gebhart/patrepeval huggingface dataset:
Theory for a gas composition sensor based on acoustic properties (2002)

Sound travelling through a gas propagates at different speeds and its intensity attenuates to different degrees depending upon the composition of the gas. Theoretically, a real-time gaseous composition sensor could be based on measuring the sound speed and the acoustic attenuation. To this end, the speed of sound was modelled using standard relations, and the acoustic attenuation was modelled using the theory for vibrational relaxation of gas molecules. The concept for a gas composition sensor is demonstrated theoretically for nitrogen-methane-water and hydrogen-oxygen-water mixtures. For a three-component gas mixture, the measured sound speed and acoustic attenuation each define separate lines in the composition plane of two of the gases. The intersection of the two lines defines the gas composition. It should also be possible to use the concept for mixtures of more than three components, if the nature of the gas composition is known to some extent.
The Assessment of α<sub><b>1</b></sub>Proteinase Inhibitor Form and Function in Lung Lavage Fluid from Healthy Subjects (1988)

The form and function of alpha 1 proteinase inhibitor in lung lavage fluid from healthy smoking and non smoking individuals has been accurately assessed using critically appraised techniques. The present study demonstrated that it is possible to accurately assess alpha 1 PI function in unconcentrated lavage fluid but that sample collection, storage and subsequent processing may all affect the results. Absolute levels of alpha 1 PI were elevated in subjects who smoke and a substantial quantity of inactive protein was found in both smokers and non smokers. The proportion of inactive alpha 1 PI was similar for both groups, which by inference implies that normal smoking subjects do not have decreased protection by this inhibitor at the bronchoalveolar level. Physicochemical analysis of the alpha 1 PI in these normal subjects showed that it was different from alpha 1 PI previously reported from patients with established disease and this may have important implications regarding the pathogenesis of their condition. Western immunoblotting of bronchoalveolar lavage fluid (BALF) showed that all of the alpha 1 PI was present in the native molecular mass form (54,000 Da). Pre-incubation of samples with methionine sulphoxide peptide reductase restored alpha 1 PI function only by approximately 10% suggesting the presence of little reversibly oxidised alpha 1 PI in either group. Anion exchange HPLC of BALF revealed the presence of two alpha 1 PI species, one of which co-eluted with native, oxidised or proteolyzed forms and the other which was more cationic and did not inhibit porcine pancreatic elastase. Finally, thirteen out of sixteen BALF samples inhibited more neutrophil elastase than could be accounted for by the amounts of functional alpha 1 PI present, suggesting that the presence of other inhibitors is a feature of normal lavage fluids.
Low temperature cultivation of <i>Escherichia coli</i> carrying a rice lipoxygenase L‐2 cDNA produces a soluble and active enzyme at a high level (1990)

Using a T7 RNA polymerase promoter system, rice lipoxygenase L-2 cDNA was expressed in E. coli as a fusion protein with 18 amino acid residues at the amino terminal end of the original enzyme. Incubation at 37 degrees C for 3 h in the presence of the inducer resulted in the production of inactive lipoxygenase. However, when induction was carried out at 15 degrees C for 16 h, active lipoxygenase, amounting to 3% of the total soluble protein, was produced. The enzyme was purified by ammonium sulfate precipitation and Mono-Q column chromatography to homogeneity at a yield of 80%. Expression of this protein should permit future site-directed mutagenesis of the gene and crystallization of the enzyme.
Differential QoS and pricing in networks: Where flow control meets game theory (1999)

The paper looks at ways of providing Quality of Service to users based on a simple pricing scheme. It is primarily aimed at elastic traffic, and it is users rather than the network who define the flow control schemes. A framework for assessing schemes and algorithms via a distributed game is presented.
Dynamics of the Microglial/Amyloid Interaction Indicate a Role in Plaque Maintenance (2008)

Microglial cells aggregate around amyloid plaques in Alzheimer's disease, but, despite their therapeutic potential, various aspects of their reactive kinetics and role in plaque pathogenesis remain hypothetical. Through use of in vivo imaging and quantitative morphological measures in transgenic mice, we demonstrate that local resident microglia rapidly react to plaque formation by extending processes and subsequently migrating toward plaques, in which individual transformed microglia somata remain spatially stable for weeks. The number of plaque-associated microglia increased at a rate of almost three per plaque per month, independent of plaque volume. Larger plaques were surrounded by larger microglia, and a subset of plaques changed in size over time, with an increase or decrease related to the volume of associated microglia. Far from adopting a more static role, plaque-associated microglia retained rapid process and membrane movement at the plaque/glia interface. Microglia internalized systemically injected amyloid-binding dye at a much higher rate in the vicinity of plaques. These results indicate a role for microglia in plaque maintenance and provide a model with multiple targets for therapeutic intervention.
Medical data abstractionism: fitting an EMR to radically evolving medical information systems. (2004)

Growing and maintaining a simple and flexible EMR (Electronic Medical Record) becomes a complicated task in light of diverse and distributed legacy data representation, advancing technologies, changes in medical practice and procedure, and changes in data regulation. Utilizing several abstraction mechanisms can simplify application development and maintenance, and provide flexibility for data evolution and migration. Newer applications built on these abstractions can be the beneficiary of slower obsolescence and lower maintenance costs.
Learning Sampling and Model-Based Signal Recovery for Compressed Sensing MRI (2020)

Compressed sensing (CS) MRI relies on adequate under-sampling of the k-space to accelerate the acquisition without compromising image quality. Consequently, the design of optimal sampling patterns for these k-space coefficients has received significant attention, with many CS MRI methods exploiting variable-density probability distributions. Realizing that an optimal sampling pattern may depend on the downstream task (e.g. image reconstruction, segmentation, or classification), we here propose joint learning of both task-adaptive k-space sampling and a subsequent model-based proximal-gradient recovery network. The former is enabled through a probabilistic generative model that leverages the Gumbel-softmax relaxation to sample across trainable beliefs while maintaining differentiability. The proposed combination of a highly flexible sampling model and a model-based (sampling-adaptive) image reconstruction network facilitates exploration and efficient training, yielding improved MR image quality compared to other sampling baselines.
CD4<sup>+</sup> helper T cells are required for resistance to a highly metastatic murine tumor (1987)

A role of CD4+ T helper cells in induction of tumor transplant rejection leading to complete regression of a highly metastatic DBA/2 mouse lymphoma was analyzed. Using an anti-CD4 monoclonal antibody (GK1.5) which eliminates T helper cells in vivo and in vitro, we found that CD4+ cells are required for tumor resistance in syngeneic DBA/2 mice or allogeneic but major histocompatibility complex-identical B10.D2 mice. In contrast, in allogeneic C57BL/6 mice tumor rejection was independent of CD4+ cells. An analogous requirement for immune CD4+ cells for in vitro induction of CD8+ tumor-specific cytotoxic T cells was found in these respective strains. The requirement for immune CD4+ cells in vitro could be replaced by recombinant interleukin 2. These results demonstrate a role of CD4+ regulatory T cells and T-T cell cooperation in the induction of anti-tumor immunity and tumor rejection, and point to possible therapeutic interventions in the afferent phase of anti-tumor immune responses.
Partial purification and characterization of fatty acid binding protein(s) in Escherichia coli membranes and reconstitution of fatty acid transport system. (1986)

Fatty acid binding protein(s) in E. coli membranes was solubilized and partially purified by oleate-AH Sepharose 4B column chromatography. The binding of palmitate to the protein was saturable. The protein bound all fatty acids with chain lengths of 10-18 tested, and its maximum activity was observed with palmitate. The incorporation of the protein into liposomes which contained a system for acyl-CoA synthesis significantly increased the uptake of the extracellular [14C] palmitate by the liposomes in comparison with the liposomes without the protein. The uptake of [14C] palmitate was also saturable, and the accumulated radioactive compound was found to be palmitoyl-CoA.
Developmental and genetic aspects of congenital diaphragmatic hernia (2012)

Congenital diaphragmatic hernia (CDH) is a frequent occurring cause of neonatal respiratory distress and occurs 1 in every 3,000 liveborns. Ventilatory support and pharmaceutical treatment of the co-occurring lung hypoplasia and pulmonary hypertension are insufficient in, respectively, 20% of isolated cases and 60% of complex ones leading to early perinatal death. The exact cause of CDH remains to be identified in the majority of human CDH patients and prognostic factors predicting treatment refraction are largely unknown. Their identification is hampered by the multifactorial and heterogenic nature of this congenital anomaly. However, application of high-resolution molecular cytogenetic techniques to patients' DNA now enables detection of chromosomal aberrations in 30% of the patients. Furthermore, recent insights in rodent embryogenesis pointed to a specific disruption of the early mesenchymal structures in the primordial diaphragm of CDH-induced offspring. Together, these data allowed for the introduction of new hypotheses on CDH pathogenesis, although many issues remain to be resolved. In this review, we have combined these new insights and remaining questions on diaphragm pathogenesis with a concise overview of the clinical, embryological, and genetic data available.
Specific Cleavage of Cystine Peptides by Cyanide (1966)

Abstract The mechanism of cyanide cleavage of peptide bonds involving the cystine amino group has been shown to involve scission of the disulfide bond to yield a sulfhydryl and a thiocyano group. In pH ranges below 8, the latter cyclizes to produce an acyliminothiazolidine moiety on the peptide chain. This product is unstable and hydrolyzes spontaneously to effect cleavage of the peptide link on the cystine amino group. Increasing the pH favors disulfide scission but decreases the rate of ring closure. Above pH 10, thiocyanate ion is eliminated from the primary reaction products. Since the disulfide scission is unsymmetrical, reoxidation of the newly formed sulfhydryl groups is necessary to convert all cysteine residues to iminothiazolidine rings at the NH2-terminal ends of peptide chains.
Identification of equine herpesvirus-1 antigens recognized by cytotoxic T lymphocytes (2003)

Equine herpesvirus-1 (EHV-1) causes serious disease in horses throughout the world, despite the frequent use of vaccines. CTLs are thought to be critical for protection from primary and reactivating latent EHV-1 infections. However, the antigen-specificity of EHV-1-specific CTLs is unknown. The aim of this study was to identify EHV-1 genes that encode proteins containing CTL epitopes and to determine their MHC I (or ELA-A in the horse) restriction. Equine dendritic cells, transfected with a series of EHV-1 genes, were used to stimulate autologous CTL precursor populations derived from previously infected horses. Cytotoxicity was subsequently measured against EHV-1-infected PWM lymphoblast targets. Dendritic cells were infected with EHV-1 (positive control) or transfected with plasmids encoding the gB, gC, gD, gE, gH, gI, gL, immediate-early (IE) or early protein of EHV-1 using the PowderJect XR-1 research device. Dendritic cells transfected with the IE gene induced CTL responses in four of six ponies. All four of these ponies shared a common ELA-A3.1 haplotype. Dendritic cells transfected with gC, gD, gI and gL glycoproteins induced CTLs in individual ponies. The cytotoxic activity was ELA-A-restricted, as heterologous targets from ELA-A mismatched ponies were not killed and an MHC I blocking antibody reduced EHV-1-specific killing. This is the first identification of an EHV-1 protein containing ELA-A-restricted CTL epitopes. This assay can now be used to study CTL specificity for EHV-1 proteins in horses with a broad range of ELA-A haplotypes, with the goal of developing a multi-epitope EHV-1 vaccine.
P2Y<sub>2</sub> nucleotide receptor signaling in human monocytic cells: Activation, desensitization and coupling to mitogen‐activated protein kinases (2001)

Activation of P2Y(2) receptors by extracellular nucleotides has been shown to induce phenotypic differentiation of human promonocytic U937 cells that is associated with the inflammatory response. The P2Y(2) receptor agonist, UTP, induced the phosphorylation of the MAP kinases MEK1/2 and ERK1/2 in a sequential manner, since ERK1/2 phosphorylation was abolished by the MEK1/2 inhibitor PD 098059. Other results indicated that P2Y(2) receptors can couple to MAP kinases via phosphatidylinositol 3-kinase (PI3K) and c-src. Accordingly, ERK1/2 phosphorylation induced by UTP was inhibited by the PI3K inhibitors, wortmannin and LY294002, and the c-src inhibitors, radicicol and PP2, but not by inhibitors of protein kinase C (PKC). The phosphorylation of ERK1/2 was independent of the ability of P2Y(2) receptors to increase the concentration of intracellular free calcium, since chelation of intracellular calcium by BAPTA did not diminish the phosphorylation of ERK1/2 induced by UTP. A 5-minute treatment with UTP reduced U937 cell responsiveness to a subsequent UTP challenge. UTP-induced desensitization was characterized by an increase in the EC(50) for receptor activation (from 0.44 to 9.3 microM) and a dramatic ( approximately 75%) decrease in the maximal calcium mobilization induced by a supramaximal dose of UTP. Phorbol ester treatment also caused P2Y(2) receptor desensitization (EC(50) = 12.3 microM UTP and maximal calcium mobilization reduced by approximately 33%). The protein kinase C inhibitor GF 109203X failed to significantly inhibit the UTP-induced desensitization of the P2Y(2) receptor, whereas the protein phosphatase inhibitor okadaic acid blocked receptor resensitization. Recovery of receptor activity after UTP-induced desensitization was evident in cells treated with agonist for 5 or 30 min. However, P2Y(2) receptor activity remained partially desensitized 30 min after pretreatment of cells with UTP for 1 h or longer. This sustained desensitized state correlated with a decrease in P2Y(2) receptor mRNA levels. Desensitization of ERK1/2 phosphorylation was induced by a 5-minute pretreatment with UTP, and cell responsiveness did not return even after a 30-minute incubation of cells in the absence of an agonist. Results suggest that desensitization of the P2Y(2) receptor may involve covalent modifications (i.e., receptor phosphorylation) that functionally uncouple the receptor from the calcium signaling pathway, and that transcriptional regulation may play a role in long-term desensitization. Our results indicate that calcium mobilization and ERK1/2 phosphorylation induced by P2Y(2) receptor activation are independent events in U937 monocytes.
Interprétation des discontinuités de Grandjean (1968)

La théorie de De Vries explique la réflexion sélective de la lumière par les préparations cholestériques sans faire intervenir les « plans » de Grandjean ; cette réflexion était jusqu'alors la meilleure justification de leur existence. L'hypothèse de distorsions imposées à la structure hélicoïdale normale d'une préparation cholestérique d'épaisseur variable conduit à remplacer les « plans » de Grandjean perpendiculaires à l'axe hélicoïdal par des surfaces de discontinuité parallèles à cet axe. Ces surfaces que nous appelons cloisons de Grandjean séparent des structures de pas d'autant plus différents que l'épaisseur est plus faible. Les cloisons de Grandjean permettent d'interpréter toutes les observations sans introduire les contradictions inhérentes aux « plans » : les conséquences que les distorsions de la structure entraînent pour la variation du pouvoir rotatoire en fonction de l'épaisseur sont vérifiées expérimentalement et confirment cette interprétation.
Novel CAR-mediated Mechanism for Synergistic Activation of Two Distinct Elements within the Human Cytochrome P450 2B6 Gene in HepG2 Cells (2004)

The constitutive active receptor (CAR) regulates the induction of the cytochrome P450 2B6 (CYP2B6) gene by phenobarbital-type inducers, such as 1,4 bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP) via the distal phenobarbital-responsive enhancer module (PBREM, at -1732/-1685 bp). Activation of the PBREM by TCPOBOP generated a 10-fold induction of CYP2B6 mRNA in HepG2 cells stably expressing mouse CAR (Ym17). Co-treatment with the protein phosphatase inhibitor okadaic acid (OA) synergistically increased this induction over 100-fold without directly activating CAR or the PBREM. Although OA synergy required the presence of PBREM, deletion assays delineated the OA-responsive activity to a proximal 24-bp (-256/-233) sequence (OARE) in the CYP2B6 promoter. CAR did not directly bind to the OARE in electrophoretic mobility shift assays. However, both DNA affinity and chromatin immunoprecipitation assays showed a significant increase in CAR association with the OARE after co-treatment with TCPOBOP and OA, indicating the indirect binding of CAR to the OARE. The two cis-acting elements, the distal PBREM and the proximal OARE, within the chromatin structure are both regulated by CAR in response to TCPOBOP and OA, respectively, to maximally induce the CYP2B6 promoter. This functional interaction between the two sites expands the current understanding of the mechanism of CAR-mediated inducible transcription.
Specialized Color Targets for Spectral Reflectance Reconstruction of Magnified Images (2015)

Digital images are used almost exclusively instead of film to capture visual information across many scientific fields. The colorimetric color representation within these digital images can be relayed from the digital counts produced by the camera with the use of a known color target. In image capture of magnified images, there is currently no reliable color target that can be used at multiple magnifications and give the user a solid understanding of the color ground truth within those images. The first part of this dissertation included the design, fabrication, and testing of a color target produced with optical interference coated microlenses for use in an off-axis illumination, compound microscope. An ideal target was designed to increase the color gamut for colorimetric imaging and provide the necessary "Block Dye" spectral reflectance profiles across the visible spectrum to reduce the number of color patches necessary for multiple filter imaging systems that rely on statistical models for spectral reflectance reconstruction.\nThere are other scientific disciplines that can benefit from a specialized color target to determine the color ground truth in their magnified images and perform spectral estimation. Not every discipline has the luxury of having a multi-filter imaging system. The second part of this dissertation developed two unique ways of using an interference coated color mirror target: one that relies on multiple light-source angles, and one that leverages a dynamic color change with time. The source multi-angle technique would be used for the microelectronic discipline where the reconstructed spectral reflectance would be used to determine a dielectric film thickness on a silicon substrate, and the time varying technique would be used for a biomedical example to determine the thickness of human tear film.
Lasers and CCDs For Flash Measurement Of Small Diameters (1987)

A pulsed diode laser casting a diffraction pattern shadow on a CCD is investigated as a non-contact micrometer. Data collected with a prototype instrument are compared with calculated diffraction patterns. Computational needs and possible techniques for diameter extraction are discussed.
Monoclonal antibodies to a 28,000 mol. wt protein antigen of Mycobacterium leprae. (1985)

Monoclonal antibodies (MoAb) have been used to analyse a protein antigen from Mycobacterium leprae with a subunit mol. wt of 28,000 daltons. Three different patterns of species specificity were observed with two antibodies being specific for M. leprae, two partially specific, and one broadly cross-reactive amongst all mycobacteria. Competitive binding and sandwich assays demonstrated that the specific and partially specific antibodies recognized closely related regions of the molecule while the cross-reactive antibody recognized a spatially separate epitope on the same polypeptide chain. Identification of specific and cross-reactive epitopes on a single antigenic molecule may be of considerable importance for understanding the functioning of the cell-mediated immune system during leprosy infection and the use of MoAb for such analyses is discussed.
The prognostic value of P-glycoprotein (ABCB) and breast cancer resistance protein (ABCG2) in adults with de novo acute myeloid leukemia with normal karyotype. (2006)

Multidrug resistance is a major cause of treatment failure in acute myeloid leukemia (AML). P-glycoprotein (PGP) over-expression has an unfavorable prognostic significance, while the role of breast cancer resistance protein (BCRP) is less clear, especially in AML patients with a normal karyotype. We studied 73 consecutive AML patients with a normal karyotype. BCRP was over-expressed in 24 patients (33%) and was significantly co-expressed with PGP (13/24 vs 11/49, p=0.006) and with CD56. Only PGP, along with age and CD34, affected the achievement of complete remission (p=0.02), while BCRP-positive cases showed an increased risk of relapse (p=0.005) and a shorter disease-free survival (p=0.027). BCRP over-expression did not influence the achievement of remission, but significantly affected the duration of complete remissions. BCRP may, therefore, be regarded as a prognostic factor in patients with normal karyotype AML, for the design of risk-adapted post-remission therapy.