in restoration of ion transport and completely protected against obstruction and histopathological anomalies, but growth was indistinguishable from CF mice. These results indicate that absence of Cftr in the intestinal epithelium is an important contributor to the intestinal obstruction phenotype in CF but does not correlate with the observed growth reduction in CF.
Thiophenol‐Mediated 1,5‐Hydrogen Atom Abstraction: Easy Access to Mono‐ and Bicyclic Compounds (2005)

Abstract A thiophenol‐mediated method for cyclization of alkynes is described. The reaction cascade involves the intermolecular addition of a phenylthiyl radical to a terminal triple bond generating an alkenyl radical, followed by a 1,5‐hydrogen atom transfer and a 5‐ exo‐ trig radical cyclization. This very efficient tin‐free procedure allows one to prepare highly functionalized cyclopentane derivatives as well as fused bicyclic and spirocyclic compounds from easily available precursors. During this cyclization process, a phenylthio moiety is incorporated into the final cyclized products. This functionalization is particularly attractive for further transformation of the products.
Effects of irradiation on intestinal cells in vivo and in vitro. (2002)

The effects of irradiation on intestinal epithelial cells were analyzed in vivo and in vitro. The in vivo study was carried out on the rat small intestine and for the in vitro study the intestinal crypt cell-line IEC-6 was used. Rat intestine and IEC-6 cells were irradiated with X-ray doses ranging between 1-16 Gy. Energy-dispersive X-ray microanalysis was used for detection of the elemental changes in the cells. Cell morphology was investigated in the scanning electron microscope, DNA-synthesis by autoradiography of 3H-thymidine incorporating nuclei and proliferation by cell counting. Our results indicate that in vivo, in the crypt cells, the increasing doses of irradiation led to increased sodium and lowered potassium and phosphorus concentrations. Corresponding ion shifts were found in the irradiated IEC-6 cells. Cells continued to proliferate up to the dose of 8 Gy, although the proliferation rate became lower with increasing dose of irradiation. The increasing dose of irradiation significantly reduced DNA-synthesis (16 Gy decreased DNA-synthesis by 50%) which resulted in a complete inhibition of cell proliferation. Analysis of goblet cells also showed characteristic radiation-dependent elemental changes. Scanning electron microscopical investigation of cells in culture revealed that most of the control cells were flat and had rather smooth cell membranes. Irradiation led to the appearance of numerous different membrane manifestations (microvilli of varying length and distribution, and blebs). Frequency of differences in the topology of the cells was related to the dose of irradiation. Our study clearly demonstrates that even low doses of irradiation cause changes in the ionic composition of the cells and inhibit DNA-synthesis and cell proliferation. The effects observed in the crypt cells in vivo were the same as in the intestinal cell line in vitro, which indicates that IEC-6 cells can be used for investigation of side effects of radiation to the abdomen.
Branched Diacylglycerol-Lactones as Potent Protein Kinase C Ligands and α-Secretase Activators (2006)

Using as our lead structure a potent PKC ligand (1) that we had previously described, we investigated a series of branched DAG-lactones to optimize the scaffold for PKC binding affinity and reduced lipophilicity, and we examined the potential utility of select compounds as alpha-secretase activators. Activation of alpha-secretase upon PKC stimulation by ligands causes increased degradation of the amyloid precursor protein (APP), resulting in enhanced secretion of sAPPalpha and reduced deposition of beta-amyloid peptide (Abeta), which is implicated in the pathogenesis of Alzheimer's disease. We modified in a systematic manner the C5-acyl group, the 3-alkylidene, and the lactone ring in 1 and established structure-activity relationships for this series of potent PKC ligands. Select DAG-lactones with high binding affinities for PKC were evaluated for their abilities to lead to increased sAPPalpha secretion as a result of alpha-secretase activation. The DAG-lactones potently induced alpha-secretase activation, and their potencies correlated with the corresponding PKC binding affinities and lipophilicities. Further investigation indicated that 2 exhibited a modestly higher level of sAPPalpha secretion than did phorbol 12,13-dibutyrate (PDBu).
Active control of noise radiated from an x-ray tube (2016)

The application of implementing an active noise control system to globally attenuate noise radiated from a medical x-ray tube has been investigated. The noise radiated from the x-ray tube is characterized by the presence of numerous tonal peaks distributed over a broad frequency bandwidth. Furthermore, there is sufficient variability in the radiated field that coherence in the acoustic field was also found to be a challenge. It was determined that a properly placed structural sensor could be used as a reference signal to achieve good coherence between the reference signal and error microphone. In order to achieve global control, speakers were placed in close proximity to areas that had been identified as source regions through the use of SLDV and acoustic intensity measurements. The frequency band below 1500 Hz was targeted, and it was found that effective attenuation could be achieved at over ten of the most prominent frequencies, resulting in attenuations in that bandwidth on the order of 7 dB. Some of the challenges encountered and results obtained will be discussed and presented.
Active devices in next-generation access networks (2013)

Next generation access networks present many more opportunities and challenges in the optical layer than the present generation of such networks do. I will review the optical components that can be used advantageously in this environment, with an emphasis on optical amplifiers in PON extension and WDM-PON.
Transportation Safety and the Allocation of Safety Improvements (2012)

Commercial air carriers are commonly regarded as one of the safest modes of transportation, largely due to oversight from organizations such as the Federal Aviation Administration (FAA), European Aviation Safety Agency (EASA), and the National Transportation Safety Board (NTSB.) Yet, many people are still apprehensive about air travel, and there is a continued effort by these regulatory agencies and NASA to improve the safety records of airlines. In comparison, other modes of transportation, such as private automobiles, are much more dangerous, but arouse less anxiety and receive less attention from regulators. In this paper, we first review the safety records of various modes of transportation in recent years and compare that to the number of investigations performed by the NTSB as well as the total cost of all new regulations. This comparison is used to determine whether enough resources are being allocated to areas with the worst safety records. We find a significant bias in allocating resources toward airlines and buses, roughly 60 and 600 times their private counterparts, respectively. We propose 3 possible explanations for this bias: the news-worthiness of an accident, the level of personal responsibility for safety, and an individual’s perception of the safety of a given mode of transport. We also demonstrate the negative implications of misallocating resources among modes, showing that substitution effects can cause improvements in safety in a single mode to result in a net decrease in safety of overall transportation by increasing costs. We propose that regulators, as well as the public, should consider these effects when determining policy in the future.