gebhart/patrepeval huggingface dataset:
Potential prognostic biomarker CD73 regulates epidermal growth factor receptor expression in human breast cancer (2012)

CD73, an ecto-enzyme overexpressed in breast-cancer cells, catalyzes the dephosphorylation of adenosine monophosphates into adenosine. Anti-CD73 slows breast cancer growth and its spread both in vivo and in vitro. In this study, we investigated the relation of CD73 to epidermal growth factor receptor (EGFR) expression using tissue array and breast cancer cell lines. We found that CD73 expression correlated positively to EGFR expression in vivo (n = 80, r = 0.425, P < 0.01) and in vitro. EGFR expression can be decreased by suppressing CD73 with an inhibitor or small shRNA, and this effect was reversed by adenosine and NECA (adenosine A2 receptor agonist), which suggested that adenosine is involved in EGFR expression regulated by CD73 (P < 0.01). We also showed that CD73 regulates EGFR phosphorylation by Src (P < 0.01). By transcription factor (TF) assay, CD73 was found to regulate some associated TFs activity such as PPARγ, which mediates EGFR expression, although whether PPARγ mediates the effect of CD73 on EGFR expression needs further study. The Kaplan-Meier recurrence-free survival curves for CD73 were also plotted in www.kmplot.com. The curves show that CD73 expression separates the cases into significantly different prognostic groups among the estrogen receptor-negative cancers (P < 0.01). Our results suggest that CD73 may be a potential prognostic biomarker associated with coexpression of EGFR in human breast cancer.
Investigations of PEGylated Recombinant Adenovirus, Using Fluorescein-Labeled Polyethylene Glycol (2007)

As with certain successful protein drug treatments, the attachment of polyethylene glycol (PEG) molecules to recombinant adenovirus (rAd) can augment their therapeutic potential. Unlike these proteins, the rAd particle has thousands of target sites for PEG conjugation. The reliable measurement of the average number of PEG molecules attached to the virion, or the degree of PEGylation (DP), is crucial not only for the characterization of PEGylated virus but also for optimization of the PEGylation reaction. Using a fluorescein-labeled PEG-SPA linker (SPA, succinimidyl ester of PEG propionic acid) with a 5-kDa linear PEG moiety, multiple preparations of fluoro-PEG-rAds were produced under various reaction conditions, purified, and analyzed by size-exclusion high-performance liquid chromatography (HPLC) with fluorescence quantification of the virus peak. The DP was strongly dependent on the percent linker concentration in the reaction. For example, under one set of conditions, fluoro-PEG-rAd samples prepared at 1.3, 2.5, 5.0, 7.4, and 10.0% linker concentration had DPs of approximately 540, 1,000, 1,590, 1,990, and 2,170, respectively. The fluoro-PEG-rAds were compared with a set of nonfluorescent PEG-rAds. Analytical ultracentrifugation in CsCl density gradients showed distinct peaks at decreased buoyant density corresponding to the increased DP of the rAd samples; sodium dodecyl sulfate-polyacrylamide gel electrophoresis/scanning densitometry showed decreased hexon monomer and penton base. Both techniques were used to estimate the DP of nonfluorescent PEG-rAds versus fluoro-PEG-rAds, and anion-exchange HPLC revealed the different surface chemistries of the two vector types. In summary, these studies should provide investigators with the ability to reproducibly prepare and characterize PEGylated rAds or other large viral or nonviral particles for further in vivo studies.
Identification of elf1, a beta-spectrin, in early mouse liver development (1998)

Beta-spectrins play essential roles in cell-cell interactions and in the maintenance of cell polarity. Our aim was to identify beta-spectrin genes important for the establishment of hepatocyte polarity and differentiation. Using subtractive screening of cDNA libraries from early embryonic mouse livers (post-coital days 10, 11, and 12), we have isolated elf1 (embryonic liver fodrin 1), a differentially expressed beta-spectrin or fodrin (betaSpIIsigmaI). Elf1 encodes a 220-amino acid protein with an NH2 terminal actin-binding domain. In situ hybridization studies demonstrate elf1 expression initially in day 10 embryonic heart tissue, then in day 11-11.5 hepatic tissue. These studies suggest that elf1 may play a role in the emergence of hepatocyte polarity during liver development.
Linguistically Motivated Information Retrieval (1999)

Information Retrieval (IR) has been developed to provide practical solutions tp people&apos;s need to find desired information...
Vaporizing Microdroplet Inhalation, Transport, and Deposition in a Human Upper Airway Model (2004)

Evaluation of injuries from inhalation exposure to toxic fuel requires detailed knowledge of inhaled aerosol transport and deposition in human airways. Focusing on highly toxic, easily volatized JP-8 fuel droplets, the three-dimensional airflow, temperature distributions, and fluid-particle thermodynamics, i.e., droplet motion as well as evaporation, are simulated and analyzed for laminar as well as locally turbulent flow conditions. Specifically, using a commercial finite-volume software with user-supplied programs as a solver, the Euler-Lagrange approach for the fluid-particle thermodynamics is employed with: (1) a low Reynolds number k-ω model for laminar-to-turbulent airflow, and (2) a stochastic model for random fluctuations in the droplet trajectories with droplet evaporation. Presently, the respiratory system consists of two major segments of a simplified human cast replica, i.e., a representative oral airway from mouth to trachea (Generation 0) and a symmetric four-generation upper bronchial tree model (G0 to G3). Experimentally validated computational fluid-particle thermodynamics results show that evaporation of JP-8 fuel droplets is greatly affecting deposition in the human airway. Specifically, droplet deposition fractions due to vaporization decrease with increasing ambient temperatures and decreasing inspiratory flow rates. It is also demonstrated that assuming idealized velocity profiles and particle distributions in or after the trachea may greatly overpredict particle deposition efficiencies in the upper bronchial tree.
Ultrasonic Absorption and Velocity Measurements in Numerous Liquids (1941)

By means of ultrasonic light-diffraction phenomena the velocity and absorption of sound in some forty transparent liquids were measured in the frequency range of 6 to 30 Mc. Among the list of materials studied are mixtures of liquids in varying proportions, several solutions of solids in liquids, and a nonliquid jell. A novel-construction glass-to-metal-to-quartz cell made possible the study of highly solvent liquids. Velocity values were obtained from measurements of the diffraction spectra spacing. Absorption values were obtained by measurement of the sound radiator voltages required to produce certain color transmission effects at measured distances from the sound radiator. The use of a mercury arc light-source enhanced the necessary color effects. The relation between sound beam width (in the optical direction) and light transmission was studied. In general, the values of velocity obtained were found to be independent of frequency, and the absorption to be proportional to frequency squared and unrelated to calculated viscous and thermal losses. A simple calculation is proposed for estimating absorption errors caused by sound beam diffraction and spreading. These apply as well to absorption measured in other methods than here used.
The Effect of High Concentrations of Iron on Impounded American Lobsters: A Case Study (1993)

Iron precipitates are reported from American lobsters Homarus americanus held in cold saline water of high iron concentration (11.0 mg/L). Upon aeration, an insoluble ferric oxide precipitate or hydroxide precipitate (or both) formed and was deposited within the carapace matrix and the gills, occluding the respiratory lamellae. Clinical signs included a darkened carapace and lethargy.
Scrapie in mice deficient in apolipoprotein E or glial fibrillary acidic protein (1996)

In the prion diseases, extensive reactive gliosis is often found to be out of proportion to the degree of apparent neuronal damage. To evaluate the role of astrocytic gliosis in experimental scrapie of the mouse, we inoculated mice deficient in apolipoprotein E (apoE) or the glial fibrillary acidic protein (GFAP) with mouse prions. The expression of both apoE and GFAP in astrocytes increases as part of the reactive gliosis that accompanies scrapie. Null mice deficient in either apoE or GFAP inoculated with prions exhibited incubation times indistinguishable from untargeted control mice. The level of PrPSc and its regional deposition in the brains of ill mice deficient in either protein were also similar to control mice. Our findings demonstrate that neither apoE nor GFAP participates in the pathogenesis of the disease or in the production of PrPSc.
A view of three decades of linear filtering theory (1974)

Developments in the theory of linear least-squares estimation in the last thirty years or so are outlined. Particular attention is paid to early mathematica[ work in the field and to more modern developments showing some of the many connections between least-squares filtering and other fields.
Effect of line broadening on the performance of Faraday filters (2015)

We show that homogeneous line broadening drastically affects the performance of atomic Faraday filters. We use a computerized optimization algorithm to find the best magnetic field and temperature for Faraday filters with a range of cell lengths. The effect of self-broadening is found to be particularly important for short vapour cells, and for `wing-type' filters. Experimentally we realize a Faraday filter using a micro-fabricated $^{87}$Rb vapour cell. By modelling the filter spectrum using the ElecSus program we show that additional homogeneous line broadening due to the background buffer-gas pressure must also be included for an accurate fit.
Evidence for Altered NMDA Receptor Function as a Basis for Metaplasticity in Visual Cortex (2003)

Sensory deprivation alters the properties of synaptic plasticity induced in the superficial layers of the visual cortex, facilitating long-term potentiation and reducing long-term depression (LTD) across a range of stimulation frequencies. Available data are compatible with either a downregulation of the mechanisms of LTD or an upregulation of NMDA receptor function in the visual cortex of dark-reared animals. Here, we provide evidence for enhanced NMDA receptor function by showing that deprivation produces a horizontal shift in the frequency-response function, decreasing LTD in response to 1 Hz stimulation, but increasing LTD in response to 0.5 Hz stimulation. In addition, we show that the effects of dark-rearing on the frequency dependence of LTD can be reversed acutely by partial NMDA receptor blockade. Finally, we show that an in vivo manipulation that rapidly downregulates NMDA receptor function in the visual cortex, brief light exposure, also rapidly reverses the effect of dark-rearing on LTD.
Analysis of a Tertiary CO2 Flood Pilot in a Naturally Fractured Reservoir (1991)

Abstract Typical EOR screening criteria suggest that naturally fractured reservoirs are poor candidates for miscible CO2 flooding. Despite this rule of thumb, the unusual geology and considerable EOR target of the fractured Midale field persuaded its owners to study implementation of CO2 flood technology. The 31,000 acre Midale field (Figure 1) is part of a trend of Mississippian carbonate reservoirs in southeastern Saskatchewan. Since 1962, the Midale Unit waterflood has recovered 20% of the 500 million barrels of original oil in place (OOP); ultimate waterflood recovery is expected to be 24%. The reservoir section consists of a heavily-fractured vuggy limestone (the "Vuggy") overlain by a less-fractured chalky dolomite (the "Marly"). Although naturally fractured, well productivities are modest, with average rates of 75-100 STB/D. In 1984 the Unit owners began a 4.4 acre tertiary miscible CO2 flood pilot. Important pilot data sources included residual oil measurements; single- and multi-well pressure transient tests; fluid analyses; time-lapse logging programs at injectors, producers, and observation wells; chemical, radioactive, halogen, and alcohol tracer programs; phase behavior studies focussing on wax-asphaltene deposition; geotomographic efforts to track flood fronts and displacement insitu; and core/CATSCAN studies of CO2 diffusion in Midale core. The $18.6 million pilot project was completed in 1989.
Coupling of Local Folding to Site-Specific Binding of Proteins to DNA (1994)

Thermodynamic studies have demonstrated the central importance of a large negative heat capacity change (delta C degree assoc) in site-specific protein-DNA recognition. Dissection of the large negative delta C degree assoc and the entropy change of protein-ligand and protein-DNA complexation provide a thermodynamic signature identifying processes in which local folding is coupled to binding. Estimates of the number of residues that fold on binding obtained from this analysis agree with structural data. Structural comparisons indicate that these local folding transitions create key parts of the protein-DNA interface. The energetic implications of this "induced fit" model for DNA site recognition are considered.
Microwave Extraction of Volatiles for Mars Science and ISRU (2012)

Results from the present study demonstrated significant differences between groups, particularly listening in noise. Females who present with auditory complaints in spite of normal hearing thresholds should have a more extensive audiological evaluation to further evaluate possible central deficits.
Modified Bisection Search for Faster Metastability Characterization (2010)

Abstract—Circuit state bisection is a robust technique to characterize the performance of multi-stage synchronizers. The passage of metastability between synchronizer stages introduces effects that are not captured by small-signal models and thus numerical integration remains the most reliable method for characterizing this behavior. However, the large number of transient simulations required to characterize one circuit through bisection makes it very difficult to use this technique to run variability analysis or parametric optimization on synchronizer circuits. We present a modified bisection search algorithm that performs 2.5 to 3.2 times faster than conventional bisection without any loss of accuracy. Our method is not restricted to any latch topology or behavior and can safely replace conventional bisection for characterizing any synchronizer circuit. Index Terms—synchronizers, metastability, bisection. I.
Genomic response, bioinformatics, and mechanics of the effects of forces on tissues and wound healing (2005)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2005.
Biodegradation of sulfur mustard hydrolysate in the sequencing batch reactor (1997)

The United States Army is currently examining chemical neutralization followed by biodegradation for disposal of the chemical warfare agent sulfur mustard. The acidic hydrolysis of sulfur mustard (“mustard gas”, 2,2′-dichlorodiethyl sulfide), yields a detoxified and biodegradable product typically containing from 80 to 95% thiodiglycol. The hydrolyzed product was typically amended with 1,450 mg/L of ammonium chloride (NH 4 Cl), 280 mg/L of potassium phosphate monobasic (KH 2 PO 4 ), and mineral salts and fed to aerobic Sequencing Batch Reactors (SBRs). The SBRs were operated with 3-5 hour aerated Fill, 17-18 hour React, 1 hour Settle and 1 hour Draw periods. The efficiency of carbon removal was greater than 90% and the effluent was non-toxic as determined by aquatic toxicity tests.
Surface potential and gravity changes due to internal dislocations in a spherical earth-II. Application to a finite fault (2002)

We present a numerical formulation for computing elastic deformations caused by a dislocation on a finite plane in a spherically symmetric earth. It is based on our previous work for a point dislocation (Sun & Okubo 1993). The formulation enables us to compute the displacement, potential and gravity changes due to an earthquake modelled as spatially distributed dislocations. As an application of the finite-fault dislocation theory, we make a case study of the theoretical and observed gravity changes The computed results are in excellent agreement with the observed gravity changes during the earthquake. The gravity changes in the near field can reach some 100 μgal, which can be easily detected by any modern gravimeter. In the far field they are still significantly large: |δg|>10 μgal within the epicentral distance θ<6° ; |δg|>1 μgal within θ<16° ; |δg|>0.1 μgal within θ<40° ; and |δg|>0.01 μgal globally. We also calculate the geoid height changes caused by the 1964 Alaska earthquake and by the same earthquake with revised parameters and an assumed barrier. We find that the earthquake should have caused geoid height changes as large as 1.5 cm.
Nanoparticle distribution during systemic inflammation is size-dependent and organ-specific (2015)

This study comprehensively investigates the changing biodistribution of fluorescent-labelled polystyrene latex bead nanoparticles in a mouse model of inflammation. Since inflammation alters systemic circulatory properties, increases vessel permeability and modulates the immune system, we theorised that systemic inflammation would alter nanoparticle distribution within the body. This has implications for prospective nanocarrier-based therapies targeting inflammatory diseases. Low dose lipopolysaccharide (LPS), a bacterial endotoxin, was used to induce an inflammatory response, and 20 nm, 100 nm or 500 nm polystyrene nanoparticles were administered after 16 hours. HPLC analysis was used to accurately quantify nanoparticle retention by each vital organ, and tissue sections revealed the precise locations of nanoparticle deposition within key tissues. During inflammation, nanoparticles of all sizes redistributed, particularly to the marginal zones of the spleen. We found that LPS-induced inflammation induces splenic macrophage polarisation and alters leukocyte uptake of nanoparticles, with size-dependent effects. In addition, spleen vasculature becomes significantly more permeable following LPS treatment. We conclude that systemic inflammation affects nanoparticle distribution by multiple mechanisms, in a size dependent manner.
Modification of pyridine‐3‐carboxamide (nicotinamide) by radical substitution (1989)

Abstract Pyridine‐3‐carboxamide ( 1 ) was reacted with alkyl radicals to give mono‐, di‐, and tri‐alkylated products. The t ‐butyl radical gives only 6‐ t ‐butylpyridine‐3‐carboxamide ( 4a ). The reactivity decreases in the order of t ‐butyl, isopropyl, and ethyl radicals. The product 4a reacts further with the 2‐phthalimidoethyl radical to give 2‐ and 4‐substituted products 9 and 10 , which were transformed into tetrahydronaphthyridinone derivatives 11 and 12 .
Automatic fluoroscopic Image Calibration for Traumatology Intervention Guidance (2005)

Fluoroscopic images are often used in surgery but they are difficult to exploit in computer aided medical intervention because of their numerous disadvantages. A simple method, compatible with surgical use, is presented and applied to a common operation in traumatology: the distal targeting during intra-medullary nailing. We also show how calibrated data from fluoroscopy imaging system combined to virtual reality techniques can guide the surgeon in such difficult tasks
AI trends in virus control (1991)

It is suggested that modern forms of programming techniques through the use of artificial intelligence (AI) can be used in the fight against computer viruses. Through the use of AI programming techniques, systems will be capable of dynamically representing human expertise through investigating, analyzing, and simulating human problem-solving behavior.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Developmental Outcomes of Aicardi Goutières Syndrome (2019)

Aicardi Goutières syndrome is a monogenic interferonopathy caused by abnormalities in the intracellular nucleic acid sensing machinery (<i>TREX1</i>, <i>RNASEH2A</i>, <i>RNASEH2B</i>, <i>RNASEH2C</i>, <i>SAMHD1</i>, <i>ADAR1</i>, or <i>IFIH1</i>). Most individuals affected by Aicardi Goutières syndrome exhibit some degree of neurologic impairment, from spastic paraparesis with relatively preserved cognition to tetraparesis and severe intellectual disability. Because of this heterogeneity, it is important to fully characterize the developmental trajectory in Aicardi Goutières syndrome. To characterize the clinical presentation in Aicardi Goutières syndrome, early features were collected from an international cohort of children (n = 100) with genetically confirmed Aicardi Goutières syndrome. There was a heterogeneous age of onset, with overlapping clusters of presenting symptoms: altered mental status, systemic inflammatory symptoms, and acute neurologic disability. Next, we created genotype-specific developmental milestone acquisition curves. Individuals with microcephaly or <i>TREX1-</i>related Aicardi Goutières syndrome secondary were the most severely affected and less likely to reach milestones, including head control, sitting, and nonspecific mama/dada. Individuals affected by <i>SAMHD1</i>, <i>IFIH1</i>, and <i>ADAR</i> attained the most advanced milestones, with 44% achieving verbal communication and 31% independently ambulating. Retrospective function scales (Gross Motor Function Classification System, Manual Ability Classification System, and Communication Function Classification System) demonstrated that two-thirds of the Aicardi Goutières syndrome population are severely affected. Our results suggest multifactorial influences on developmental trajectory, including a strong contribution from genotype. Further studies are needed to identify the additional factors that influence overall outcomes to better counsel families and to design clinical trials with appropriate clinical endpoints.
Evaluation of Histologic, Serologic, and Clinical Changes in Response to Abatacept Treatment of Primary Sjögren's Syndrome: A Pilot Study (2013)

CTLA-4Ig treatment significantly reduces glandular inflammation in primary SS, induces several cellular changes, and increases saliva production. Remarkably, this increase in saliva production is significantly influenced by disease duration.
Dependence of vascular permeability enhancement on cysteine proteinases in vesicles of Porphyromonas gingivalis (1995)

Infection with Porphyromonas gingivalis is strongly associated with adult periodontitis, and proteinases are considered to be important virulent factors of the bacterium. In order to investigate the function of proteinases in disease development we examined vesicles, a biological carrier of these enzymes, for the generation of vascular permeability enhancement (VPE) activity, believed to correlate with the exudation of gingival crevicular fluid. The vesicles generated VPE activity from human plasma in a dose-dependent manner which could be inhibited 90% by antipain, a specific inhibitor of the Arg-specific cysteine proteinases (Arg-gingipains [RGPs] from P. gingivalis. Incubation of vesicles with high-molecular-weight-kininogen (HMWK)-deficient plasma did not result in VPE activity. On this basis, RGPs associated with vesicles were assumed to be responsible for most of the VPE activity generation via plasma prekallikrein activation and subsequent bradykinin production. The secondary pathway for VPE activity production was dependent on the direct release of bradykinin from HMWK by the concerted action of RGP and a Lys-specific cysteine proteinase (Lys-gingipain [KGP]), also associated with vesicles. These results indicate that RGP and KGP are biologically important VPE factors acting either via prekallikrein activation (RGP) and/or HMWK cleavage (RGP and KGP) to release BK and, thereby, contributing to the production of gingival crevicular fluid at periodontal sites infected with P. gingivalis.