gebhart/patrepeval huggingface dataset:
Alternate Catalytic States of Bovine Kidney Diamine Oxidase Resolved by Hydroxyapatite Chromatography (2006)

Diamine oxidase (DAO, EC 1.4.3.6) has a crucial role in the down‐regulation of biogenic amines known to be involved in cellular proliferation and differentiation. Through the oxidative diamination of polyamines and production of their corresponding aminoaldehydes, DAO acts as the principal mechanism for down regulating the immediate effects of polyamine synthesis. Various isoforms of copper and TPQ‐dependent diamine oxidases are prevalent in various tissues, where the compartmentalization of these enzymes further defines their physiological functions. We have developed a purification scheme for the isolation of the bovine kidney isoform of diamine oxidase (BKDAO), and find that the purified enzyme can be resolved into two distinct populations by calcium phosphate chromatography. Each form is quite stable in solution, but the interconversion between these two peaks is possible by passage through the column a second time. This salt‐dependence of DAO was further examined by the measurement of steady‐state parameters in presence of various salts (KCl, KPi, NaCl, and NaPi). Global fitting of steady‐state kinetic data recorded over a broad range of substrate and salt concentrations suggests that this enzyme exists in solution in interchangeable allosteric states each having unique sensitivity to substrate inhibition. The close structural homology of BKDAO and other closely related enzymes suggests that this may represent a general catalytic mechanism for this group of enzymes. FUNDING RIMI Program NIH GM0651158
Immunohistochemical correlates of response to recombinant interleukin-2-based immunotherapy in humans. (1989)

We have evaluated immunohistochemical characteristics of tumors and the infiltrating cells in patients treated with various immunotherapy regimens. Forty-eight patients with advanced malignancies were treated with high dose i.v. recombinant interleukin-2 alone or in combination with cyclophosphamide, recombinant tumor necrosis factor, recombinant interferon-alpha, antimelanoma antibody 9.2.27, adoptively transferred tumor infiltrating lymphocytes, or lymphokine-activated killer cells. Thirty-four patients with metastatic melanoma and two patients with breast carcinoma underwent excision of one or more s.c. metastases either before, during, or after treatment. Twelve patients with metastatic renal cell carcinoma underwent pretreatment nephrectomy and these tumors were also studied. Tumor cells were evaluated for class I (HLA-A,B,C) and II (HLA-DR) antigen expression and the mononuclear infiltrate was characterized using an avidin-biotin immunoperoxidase technique. All melanomas were class I antigen positive. Fifty-three % of biopsied metastatic melanoma lesions, 58% of primary renal cell carcinomas, and neither of the two breast carcinomas expressed class II antigen prior to therapy. The pretreatment expression of class II antigens by a tumor was not predictive of a clinical response to recombinant interleukin 2-based therapy. After treatment, however, seven of seven biopsied regressing individual metastases intensely expressed DR antigen on over fifty percent of the cells while only three of ten nonresponding lesions did so. Regressing lesions were permeated with macrophages and both CD4 and CD8 T-cell subsets. There were no CD1 or NKH-1 positive infiltrating cells detected in any lesion. The response to recombinant interleukin 2-based immunotherapy is associated with T-cell as well as macrophage infiltration. DR antigen expression by tumor cells and T-cell infiltrate appear in individual lesions to be associated with this response.
Direct Excitatory Interactions Between Cones of Different Spectral Types in the Turtle Retina (1984)

Cone linear sensitivities to red and green stimuli were measured intracellularly in the dark- and light-adapted turtle retina. Test flashes of small diameter were used to minimize horizontal cell feedback. Light adaptation was achieved with either green or red background illumination. The ratio of cone sensitivities to red and green light depended on the color of the background light and differed from the ratio measured in the dark. Electron microscope studies of Golgi-stained turtle cones revealed direct synaptic connections between red and green cones mediated by cone telodendria. These data indicate that the red cone photoresponse is not univariant as has been previously supposed and suggest that mixing of signals from different spectral classes of cones can occur via direct excitatory connections between cones.
Dielectric investigation of the sliding charge-density wave inTl0.3MoO3 (1988)

We have investigated the low-frequency complex conductivity of the charge-density-wave condensate in ${\mathrm{Tl}}_{0.3}$${\mathrm{MoO}}_{3}$, in the temperature range 40--90 K, by the measurement of admittance sampled in the frequency interval 5 Hz--13 MHz. The observed response can be characterized in terms of a simple Debye relaxation model with a distribution of relaxation times by analogy with the reported behavior of its isostructural analog ${\mathrm{K}}_{0.3}$${\mathrm{MoO}}_{3}$. Despite qualitative similarities with the general trends observed in ${\mathrm{K}}_{0.3}$${\mathrm{MoO}}_{3}$, the relaxational response in ${\mathrm{Tl}}_{0.3}$${\mathrm{MoO}}_{3}$ differed significantly in detail. Both the mean relaxation times (${\ensuremath{\tau}}_{0}$) and static dielectric constants (${\ensuremath{\epsilon}}_{0}$) are shown to have Arrhenius temperature dependence with activation energies of 743 and 152 K, respectively. For applied dc biases above the threshold field (${E}_{T}$) for nonlinear conduction, the response shows structure at frequencies that resemble ``washboard'' characteristics of a moving charge condensate. From the values of the high-frequency real and imaginary parts of the dielectric constants, the existence of yet another relaxation process is proposed.
On-stack replacement to improve JIT-based obfuscation a preliminary study (2013)

As more devices are connecting together, more effective security techniques are needed to protect running software from hackers. One possible security technique is to continuously change the binary code running of given software by recompiling it on the fly. This switching need to be done frequently, quickly, and randomly, not constrained by specific locations in code, to make it difficult for the hacker to track the behavior of the running code or predict its functionality. In our research we are working on a technique that recompiles speculatively and concurrently with current execution, and switches to the new compiled version dynamically, at arbitrary points. This paper presents an early analytical study augmented by experimental analysis on manually applying this technique on simple kernels, to study the concept in comparison with other similar techniques.
Prenatal cadmium exposure does not induce greater incidence or earlier onset of autoimmunity in the offspring (2021)

We previously demonstrated that exposure of adult mice to environmental levels of cadmium (Cd) alters immune cell development and function with increases in anti-streptococcal antibody levels, as well as decreases in splenic natural regulatory T cells (nTreg) in the adult female offspring. Based on these data, we hypothesized that prenatal Cd exposure could predispose an individual to developing autoimmunity as adults. To test this hypothesis, the effects of prenatal Cd on the development of autoimmune diabetes and arthritis were investigated. Non-obese diabetic (NOD) mice were exposed to Cd in a manner identical to our previous studies, and the onset of diabetes was assessed in the offspring. Our results showed a similar time-to-onset and severity of disease to historical data, and there were no statistical differences between Cd-exposed and control offspring. Numerous other immune parameters were measured and none of these parameters showed biologically-relevant differences between Cd-exposed and control animals. To test whether prenatal Cd-exposure affected development of autoimmune arthritis, we used SKG mice. While the levels of arthritis were similar between Cd-exposed and control offspring of both sexes, the pathology of arthritis determined by micro-computed tomography (μCT) between Cd-exposed and control animals, showed some statistically different values, especially in the female offspring. However, the differences were small and thus, the biological significance of these changes is open to speculation. Overall, based on the results from two autoimmune models, we conclude that prenatal exposure to Cd did not lead to a measurable propensity to develop autoimmune disease later in life.
Detection of Methicillin Resistance in Staphylococcus aureus From Agar Cultures and Directly From Positive Blood Cultures Using MALDI-TOF Mass Spectrometry-Based Direct-on-Target Microdroplet Growth Assay (2020)

Matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry (MALDI-TOF MS)-based direct-on-target microdroplet growth assay (DOT-MGA) was recently described as a novel method of phenotypic antimicrobial susceptibility testing (AST). Here, we developed the application of MALDI-TOF MS-based DOT-MGA for Gram-positive bacteria including AST from agar cultures and directly from positive blood cultures (BCs) using the detection of methicillin resistance as example. Consecutively collected, a total of 14 methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) and 14 methicillin-susceptible <i>S. aureus</i> (MSSA) clinical isolates were included. Furthermore, a collection of MRSA challenge strains comprising different <i>SCCmec</i> types, <i>mec</i> genes, and <i>spa</i> types was tested. Blood samples were spiked with MRSA and MSSA and positive BC broth processed by three different methods: serial dilution of BC broth, lysis/centrifugation, and differential centrifugation. Processed BC broth was directly used for rapid AST using DOT-MGA. Droplets of 6 μl with and without cefoxitin at the EUCAST breakpoint concentration were spotted in triplicates onto the surface of a MALDI target. Targets were incubated in a humidity chamber, followed by medium removal and on-target protein extraction with formic acid before adding matrix with an internal standard as a quality control (QC). Spectra were acquired and evaluated using MALDI Biotyper software. First, tests were considered as valid, if the growth control achieved an identification score of ≥1.7. For valid tests, same score criterion was used for resistant isolates when incubated with cefoxitin. An identification score <1.7 after incubation with cefoxitin defined susceptible isolates. On-target protein extraction using formic acid considerably improved detection of methicillin resistance in <i>S. aureus</i> and DOT-MGA showed feasible results for AST from agar cultures after 4 h incubation time. Comparing the different processing methods of positive BC broth, lysis/centrifugation method with a final dilution step 10<sup>-1</sup> of the 0.5 McFarland suspension resulted in best test performance after 4 h incubation time. Overall, 96.4% test validity, 100% sensitivity, and 100% specificity were achieved for detection of methicillin resistance in clinical isolates. All strains of the MRSA challenge collection were successfully tested as methicillin-resistant. This first study on Gram-positive organisms showed feasibility and accuracy of MALDI-TOF MS-based DOT-MGA for rapid AST of <i>S. aureus</i> from agar cultures and directly from positive BCs.
Supplementary Figure Legend from Quantification of Excision Repair Cross-Complementing Group 1 and Survival in p16-Negative Squamous Cell Head and Neck Cancers (2023)

&lt;p&gt;PDF file - 56K&lt;/p&gt;
Different spatial distributions of brain metastases from lung cancer by histological subtype and mutation status of epidermal growth factor receptor (2015)

The purpose of this study was to test the hypothesis that the genetic backgrounds of lung cancers could affect the spatial distribution of brain metastases. CT or MR images of 200 patients with a total of 1033 treatment-naive brain metastases from lung cancer were retrospectively reviewed (23 by CT and 177 by MRI). All images were standardized to the human brain MRI atlas provided by the Montreal Neurological Institute 152 database. Locations, depths from the brain surface, and sizes of the lesions after image standardization were analyzed. The posterior fossa, the anatomic “watershed areas,” and the gray-white matter junction were confirmed to be more commonly affected by lung cancer brain metastases, and brain metastases with epidermal growth factor receptor (EGFR) L858R mutation occurred more often in the caudate, cerebellum, and temporal lobe than those with exon 19 deletion of EGFR. Median depths of the lesions from the brain surface were 13.7 mm (range, 8.6–21.9) for exon 19 deleted EGFR, 11.5 mm (6.6–16.8) for L858R mutated, and 15.0 mm (10.0–20.7) for wild-type EGFR. Lesions with L858R mutated EGFR were located significantly closer to the brain surface than lesions with exon 19 deleted or wild-type EGFR (P = .0032 and P < .0001, respectively). Furthermore, brain metastases of adenocarcinoma lung cancer patients with a history of chemotherapy but not molecular targeted therapy were located significantly deeper from the brain surface (P = .0002). This analysis is the first to reveal the relationship between EGFR mutation status and the spatial distribution of brain metastases of lung cancer.
Modular Point-of-Care Breath Analyzer and Shape Taxonomy-Based Machine Learning for Gastric Cancer Detection (2022)

The results show that this point-of-care breath analyzer and data analysis approach constitute a promising combination for the detection of gastric cancer-specific breath. The cluster taxonomy-based sensor reaction curve representation improved the results, and could be used in other similar applications.
Ibex (2014)

Modern data appliances face severe bandwidth bottlenecks when moving vast amounts of data from storage to the query processing nodes. A possible solution to mitigate these bottlenecks is query off-loading to an intelligent storage engine , where partial or whole queries are pushed down to the storage engine. In this paper, we present Ibex , a prototype of an intelligent storage engine that supports off-loading of complex query operators. Besides increasing performance, Ibex also reduces energy consumption, as it uses an FPGA rather than conventional CPUs to implement the off-load engine. Ibex is a hybrid engine, with dedicated hardware that evaluates SQL expressions at line-rate and a software fallback for tasks that the hardware engine cannot handle. Ibex supports GROUP BY aggregation, as well as projection - and selection - based filtering. GROUP BY aggregation has a higher impact on performance but is also a more challenging operator to implement on an FPGA.
CO2 Removal from Contaminated Natural Gas Mixtures by Hydrate Formation (2009)

We analyzed the formation rates of gas hydrates from methane/CO2 mixtures associated with contaminated well gas streams, which results in a methane-enriched gas product. The initial pressure affects both the final clean gas composition and the time taken to achieve it. Although promoters have been described, we note that this term often refers to interstitial materials that stabilize equilibrium hydrate structures rather than classical chemical rate promoters (i.e., catalysts). We also show that previously reported hydrate rate improvers are irrelevant for commercial purposes because they merely overcome inadequate mixing systems. We identify the key process requiring rate acceleration and show the potential for reducing the time for this process to make selective CO2 hydrate formation commercially attractive. We also examine the effect of salinity on the selective formation of CO2 hydrates. The phase boundary pressures increase with increasing salt concentration, and the rate of formation decreases. Formation times are on the order of 1 h, so catalysts are required to make this process commercially viable.
Prometheus: From Legend to the Real Liver Support Therapy (2007)

A large number of patients develop liver disease that may evolve into progressive chronic failure. Artificial liver support systems (e.g., MARS and Prometheus) are considered in the framework of the steady increase in the number of patients who could possibly benefit from these blood purification devices. Albumin dialysis and adsorption are now two integrated concepts. The present know-how enabling us to appropriately modify several intrinsic characteristics of the adsorbents--e.g., their chemical nature, the particle and pore size distribution, as well as a larger surface offered to adsorption--has helped in better fine-tuning liver support systems to improve adsorption kinetics and flow characteristics specifically for the intended clinical application. These properties together with an improved biocompatibility have made possible the development of adsorptive techniques for which clearances and total removal rates of target compound would be unthinkable with conventional hemodialysis or hemofiltration. Several adsorptive techniques are already available commercially for the treatment of sepsis and septic shock and of acute liver failure, but controlled studies with clinical end points are still lacking.
Electronic removal of lesions for more robust BPE scoring on breast DCE-MRI (2021)

During radiologists’ visual assessment of background parenchymal enhancement (BPE) on dynamic contrast enhanced (DCE)-MR images, presence of a tumor may erroneously inflate the BPE estimation due to angiogenesis within the tumor. With a dataset of 426 MRIs, we present an automated method to segment breasts, electronically remove the influence of lesion presence, and calculate scores to estimate BPE levels. A U-Net was trained for breast segmentation from maximum intensity projection (MIP) images. Next, fuzzy c-means (FCM) clustering was used to segment the lesions from the breast DCE-MRIs, and the lesion volume was removed to create MIP images without the influence of the lesion. U-Net outputs were applied to create MIP images of both breasts, affected breasts, and unaffected breasts before and after lesion removal. On an independent test set, a statistically significant trend was found between the radiologist BPE ratings and the calculated BPE scores for all breast regions (Kendall correlation, p &lt; 0.001). Receiver operating characteristic (ROC) analysis was performed to determine the predictive value of the computed scores from each breast region in the binary tasks of classifying Minimal vs. Marked and Low vs. High BPE relative to a radiologist rating. Scores from all breast regions performed significantly better than guessing (p &lt; 0.025 from the z-test) with BPE scores of the affected breast after lesion removal performing the best (AUC = 0.87). Results demonstrate the potential for an automatic BPE prediction from breast DCE-MR without the influence of lesion enhancement.
Characterization of Thermal Modulation of Electrical Conductivity for Small Volume Absorbance Measurements (1989)

Laser-induced thermal modulation of electrical conductivity is a new photothermal method for the measurement of minute absorbance in sub-nanoliter liquid samples. In this paper, a model is presented for the technique. This model is based upon the interaction of a Gaussian laser beam with a cylindrical, homogeneous electrolytic resistor. Particularly simple results are produced if the laser beam spot size is much smaller than the diameter of the electrodes. The theory is verified with respect to the electrode spacing and to the laser power, spot size, and chopping frequency; the highest sensitivity occurs with low chopping frequency, high laser power, and small electrode spacing. The signal is independent of laser spot size, as long as the beam does not illuminate the electrode surface. The precision of the measurement is dominated by shot noise in the current flow through the electrolytic resistor. One point absorbance detection limits of 5.5 × 10−6 measured across the 76-μm diameter electrode wires are obtained in aqueous solution with a 5- mW helium–neon laser. With this instrument, the difference in the absorbance of water and deuterated water is easily determined at 632.8 nm. Keywords: thermal modulation of electrical conductivity.
Optimizing Dispersants in a Lubricant Formulation by Statistical Design - A Simplex Model (1992)

&lt;div class="htmlview paragraph"&gt;A simplex statistical design was used to model the Sequence VE engine performance of two dispersants, P and L, in a lubricant formulation. Dispersant P is a polyisobutylene succinimide, and L a low molecular weight ethylene propylene succinimide dispersant. The model showed that in the Sequence VE test, dispersant L gives superior sludge and varnish performance as compared to dispersant P. Furthermore, there is a synergism in the Sequence VE sludge performance when the two dispersants are mixed in the formulation.&lt;/div&gt;
Cyclostationary spectrum sensing under four-level hypothesis for spectrum sharing (2011)

This paper presents a new multiple hypothesis problem for spectrum sharing between primary users (PUs) and secondary users (SUs) with cognitive radio technique. The considered four hypotheses are as follows; the studied frequency band is vacant (hypothesis H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> ), the studied frequency band is occupied only by a PU (hypothesis H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> ), the studied frequency band is occupied only by another SU (hypothesis H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) and the studied frequency band is occupied by PU and another SU simultaneously (hypothesis H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ). Most of the related works have considered the binary hypothesis testing problem (H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> and H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> ). By applying the multiple hypothesis testing problem, we can enhance the protection of the PU but also fairness among multiple SUs. To avoid difficulties in forming decision regions in the multiple hypothesis problem, a framework where two binary hypothesis tests are combined to form the final decision is introduced. The problem in implementing this framework is that a SU signal can cause interference to the binary hypothesis test for the PU signal (and vice versa), so that we may falsely detect presence of a PU even when only a SU is present. To reduce the leakage due to interference, we propose an implementation using cyclostationary based detection. However, under H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , the correlation between the PU and SU signals is difficult to avoid. We theoretically analyze the correlation under H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and show its impact on the detection performances.