gebhart/patrepeval huggingface dataset:
The cat lipocalin Fel d 7 and its cross‐reactivity with the dog lipocalin Can f 1 (2016)

We investigated the prevalence of sensitization to the cat lipocalin Fel d 7 among 140 cat-sensitized Swedish patients and elucidated its allergenic activity and cross-reactivity with the dog lipocalin Can f 1. Sixty-five of 140 patients had IgE to rFel d 7 whereof 60 also had IgE to rCan f 1. A moderate correlation between IgE levels to rFel d 7 and rCan f 1 was found. rFel d 7 activated basophils in vitro and inhibited IgE binding to rCan f 1 in 4 of 13 patients, whereas rCan f 1 inhibited IgE binding to rFel d 7 in 7 of 13 patients. Fel d 7 and Can f 1 showed high similarities in protein structure and epitopes in common were found using cross-reactive antisera. Fel d 7 is a common allergen in a Swedish cat-sensitized population that cross-reacts with Can f 1, and may contribute to symptoms in cat- but also in dog-allergic patients.
Dietary and hormonal regulation of L-type pyruvate kinase gene expression in rat small intestine (1987)

L-type pyruvate kinase is an enzyme of the glycolytic pathway whose activity and mRNA levels fluctuate in the small intestine according to dietary status. Both the enzyme activity and mRNA concentration decline during fasting and increase upon refeeding either a glucose-rich or a fructose-rich diet. Using a single-strand M 13 phage complementary to L-type pyruvate kinase mRNA as probe, we determined the level of the mRNA in the small intestine of normal, adrenalectomized, thyroidectomized, diabetic and glucagon-treated or cAMP-treated animals refed either a glucose-rich or a fructose-rich diet. The specific mRNA is present in the small intestine of normal fasted rats and increases twofold and threefold on refeeding glucose and fructose respectively. However, the hormonal control of the gene expression differs according to the dietary carbohydrate. The L-type pyruvate kinase mRNA increase, induced by glucose feeding, is hormone-dependent and requires the presence of thyroid hormones and insulin. In fructose-fed rats a certain level of mRNA increase occurs regardless of the hormonal status of the animals, but the full induction of the mRNA by fructose requires the presence of glucocorticoids, thyroid hormones and insulin. Thus, the hormonal regulation of L-type pyruvate kinase gene expression in the small intestine is largely similar to that described in normal rat liver but the basal mRNA level and the stimulation of the mRNA increase by fructose are higher in the small intestine.
EIT of the Human Body with Optimal Current Patterns and Skin-Electrode Impedance Compensation (2014)

Following the lead of the EIT research group at Rensselaer Polytechnic Institute, we have designed and implemented a system comprising 32 independent current sources, in which it is possible to apply current patterns optimizing distinguishability. One potential technical problem is that we are measuring voltages on current-carrying electrodes, giving some sensitivity to time varying skinelectrode impedances. We demonstrate here an algorithm to estimate simultaneously changes in the medium and timevarying skin-electrode impedances.
Purification of the Human Immunodeficiency Virus-1 Aspartyl Proteinase Substrate Peptide (1995)

A rapid and sensitive assay for the aspartyl protease enzyme of the HIV-1 virus is being developed for detecting potential inhibitors. A tritiated peptide serves as the substrate and after the reaction, the radiolabeled product is counted in solution while the substrate is removed from solution by adsorption onto charcoal added to the tube as a tablet. The labeled substrate was synthesized with an unsaturated proline in the sequence. After tritiation the radiolabeled substrate peptide was isolated by rapid countercurrent chromatography. The tritiation reaction was loaded on a multi-layer coil planet centrifuge in the solvent system t-butyl methyl ether, acetonitrile and 1% aq. trifluoroacetic acid (2:2:3 by volume) and chromatographed at a flow of 120 ml/hr and a centrifugation rate of 800 rpm. The excess radioactive side products were eluted after the solvent front followed by the peptide. The peptide was separated within 1 hr and could be directly used in the experiments.
High-speed X-ray analysis of liquid delivery during jet injection (2017)

The effect of varying velocity during jet injection on the dispersion of fluid into tissue is investigated using a custom-built X-ray imaging system. Injections are performed into ex-vivo porcine abdominal tissue using a voice coil actuated injection device. Single velocity and two-phase velocity injections reveal the complex nature of the dispersion of the fluid jet in layered tissue and highlight the effects of changing the jet velocity following the initial penetration of the liquid into the tissue.
Perspective: Drawing on Findings From Critical Illness to Explain Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (2022)

We propose an initial explanation for how myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) could originate and perpetuate by drawing on findings from critical illness research. Specifically, we combine emerging findings regarding (a) hypoperfusion and endotheliopathy, and (b) intestinal injury in these illnesses with our previously published hypothesis about the role of (c) pituitary suppression, and (d) low thyroid hormone <i>function</i> associated with redox imbalance in ME/CFS. Moreover, we describe interlinkages between these pathophysiological mechanisms as well as "vicious cycles" involving cytokines and inflammation that may contribute to explain the chronic nature of these illnesses. This paper summarizes and expands on our previous publications about the relevance of findings from critical illness for ME/CFS. New knowledge on diagnostics, prognostics and treatment strategies could be gained through active collaboration between critical illness and ME/CFS researchers, which could lead to improved outcomes for both conditions.
Sulfate Metabolism in Mycobacteria (2006)

Pathogenic bacteria have developed numerous mechanisms to survive inside a hostile host environment. The human pathogen Mycobacterium tuberculosis (M. tb) is thought to control the human immune response with diverse biomolecules, including a variety of exotic lipids. One prevalent M. tb-specific sulfated metabolite, termed sulfolipid-1 (SL-1), has been correlated with virulence though its specific biological function is not known. Recent advances in our understanding of SL-1 biosynthesis will help elucidate the role of this curious metabolite in M. tb infection. Furthermore, the study of SL-1 has led to questions regarding the significance of sulfation in mycobacteria. Examples of sulfated metabolites as mediators of interactions between bacteria and plants suggest that sulfation is a key modulator of extracellular signaling between prokaryotes and eukaryotes. The discovery of novel sulfated metabolites in M. tb and related mycobacteria strengthens this hypothesis. Finally, mechanistic and structural data from sulfate-assimilation enzymes have revealed how M. tb controls the flux of sulfate in the cell. Mutants with defects in sulfate assimilation indicate that the fate of sulfur in M. tb is a critical survival determinant for the bacteria during infection and suggest novel targets for tuberculosis drug therapy.
Supplementary Table S2 from Anagrelide for Gastrointestinal Stromal Tumor (2023)

&lt;p&gt;Supplemantary Table S2. KIT and ANO1 expression in 630 human cancers.&lt;/p&gt;
Multi‐Level Micro/Nanotexturing by Three‐Dimensionally Controlled Photofluidization and its Use in Plasmonic Applications (2013)

The Field-Gradient Effect extends the photofluidization of azobenzene materials to 3D, multi-level micro/nanotexturing with a newly conceptualized design strategy based on "field-gradient photofluidization". In particular, we successfully characterized the vertical gradient optical absorption within the azobenzene material and the resulting field-gradient photofluidization both theoretically and experimentally. Furthermore, we could create the heterogeneously integrated micro/nanotextures at any desired surface heights, capability that is potentially beneficial for plasmonic applications.
ChemInform Abstract: Synthesis of Alkanols by Addition of Organometallics to Carbon Dioxide, Carboxylic Acids, and Derivatives (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Preferential Nuclear and Cytoplasmic NY-BR-1 Protein Expression in Primary Breast Cancer and Lymph Node Metastases (2006)

This study supports the notion that NY-BR-1 is a differentiation antigen of the breast, which is present in normal and tumorous mammary epithelium. The organ-specific expression of NY-BR-1 and its high prevalence in metastases indicate that it could be a valuable target for cancer immunotherapy.
Experimental Characterization of an Open Loop Pulsating Heat Pipe Cooler (2014)

Pulsating heat pipes (PHP) have emerged in the last years as suitable cooling devices for dissipating the high heat loads generated by electronic devices since they allow to extend the applicability of air cooling in area nowadays covered by water cooling. Two-phase cooling technologies based on the two phase pulsating heat pipe principle are promising solutions because, being entirely passive they can comply with long term operation without maintenance. The main advantage of a PHP compared to conventional thermosyphon technologies for electronics cooling is that a PHP is orientation independent. The authors has developed a novel, compact, and low cost PHP based on automotive technology. The present paper presents the experimental results of an air cooled open loop pulsating heat pipe with optimized manifold design to minimize fluid pressure drops in the fluid turns. The effect of several parameters including filling ratio and heat load are presented. Tests have been done with the refrigerant fluid R245fa in vertical and horizontal orientations. The measurements showed a maximum thermal resistance ranging between 40 and 48 K/kW in vertical and horizontal position respectively for a heat load of 2 kW and air temperature of 20 °C.
Polarization beam shaping (2007)

Spatial engineering of polarization is proposed as a novel method of beam shaping. It is shown that a flat-top-shaped focus can be obtained in the far field by changing the polarization in the pupil plane in a spatially inhomogeneous manner. Experiments have been carried out to verify the validity of this method in one dimension. By comparison with traditional beam shaping methods, polarization beam shaping yields the smallest flat-top focus while maintaining high efficiency.
Functional Group Identification in Scanning Tunneling Microscopy of Molecular Adsorbates (1996)

Monolayer films of several primary substituted hydrocarbons CH3(CH2)nCH2X (X = CH3, OH, NH2, SH, Cl, Br, I; n = 16−30) have been imaged on graphite at the solution−substrate interface using a scanning tunneling microscope (STM). The straight chain hydrocarbons form well-ordered 2-D films on graphite and physisorb with their molecular axes parallel to the surface. The NH2, SH, Br, and I end groups are observed as bright spots in the STM image corresponding to an enhancement in the tunnel current in the vicinity of the functional group, relative to the remainder of the carbon chain. On the other hand, the OH and Cl substituents were not distinguishable from the alkyl chain in the STM images. Comparison of the relative “brightness” of the functional groups with respect to the carbon chain reveals an empirical relationship between increasing relative brightness and increasing molecular polarizability. A model is proposed to describe the STM imaging mechanism for these insulating, physisorbed films in which the role of the adsorbate's polarizability, electronic structure, and orientation with respect to the surface are considered.
Proton NMR study of the role of individual heme propionates in modulating structural and dynamic properties of the heme pocket in myoglobin (1990)

The relative importance of the two heme propionate salt bridges to the protein matrix in determining the equilibrium orientational preference of the synthetic hemin, heptamethyl-monopropionate-porphine-iron(III), reconstituted into sperm whale and horse myoglobin metcyano complexes was determined using the nuclear Overhauser effect, NOE. The preferences for occupying the crystallographic 7-propionate position which makes a link to interior His FG3 in both proteins, versus that of the 6-propionate group interacting with the surface CD3 residue, were found to be ~ 1:2 for the sperm whale and 3:2 for the horse protein. Since the FG3 residue is conserved (His), and the CD3 residue differs in the two proteins (Arg for spermwhale, Lys for horse), we conclude that the 6-propionate-Lys CD3 link in horse Mb is less stable by ~0.64 kcal/mol than the 6-propionate-Arg CD3 salt bridge in sperm whale Mb. Since this salt bridge, in part, holds closed a likely distal ligation channel to the heme pocket, the lower stability of this link in the horse relative to the sperm whale protein provides a structural basis for interpreting earlier highly differential labile hydrogen dynamics for the two proteins (Lecomte, J. T. J.; La Mar, G. N. Biochemistry 1985, 24, 7388-7395). Reconstitution of horse Mb with protohemin IX derivatives having individual propionates selectivityreplaced by methyls confirms that vinyl contacts are much more important than propionate contacts in determining the orientational preference of the heme in the pocket. Each of the monopropionate hemins revealed that the orientational isomer with a propionate in the crystallographic 6-position is in dynamic equilibrium (-103 s_1) with another isomeric form which isdeduced to be the heme orientation with the propionate in the crystallographic 8-position. The interconversion involves simply 90° rotational “hopping” of the heme about the iron-His bond, and this process is concluded to be significantly faster in the horse thansperm whale protein, again suggesting that the 6-propionate salt bridge is weaker in the former Mb. © 1990, American Chemical Society. All rights reserved.
Antitumor Activity of 3-Indolylmethanamines 31B and PS121912. (2015)

3-Indolylmethanamines represent a new class of antitumor agents. We have shown for the first time the in vivo anticancer effects of 3-indolylmethanamines 31B and PS121912.
T-cell receptor Vβ skewing frequently occurs in refractory cytopenia of childhood and is associated with an expansion of effector cytotoxic T cells: a prospective study by EWOG-MDS (2014)

Immunosuppressive therapy (IST), consisting of antithymocyte globulin and cyclosporine A, is effective in refractory cytopenia of childhood (RCC), suggesting that, similar to low-grade myelodysplastic syndromes in adult patients, T lymphocytes are involved in suppressing hematopoiesis in a subset of RCC patients. However, the potential role of a T-cell-mediated pathophysiology in RCC remains poorly explored. In a cohort of 92 RCC patients, we prospectively assessed the frequency of T-cell receptor (TCR) β-chain variable (Vβ) domain skewing in bone marrow and peripheral blood by heteroduplex PCR, and analyzed T-cell subsets in peripheral blood by flow cytometry. TCRVβ skewing was present in 40% of RCC patients. TCRVβ skewing did not correlate with bone marrow cellularity, karyotype, transfusion history, HLA-DR15 or the presence of a PNH clone. In 28 patients treated with IST, TCRVβ skewing was not clearly related with treatment response. However, TCRVβ skewing did correlate with a disturbed CD4(+)/CD8(+) T-cell ratio, a reduction in naive CD8(+) T cells, an expansion of effector CD8(+) T cells and an increase in activated CD8(+) T cells (defined as HLA-DR(+), CD57(+) or CD56(+)). These data suggest that T lymphocytes contribute to RCC pathogenesis in a proportion of patients, and provide a rationale for treatment with IST in selected patients with RCC.
STABLE HIGH CONDUCTIVITY BILAYERED ELECTROLYTES FOR LOW TEMPERATURE SOLID OXIDE FUEL CELLS (2001)

Solid oxide fuel cells (SOFCs) are the future of energy production in America. They offer great promise as a clean and efficient process for directly converting chemical energy to electricity while providing significant environmental benefits (they produce negligible hydrocarbons, CO, or NO{sub x} and, as a result of their high efficiency, produce about one-third less CO{sub 2} per kilowatt hour than internal combustion engines). Unfortunately, the current SOFC technology, based on a stabilized zirconia electrolyte, must operate in the region of 1000 C to avoid unacceptably high ohmic losses. These high temperatures demand (a) specialized (expensive) materials for the fuel cell interconnects and insulation, (b) time to heat up to the operating temperature and (c) energy input to arrive at the operating temperature. Therefore, if fuel cells could be designed to give a reasonable power output at low to intermediate1 temperatures tremendous benefits may be accrued. At low temperatures, in particular, it becomes feasible to use ferritic steel for interconnects instead of expensive and brittle ceramic materials such as those based on LaCrO{sub 3}. In addition, sealing the fuel cell becomes easier and more reliable; rapid start-up is facilitated; thermal stresses (e.g., those caused by thermal expansion mismatches) are reduced; radiative losses ({approx}T{sup 4}) become minimal; electrode sintering becomes negligible and (due to a smaller thermodynamic penalty) the SOFC operating cycle (heating from ambient) would be more efficient. Combined, all these improvements further result in reduced initial and operating costs. The problem is, at lower temperatures the conductivity of the conventional stabilized zirconia electrolyte decreases to the point where it cannot supply electrical current efficiently to an external load. The primary objectives of the proposed research are to develop a stable high conductivity (> 0.05 S cm{sup -1} at {le} 550 C) electrolyte for lower temperature SOFCs. This objective is specifically directed toward meeting the lowest (and most difficult) temperature criteria for the 21st Century Fuel Cell Program. Meeting this objective provides a potential for future transportation applications of SOFCs, where their ability to directly use hydrocarbon fuels could permit refueling within the existing transportation infrastructure. In order to meet this objective we are developing a functionally gradient bilayer electrolyte comprised of bismuth oxide on the air side and ceria on the fuel side. Bismuth oxide and doped ceria are among the highest ionic conducting electrolytes and in fact bismuth oxide based electrolytes are the only known solid oxide electrolytes to have an ionic conductivity that meets the program conductivity goal.
Gradient Intra Prediction for Coding of Computer Animated Videos (2006)

The increasing interest in computer animations initiated the need of efficient coding for such applications. This paper proposes two gradient based approaches to improve the efficiency of Intra Prediction. Taking advantage of a special property of computer animations, namely the gradient distribution of intensity on object surfaces, the devised methods provided a better performance over H.264/AVC. According to the simulations, up to 0.3 dB gain in PSNR has been achieved.
Usage of Object Matching Algorithms Combined with Mixed Reality for Enhanced Decision Making in Orbital Reconstruction—A Technical Note (2023)

This technical note describes the usage of object matching to virtually compare different modes of reconstruction in orbital trauma and display the results to the surgeon and the patient pre-operatively via mixed reality devices for enhanced surgical decision making and immersive patient education. A case of an orbital floor fracture is presented for which surface and volume matching were implemented to compare orbital reconstruction utilizing pre-fabricated titanium meshes versus patient-specific implants. The results could be visualized by mixed reality devices to further enhance surgical decision-making. The data sets were demonstrated to the patient in mixed reality for immersive patient education and enhanced shared decision making. The advantages of the new technologies are discussed in view of the new possibilities of improved patient education and informed consent processes, as well as new ways of teaching medical trainees.
Band Deformation at a T-Junction While Electrofocusing in a Dog-Leg Microchannel (2004)

On-chip isoelectric focusing (IEF) has been performed in both straight and dog-leg microchannels. Three-dimensional microfluidic chips were fabricated on poly di-methyl-siloxane (PDMS) using soft lithography and multilayer bonding techniques. Plasma oxidized PDMS channel surfaces were dynamically coated with methyl cellulose to discourage electroosmotic flow during separation and purification processes. In a straight microchannel, IEF was completed within 5 minutes at an applied electric field strength of 50 V/cm using broad range ampholytes. The focused bands were generally well-formed with sharp edges and were less than 100 microns across yielding a putative peak capacity in excess of 100 peaks in a 2-cm long channel. However, the conventional IEF protocol shifts the focused bands toward the cathodic well. This cathodic drift can be effectively minimized by placing highly viscous polymer solutions in the electrode reservoirs. In dog-leg microchannels, initially well formed focused band dispersed at the Tee-channel junction, but refocused at the dog-leg channels with relatively lower resolution.
Combined adaptive modulation and truncated ARQ for packet data transmission in MIMO systems (2005)

The aim of this paper is to provide a framework for cross-layer management of packet-data transmissions in MIMO systems employing orthogonal space-time block coding (STBC) over Nakagami fading channels. The framework integrates physical layer adaptive modulation and link layer truncated automatic repeat request (T-ARQ), in an attempt to maximize the system's spectral efficiency under prescribed quality of service requirements such as delay and error rate constraints. The performance of the proposed scheme is assessed via three metrics for which we derive closed-form expressions. These metrics consist of the average packet error rate, the average spectral efficiency and the outage probability. We illustrate our analysis through numerical results showing how the combined cross-layer design significantly outperforms both physical layer adaptive modulation and link layer T-ARQ when solely one of these adaptive techniques is used in conjunction with STBC.
The niching method for obtaining global optima and local optima in multimodal functions (2003)

Abstract Sometimes it is desirable to know the secondary candidates as well as the global optima of multimodal functions. The Deterministic Crowding (DC) method is an effective type of genetic algorithm for discovering multiple global optima, but it has difficulties discovering local optima. An improvement on this method called “Dispersing Deterministic Crowding” (DDC) is therefore proposed which encourages dispersion of individuals and creation of species within the population in order to increase the discovery of local optima, as well as of global optima. A method for preferential identification of solutions with a fitness exceeding some demanded level is also developed. The performance of DDC is compared with those of other niching methods, DC, sharing, RTS, GA with tabu search, and the immune algorithm, to show its effectiveness. © 2003 Wiley Periodicals, Inc. Syst Comp Jpn, 34(11): 30–42, 2003; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/scj.10480