gebhart/patrepeval huggingface dataset:
Equivalence of subpixel motion estimators based on optical flow and block matching (2002)

We compare two classes of algorithms for estimating subpixel, rigid-body translation between two images. One class is based on optical flow. Optical flow algorithms determine translations between images from estimates of spatial and temporal derivatives of brightness. The other class is based on block matching. Block matching algorithms determine translations between images by minimizing the difference between shifted (warped) versions of the original images. We show that these two classes of algorithms are equivalent for subpixel displacements. Specifically, we show that all block matching algorithms that use bilinear interpolation can be recast into equivalent optical flow formulations, and that all algorithms based on optical flow using first-order derivative estimators can be recast into equivalent block matching formulations.
Wound Healing After Excimer Laser Keratomileusis (Photorefractive Keratectomy) in Monkeys (1990)

Laser myopic keratomileusis (photorefractive keratectomy) was performed on 29 rhesus monkey corneas with an argon fluoride (193-nm) excimer laser and a computer-controlled, moving slit delivery system. The 4-mm-diameter central ablation zone ranged in depth from 11 microns (-2 diopters effect) to 46 microns (-8 diopters effect). Corneas were studied for the 9 months postoperatively by clinical slit-lamp microscopy, and periodically with light and transmission electron microscopy. By 6 weeks, mild to moderate subepithelial haze was apparent in 93% of the corneas, with considerable variability in density. Progressive clearing occurred so that by 6 to 9 months 12 of 13 surviving corneas (92%) were either completely clear (4 corneas) or trace hazy (8 corneas). The epithelium was thickened at 21 days after ablation and returned to normal thickness by 3 months. At 3 weeks, subepithelial fibroblasts were three times the density of normal keratocytes and returned to nearly normal numbers by 9 months. We concluded that the anterior monkey cornea demonstrated a mild, typical wound healing response after excimer laser keratomileusis.
Rapid synthesis of long-chain deoxyribooligonucleotides by the N-methylimidazolide phosphotriester method (1983)

A modified phosphotriester method has been employed for the efficient chemical synthesis of long-chain deoxyribooligonucleotides. During the course of this work, a general and rapid procedure was developed for the preparation of 24-62-mers in solution. Preparative reversed phase column chromatography on silanized silica gel was used to purify triester intermediates starting from 10-mers. The rapid synthesis of 32-mer and 42-mer on glass and silica gel supports using suitably protected 2-8-mer blocks as coupling units has been also accomplished. In particular, a convenient procedure for the solid-phase synthesis of oligonucleotide blocks bearing 3'-terminal phosphodiester groups is described.
Selective SiGe nanostructures (2001)

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2001.
Role of Hsp90 in Systemic Lupus Erythematosus and Its Clinical Relevance (2012)

Heat shock proteins (HSP) are a family of ubiquitous and phylogenically highly conserved proteins which play an essential role as molecular chaperones in protein folding and transport. Heat Shock Protein 90 (Hsp90) is not mandatory for the biogenesis of most proteins, rather it participate in structural maturation and conformational regulation of a number of signaling molecules and transcription factors. Hsp90 has been shown to play an important role in antigen presentation, activation of lymphocytes, macrophages, maturation of dendritic cells, and in the enhanceosome mediated induction of inflammation. Systemic lupus erythematosus (SLE) is a chronic autoimmune inflammatory disease with complex immunological and clinical manifestations. Dysregulated expression of Type I interferon α, activation of B cells and production of autoantibodies are hallmarks of SLE. The enhanced levels of Hsp90 were detected in the serum of SLE patients. The elevated level of Hsp90 in SLE has also been correlated with increased levels of IL-6 and presence of autoantibodies to Hsp90. This suggests that Hsp90 may contribute to the inflammation and disease progression and that targeting of Hsp 90 expression may be a potential treatment of SLE. The pharmacologic inhibition of Hsp90 was successfully applied in mouse models of autoimmune encephalomyelitis and SLE-like autoimmune diseases. Thus targeting Hsp90 may be an effective treatment for SLE, especially if combined with other targeted therapeutic approaches.
Usual Interstitial Pneumonia Can Be Detected in Transbronchial Biopsies Using Machine Learning (2017)

We demonstrate proof of principle that genomic analysis and machine learning improves the utility of TBB for the diagnosis of UIP, with greater sensitivity and specificity than pathology in TBB alone. Combining multiple individual subject samples results in increased test accuracy over single sample testing. This approach requires validation in an independent cohort of subjects before application in the clinic.
Chronic and Acute Effects of Dronedarone on the Action Potential of Rabbit Atrial Muscle Preparations: Comparison With Amiodarone (2002)

Dronedarone, a noniodinated derivative of amiodarone, is under evaluation as a potentially less toxic anti-arrhythmic alternative to amiodarone. The acute and chronic electrophysiologic effects of dronedarone and amiodarone were compared in isolated rabbit atrial muscle by microelectrode techniques. Four-week PO treatment with dronedarone or amiodarone increased action potential duration (APD90) (58 +/- 4 ms control versus 69 +/- 2 ms dronedarone, p < 0.01; 68 +/- 3 ms amiodarone, p < 0.01 for a 100-mg/kg/d dose) and effective refractory period (49 +/- 6 ms control versus 68 +/- 4 ms dronedarone, p < 0.01; 63 +/- 3 ms amiodarone, p < 0.01). The APD90 prolonged reverse rate-dependency. In contrast, acute superfusion with 10 microM dronedarone or amiodarone decreased APD90 (61 +/- 6 ms control versus 53 +/- 4 ms dronedarone, p < 0.05; 52 +/- 6 ms amiodarone, p < 0.05), effective refractory period (50 +/- 5 ms control versus 44 +/- 4 ms dronedarone, p < 0.05; 43 +/- 6 ms amiodarone, p < 0.05), and the maximum upstroke slope of the action potential (Vmax) (188 +/- 9 V/s control versus 182 +/- 11 V/s dronedarone p < 0.05; 182 +/- 11 V/s amiodarone, p < 0.05). Thus, chronic and acute electrophysiologic effects of dronedarone on rabbit atrial muscle are similar to those of amiodarone, suggesting a similar potential against atrial arrhythmias.
Fluorescent dyes bound to hydrophilic copolymers: Applications in aqueous halide sensing (2000)

A range of halide-sensitive fluorophores were bound to two hydrophilic copolymers. Thin films of the copolymers swelled in the aqueous media, allowing dye fluorescence to be dynamically quenched by the diffusion of halide ions. The resultant sensor films were characterized in terms of their hydrophilicity, sensitivity, and selectivity toward halide. The sensor films were reversibly capable of determining aqueous bromide and iodide at a mildly alkaline pH with typical 90% response times of 30–70 s and a shelf life in excess of 2 years. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 76: 603–615, 2000
Hydrophilic Surface Modification of PDMS Using Atmospheric RF Plasma (2006)

Control of surface properties in microfluidics systems is an indispensable prerequisite for the success of bioanalytical applications. Poly(dimethylsiloxane) (PDMS) microfluidic devices are hampered from unwanted adsorption of biomolecules and the lack of methods to control electroosmotic flow(EOF). Among the various methods of hydrophilic treatment, a new cleaner technology was chosen to treat PDMS. By using atmospheric RF plasma, hydrophilic surfaces can be created. Thus, analysis was conducted with AFM, XPS, and contact angle before and after plasma treatment. Constructing hydrophilic surfaces without changing the true character of that surface has previously been costly and time consuming. But by using atmospheric plasma cost and time are both greatly reduced. There are many other benefits of hydrophilic surface treatment, including the capability to increase adhesion and capillary effects, etc. Also, with hydrophilic treatment of the micro channels on the PDMS surface, surface tension is reduced thus allowing fluids to move easily along those channels. However, the most important aim is to increase the capillary effects without any deposition or chemical treatment.
Glycophospholipid membrane anchor attachment. Molecular analysis of the cleavage/attachment site. (1991)

The COOH terminus of decay accelerating factor (DAF) contains a signal that directs attachment of a glycophosphatidylinositol (GPI) membrane anchor in a process involving proteolytic removal of 17-31 COOH-terminal residues. Previous work suggested that two elements are required for anchor addition, a COOH-terminal hydrophobic domain (the GPI signal) and an element located NH2-terminal to it, postulated to be the cleavage/attachment site. Using [3H]ethanolamine (a component of the anchor) to tag the COOH terminus, we isolated and sequenced a COOH-terminal tryptic peptide, thereby identifying Ser-319 as the COOH-terminal residue attached to the GPI anchor. This indicates that a 28-residue peptide is removed during processing and localizes the cleavage/attachment site precisely to the region previously shown to be required for anchor attachment (between 10 and 20 residues NH2-terminal to the hydrophobic domain). Since DAF contains multiple cryptic cleavage/attachment sites, we used a GPI-linked human growth hormone-DAF fusion to study the structural requirements for cleavage/attachment. Our results show that while sequences immediately NH2-terminal to the attachment site are not required for anchor addition, deletion of Ser-319 abolishes both anchor attachment and transport to the cell surface. Systematic replacement of the attachment site serine with all possible amino acids indicated that alanine, aspartate, asparagine, glycine, or serine efficiently support GPI anchor attachment while valine and glutamate are partially effective. All other substitutions including cysteine (permitted at the attachment site in other GPI-anchored proteins) abolish both GPI anchor attachment and transport to the cell surface, resulting in accumulation of uncleaved fusion protein in internal compartments (endoplasmic reticulum and Golgi). These results support the general rule that the residue at the cleavage/attachment site must be small. Further, addition of a GPI anchor appears to be necessary for transport to the cell surface in transfected COS cells.
Tuned-circuit Johnson noise thermometry (1989)

Three tuned circuits that can be used in Johnson noise thermometry have been analyzed; series resistance-inductance-capacitance (RLC), parallel RLC, and transformer coupled. Tuned circuits allow the temperature of the sensor to be determined by a single noise voltage, which is ideally independent of the resistance of the sensor, thereby reducing the complexity of temperature-measuring systems for space applications. Direct-coupled and transformer-coupled tuned circuits may offer advantage to the SP-100 system designer interfacing with data systems. A study was performed to establish whether the advantages of the ideal tuned circuits would be obtained with real, lossy inductive components and would provide a measurement system independent of aging and temperature effects on sensor resistance. Theoretical mean-squared output voltage dependence on sensor temperature and resistance, output capacitor value, and inductor temperature and resistance are derived for the series and parallel RLC cases. It is shown for tuned circuits using lossless inductors that the mean squared voltage is kT{sub R}/C, where T{sub R} is the sensor temperature and C is the capacitance of the capacitor. For lossy inductors and transformers, the mean-squared capacitor voltage is a function of sensor resistance, which may change in an unknown manner during an extended mission. Experiments were performedmore » using a low-loss magnetic core as the core material of an inductor and also of a transformer. These results show that the effects of core loss on temperature accuracy are roughly the same in both cases. Experiments also show that for a sensor resistance of 100{Omega} at 1375K and for appropriate choices of inductance and capacitance values, the temperature measurement error due to an unknown sensor resistance change is in the range of 0.3 to 1 K/{Omega}, depending on the circuit used. 3 refs., 8 figs.« less
Preparation and properties of antigen 60 from Mycobacterium bovis BCG. (1986)

Antigen 60 (A60) is the main thermostable immunogen of both 'old tuberculin' (OT) and 'purified protein derivative' (PPD), known reagents for cutaneous tests in tuberculosis. It is recognized by bidimensional immunoelectrophoresis with anti-BCG antiserum, where it appears as the less mobile component. A60 was prepared from the cytoplasm of Mycobacterium bovis BCG, and purified by exclusion gel chromatography and lectin affinity chromatography. Labelled A60 was obtained by radioiodination and used for a radioimmunoassay. Composition of A60 was explored by use of organic solvents, chemicals and enzymes. It contained two fractions of free and bound lipids, as well as protein and polysaccharide moieties. After removal of both free and bound lipid fractions, the core still retained the ability to form immunoprecipitinogen lines with anti-BCG antiserum. The lipopolysaccharide and lipo-protein moieties of A60, as well as the free lipid fraction, were also complexed by antibodies. It is concluded that A60 is a lipopolysaccharide-protein complex of 10(6) to 10(7) daltons, which is a major immunogenic component of mycobacterial cytoplasm. The detailed structure of this antigen, its immunological properties, and its use for an ELISA type immunoassay for tuberculosis are described in two other publications.
TREATMENT OF ACUTE GRAFT-VERSUS-HOST DISEASE WITH A NONMITOGENIC ANTI-CD3 MONOCLONAL ANTIBODY (1992)

Treatment with the monoclonal antibody OKT3 specific for the CD3 complex associated with the T cell antigen receptor can reverse acute rejection of human renal allografts. However, efficacy of anti-CD3 antibodies for treatment of patients with acute graft-versus-host disease after marrow transplantation has not been established. The dose-limiting side effects resulting from T cell activation induced by some anti-CD3 antibodies in vivo have discouraged their use for this application. We now report a phase I-II study of GVHD treatment with the anti-CD3 antibody BC3, a monoclonal murine IgG2b that, unlike OKT3, does not activate T cells. Fourteen patients were treated with BC3 after progression of acute GVHD despite treatment with cyclosporine and corticosteroids, and three patients received BC3 as primary treatment for GVHD. BC3 was administered at a dose of 0.1 or 0.2 mg/kg/day for seven or eight days. Five patients achieved complete resolution of GVHD, eight patients had partial improvement, two patients had no change, and two patients had progression of GVHD on therapy. Responses were sustained in 8 of 13 patients. Mild chills, fever, hypertension, and chest discomfort occurred in various combinations following 6 of 17 (35%) initial infusions of BC3 and following 4 of 99 (4%) subsequent infusions. In each instance it was possible to continue BC3 therapy without adjusting the dose or treatment schedule. In each patient treated, the absolute count of peripheral blood lymphocytes decreased transiently but returned to baseline within 22 hr after the first infusion. Circulating T cells had surface CD3 molecules saturated by the infused antibody in all but one patient. Four patients survived longer than one year after treatment with antibody BC3, and 13 patients died of infection or organ failure. Administration of the nonmitogenic anti-CD3 antibody BC3 was associated with improvement in the clinical manifestations of GVHD with minimal acute toxicity. Efficacy of antibody treatment did not depend on depletion of circulating T cells. Therefore, antibody BC3 may be achieving therapeutic immunosuppression by modulating T cell function. Controlled studies in patients treated earlier in the course of GVHD should determine whether antibody BC3 can improve survival.
New Technologies for Evaluating Flexible Pavement Construction: Year 1 Report (2006)

Historically in Texas, acceptance of flexible pavement layers has been based upon density control, where the density of the layer must meet or exceed some minimum value. The Texas Department of Transportation (TxDOT) utilizes the nuclear density gauge to perform this acceptance testing for subgrade and base layers. However, TxDOT desires to find a non-nuclear method for measuring density; additionally, TxDOT desires to investigate the feasibility of a fundamental shift from density to mechanistic properties for acceptance. This report describes the search for a replacement for the nuclear gauge and also summarizes new techniques that could potentially be used for acceptance of flexible pavement construction. Currently no direct replacement exists for the nuclear density gauge; the most similar devices are the Pavement Quality Indicator and the Pavetracker Plus. However, these two devices are only applicable to hot-mix asphalt layers and are best suited for measuring differential density. Several systems exist that are not density-based that potentially could control flexible pavement construction. These systems include the Vertek and AquaPro moisture probes, the portable falling weight deflectometer, the dynamic cone penetrometer, instrumented vibratory rollers, automated proof rollers, ground-penetrating radar, and infrared imaging. The latter four systems provide near 100% coverage and could serve as screening tools to identify where to perform spot tests. This report describes preliminary testing of the most promising systems and outlines a framework for continued testing with the most promising devices for use during the remainder of this project.
Adrenal Gland and Lung Lesions in Gulf of Mexico Common Bottlenose Dolphins (Tursiops truncatus) Found Dead following the Deepwater Horizon Oil Spill (2015)

A northern Gulf of Mexico (GoM) cetacean unusual mortality event (UME) involving primarily bottlenose dolphins (Tursiops truncatus) in Louisiana, Mississippi, and Alabama began in February 2010 and continued into 2014. Overlapping in time and space with this UME was the Deepwater Horizon (DWH) oil spill, which was proposed as a contributing cause of adrenal disease, lung disease, and poor health in live dolphins examined during 2011 in Barataria Bay, Louisiana. To assess potential contributing factors and causes of deaths for stranded UME dolphins from June 2010 through December 2012, lung and adrenal gland tissues were histologically evaluated from 46 fresh dead non-perinatal carcasses that stranded in Louisiana (including 22 from Barataria Bay), Mississippi, and Alabama. UME dolphins were tested for evidence of biotoxicosis, morbillivirus infection, and brucellosis. Results were compared to up to 106 fresh dead stranded dolphins from outside the UME area or prior to the DWH spill. UME dolphins were more likely to have primary bacterial pneumonia (22% compared to 2% in non-UME dolphins, P = .003) and thin adrenal cortices (33% compared to 7% in non-UME dolphins, P = .003). In 70% of UME dolphins with primary bacterial pneumonia, the condition either caused or contributed significantly to death. Brucellosis and morbillivirus infections were detected in 7% and 11% of UME dolphins, respectively, and biotoxin levels were low or below the detection limit, indicating that these were not primary causes of the current UME. The rare, life-threatening, and chronic adrenal gland and lung diseases identified in stranded UME dolphins are consistent with exposure to petroleum compounds as seen in other mammals. Exposure of dolphins to elevated petroleum compounds present in coastal GoM waters during and after the DWH oil spill is proposed as a cause of adrenal and lung disease and as a contributor to increased dolphin deaths.
The Neuroimmunology of Schizophrenia (2013)

Schizophrenia (SCZ) is a polygenic, multi-factorial disorder and a definitive understanding of its pathophysiology has been lacking since it was first described more than a century ago. The predominant pharmacological approach used to treat SCZ is the use of dopamine receptor antagonists. The fact that many patients remain symptomatic, despite complying with medication regimens, emphasises the need for a more encompassing explanation for both the causes and treatment of SCZ. Recent neuroanatomical, neurobiological, environmental and genetic studies have revived the idea that inflammatory pathways are involved in the pathogenesis of SCZ. These new insights have emerged from multiple lines of evidence, including the levels of inflammatory proteins in the central nervous system of patients with SCZ and animal models. This review focuses on aberrant inflammatory mechanisms present both before and during the onset of the psychotic symptoms that characterise SCZ and discusses recent research into adjunctive immune system modulating therapies for its more effective treatment.
Vectorization of proteins across the blood–brain barrier: high transcytosis of melanotransferrin (P97) (2003)

The blood–brain barrier (BBB) performs a neuroprotective function by tightly controlling access to the brain. There is little transit across the BBB of large, hydrophilic molecules asides from some specific proteins which are taken up be receptor‐mediated endocytosis. Since melanotransferrin (P97) levels are very low in normal serum, we investigated whether P97 may cross the BBB to a greater extent than do other proteins. We thus observed that recombinant human P97 is highly accumulated into the mouse brain following intravenous injection and in situ brain perfusion. Moreover, P97 transcytosis across bovine brain capillary endothelial cell (BBCEC) monolayers is at least 14‐fold higher than that of transferrin, with no apparent changes in the BBCEC monolayer integrity. The brain accumulation, high rate of P97 transcytosis and its very low level in the blood suggest that P97 could be used as a new delivery system to target drugs directly to the brain.
Recent advances in the design of drug-loaded polymeric implants for the treatment of solid tumors (2011)

Although these implants have been shown to improve the treatment of various solid tumors, the ideal implant that is able to deliver high doses of chemotherapeutics to the tumor site, over prolonged periods with relatively few side effects on normal tissue, is yet to be formulated.