gebhart/patrepeval huggingface dataset:
Regulation of MHC Class II Expression and Antigen Processing in Murine and Human Mesenchymal Stromal Cells by IFN-γ, TGF-β, and Cell Density (2007)

Mesenchymal stromal cells (MSC) possess immunosuppressive properties, yet when treated with IFN-gamma they acquire APC functions. To gain insight into MSC immune plasticity, we explored signaling pathways induced by IFN-gamma required for MHC class II (MHC II)-dependent Ag presentation. IFN-gamma-induced MHC II expression in mouse MSC was enhanced by high cell density or serum deprivation and suppressed by TGF-beta. This process was regulated by the activity of the type IV CIITA promoter independently of STAT1 activation and the induction of the IFN regulatory factor 1-dependent B7H1/PD-L1 encoding gene. The absence of direct correlation with the cell cycle suggested that cellular connectivity modulates IFN-gamma responsiveness for MHC II expression in mouse MSC. TGF-beta signaling in mouse MSC involved ALK5 and ALK1 TGF-beta RI, leading to the phosphorylation of Smad2/Smad3 and Smad1/Smad5/Smad8. An opposite effect was observed in human MSC where IFN-gamma-induced MHC II expression occurred at the highest levels in low-density cultures; however, TGF-beta reduced IFN-gamma-induced MHC II expression and its signaling was similar as in mouse MSC. This suggests that the IFN-gamma-induced APC features of MSC can be modulated by TGF-beta, serum factors, and cell density in vitro, although not in the same way in mouse and human MSC, via their convergent effects on CIITA expression.
Structural Analysis of Tn5 (1981)

Nucleotide sequences have been determined for the 1.5-kb inverted repeats of Tn5 and for their junctions with the central unique region and with host DNA. The primary findings stemming from this analysis are: 1. Integration of Tn5 is accompanied by the duplication of 9 bp of host DNA. 2. Loss of Tn5 occurs by crossover between short, homologous nucleotide sequences near the junction between Tn5 and host DNA. 3. The IR sequences contain long, open translational reading frames that may code for transposase proteins. 4. The two IR sequences differ by a single-base change. This alteration accounts for the two functional differences observed between IRL and IRR: It shortens the reading frame for the transposase gene in IRL, and it improves the efficiency of a promoter for the nearby Km-resistance gene. 5. The NH2 terminus of the structural gene for the Km-resistance gene maps at the very left border of the unique region, i.e., very close to the end of IRL. These results support the view that the inverted repeats of Tn5 stem from two identical copies of an originally independently moving DNA element. In the transposon, one of these, IRL, seems to have evolved toward a close physical and functional linkage with the antibiotic-resistance gene.
DigitSpace (2016)

Thumb-to-fingers interfaces augment touch widgets on fingers, which are manipulated by the thumb. Such interfaces are ideal for one-handed eyes-free input since touch widgets on the fingers enable easy access by the stylus thumb. This study presents DigitSpace, a thumb-to-fingers interface that addresses two ergonomic factors: hand anatomy and touch precision. Hand anatomy restricts possible movements of a thumb, which further influences the physical comfort during the interactions. Touch precision is a human factor that determines how precisely users can manipulate touch widgets set on fingers, which determines effective layouts of the widgets. Buttons and touchpads were considered in our studies to enable discrete and continuous input in an eyes-free manner. The first study explores the regions of fingers where the interactions can be comfortably performed. According to the comfort regions, the second and third studies explore effective layouts for button and touchpad widgets. The experimental results indicate that participants could discriminate at least 16 buttons on their fingers. For touchpad, participants were asked to perform unistrokes. Our results revealed that since individual participant performed a coherent writing behavior, personalized $1 recognizers could offer 92% accuracy on a cross-finger touchpad. A series of design guidelines are proposed for designers, and a DigitSpace prototype that uses magnetic-tracking methods is demonstrated.
Polar Interactions between Stacked π Systems in Fluorinated 1,8‐Diarylnaphthalenes: Importance of Quadrupole Moments in Molecular Recognition (1995)

T-shaped arrangements in the homodimers A and C of benzene and hexafluorobenzene, respectively, are rationalized by polar effects, but face-to-face stacking dominates in the 1:1 heterodimer B. The dynamics of a series of fluorinated 1,8-diarylnaphthalenes clearly demonstrate the dependence of arene–arene interactions on the electronic characteristics of the arenes. The results are important for the design of supramolecular structures.
Phase change recording using a scanning near-field optical microscope (1996)

The formation and observation, with reflected light, of 60-nm-diam phase-changed domains in a thin GeSbTe film using a scanning near-field optical microscope with a 785 nm wavelength laser diode is demonstrated. The dependence of the domain size on incident laser power was obtained, and the size changed from 150 to 60 nm in diameter with incident power of 8.4–7.3 mW in the probe. At the threshold power of 7.3 mW, the film temperature rose to around 180 °C to partially phase change the local area of the film from amorphous to crystalline. A detected reflectivity increase due to phase change in the formed domain was 8%–2%. The observing (reading) was performed with an incident laser power of 0.2 mW, which corresponds to 10−2–10−3 times less than in a magneto-optical recording. The incident laser power shows that the phase change reading using the reflection scanning near-field optical microscope has the potential to read the recorded bit at a speed over 10 MHz.
Microtechnical Demonstration of Phosphatase in Tissue Sections. (1939)

In preliminary experiments the phosphatase activity of aqueous extracts of dog kidney cortex made (a) of fresh ground tissue, (b) of ground tissue dehydrated with several changes of 95% and absolute alcohol, (c) of dehydrated ground tissue exposed to 56°C for one hour was determined by the Berenblum-Chain modification of Kay's method. These experiments have shown that phosphatase is not destroyed either by alcohol or by exposure to 56°C in completely dehydrated state, the maximum decrease in activity observed having amounted to less than 20%. Moreover, purification of phosphatase by alcohol precipitation has been successfully used by Mart-land and Robison. It appeared possible to demonstrate phosphatase in celloidin or paraffin sections on the basis of the following principle: If tissue sections containing active phosphatase are incubated with a solution of sodium glycerophosphate or of some other suitable ester-phosphate, such as hexose-phosphate or nucleinate, at a suitable pH, at the sites where phosphatase is present, PO4 ions will be split off. These ions may be trapped at the spot by the salts of metals whose phosphates are insoluble. A precipitate of insoluble phosphate forms which, if visible, or made visible, indicates the presence of phosphatase. A useable technic has been worked out on the basis of this principle.Fixation. Phosphatase is dissolved or destroyed by most of the routine fixatives. In alcohol, however, it is preserved for many weeks at least. Thin slices of fresh tissue should be fixed in 95% alcohol for about one day.Unfortunately, decalcification is impossible, because all acids destroy phosphatase completely.Embedding. Both celloidin and paraffin embedding is suitable. If the tissue is well dehydrated, exposure to paraffin at 56 to 60°C for 2 hours will do no harm.
Automatic Focusing of a Computer-Controlled Microscope (1975)

An on-line focusing procedure for a computer-controlled microscope employed in the measurement of human chromosome images is discussed. The method is based on an algorithm proposed by Mendelsohn and Mayall. A focusing accuracy of standard deviation less than 1/20th micron in the slide-objective distance has been achieved. Changes of the focus position with time, and for individual chromosomes within a metaphase, have been investigated. The method has proved insensitive to imperfections in the scanner photocathode. The method has also been used to determine the autofocusing accuracy of an analog metaphase-finding apparatus.
Laser-Matter Interaction at Intensities of 10 Sup 12 W/Cm Sup 2 and Below (1990)

For single pulsed laser-matter interactions at sufficiently high intensity, the electron density in the ablated vapor is large enough to absorb the laser radiation before it can reach the dense target material. The resulting interaction can be described in terms of energy flows: laser energy is absorbed in the plasma in front of the target and reappears as thermal electron energy and secondary radiation, part of which impinges upon and heats the dense target material at the dense material-vapor interface. This heating in turn drives ablation, thereby providing a self-consistent mass source for the laser absorption, energy conversion, and transmission. Under typical conditions of laser intensity, pulse width and spot size, the flow patterns can be strongly two-dimensional. We have modified the inertial confinement fusion code LASNEX to simulate gaseous and some dense material aspects for the relatively low intensity, long-pulse-length conditions to interest in many laser-related applications. The unique aspect to our treatment consists of an ablation model which defines a dense material vapor interface and then calculates the mass flow across this interface. The model, at present, treats the dense material as a rigid, two-dimensional simulational mass and heat reservoir, suppressing all hydrodynamical motion in the dense material. The modeling is being developed and refined through simulation of experiments, as well as through the investigation of internal inconsistencies, and some simulations of model problems. 5 refs., 14 figs., 1 tab.
Polymer electrolytes (1993)

Polymer electrolytes are ionically conducting solid phases formed by the dissolution of salts in ion-coordinating macromolecules. Such materials may be readily fabricated as films using continuous production plant and are being considered as replacements for conventional low-molecular-weight liquid-based electrolytes for practical electrochemical devices such as power sources, variable-transmission windows and displays. The mechanism for ionic transport in polymer electrolytes is novel and quite distinct from the processes occurring in liquid solutions, molten salts or crystalline solid electrolytes. Ion mobility is associated with local structural relaxations of the polymer, although the relationship is not simple. For certain charge carriers local matrix motion simply provides time-dependent pathways or opportunities for ions to move between suitable low-energy sites; for others a mechanism involving short-range transport of ions temporarily attached to the polymer chain is important. For cations, lability of the ion–solvent bond is a necessary condition for long-range transport.The structures and morphology of polymer electrolytes have been studied using a range of techniques. Crystal structures have been reported for certain stoichiometric complexes, but it has been shown that significant ionic conductivity is restricted to amorphous phases. Ionic motion in the latter has been investigated as a function of such variables as salt type, concentration, temperature and the molecular weight of the host polymer.Research on the polymer electrolyte/electrode interface has also been reported; it has been suggested that the constraints on the reorientation of solvating groups in the double layer leads to distinctive behaviour. Polymer electrolytes are likely to hold out the best prospect for practical all-solid-state electrochemical devices since their ability to deform elastically permits efficient interfaces to be fabricated and maintained during cell cycling where volume changes take place in adjacent phases.
Star-Shaped Trimeric Quaternary Ammonium Bromide Surfactants: Adsorption and Aggregation Properties (2012)

Novel star-shaped trimeric surfactants consisting of three quaternary ammonium surfactants linked to a tris(2-aminoethyl)amine core were synthesized. Each ammonium had two methyls and a straight alkyl chain of 8, 10, 12, or 14 carbons. The adsorption and aggregation properties of these tris(N-alkyl-N,N-dimethyl-2-ammoniumethyl)amine bromides (3C(n)trisQ, in which n represents alkyl chain carbon number) were characterized by equilibrium and dynamic surface tension, rheology, small-angle neutron scattering (SANS), and cryogenic transmission electron microscopy (cryo-TEM) techniques. 3C(n)trisQ showed critical micelle concentrations (CMC) 1 order of magnitude lower than that of the corresponding gemini surfactants with an ethylene spacer and the corresponding monomeric surfactants. The logarithm of the CMC decreased linearly with increasing hydrocarbon chain length for 3C(n)trisQ. The slope of the line, which is well-known as Klevens equation, was larger than those of the monomeric and gemini surfactants; however, considering the total carbon number in the chains, the slope was shallower than the monomeric and was close to the gemini. Through the results such as surface tensions at the CMC (32-34 mN m(-1)) and the parameters of standard free energy, CMC/C(20) and pC(20), it was found that 3C(n)trisQ could adsorb densely at the air/water interface despite the strong electrostatic repulsion between multiple quaternary ammonium headgroups. Moreover, dynamic surface tension measurements showed that the kinetics of adsorption for 3C(n)trisQ to the air/water interface was slow because of their bulky structures. Furthermore, the results of rheology, SANS, and cryo-TEM determined that 3C(n)trisQ with n = 10 and 12 formed ellipsoidal micelles at low concentrations in solution and the structures transformed to threadlike micelles with very few branches for n = 12 as the concentration increased, but for n = 14 threadlike micelles formed at relatively low concentrations.
In vitro human lymphocyte proliferative responses to a glycoprotein of the yeast Saccharomyces cerevisiae. (1994)

Following reports of enhanced humoral immunity to Saccharomyces cerevisiae in patients with Crohn's disease, and identification of an immunodominant, high molecular weight glycoprotein (gp200), we have investigated the cellular immune response to this yeast in normal individuals. Following exposure to a crude saline extract (Sacc), peripheral blood mononuclear cells (PBMC) from these subjects demonstrated dose-dependent increases in tritiated thymidine incorporation, the time-course of which resembled that of the response to the known recall antigens PPD and TT. This was accompanied by increased cytotoxicity of the cultured cells for natural killer (NK)-sensitive and NK-resistant target cell lines. Furthermore, using a purified, high molecular weight, glycoprotein fraction of Sacc in culture, a dose-dependent lymphoproliferative response was again observed. Stimulation indices (SI) for thymidine incorporation by umbilical cord blood lymphocytes exposed to Sacc were low compared with those of normal adults. These results provide evidence for possible antigen-specific, cellular, immune sensitization of normal individuals to a ubiquitous dietary component.
CD47 Deficiency in Mice Exacerbates Chronic Fatty Diet-Induced Steatohepatitis Through Its Role in Regulating Hepatic Inflammation and Lipid Metabolism (2020)

Inflammation is one of the hallmarks of non-alcoholic steatohepatitis. CD47 is a widely expressed transmembrane protein that signals through inhibitory receptor signal regulatory protein α (SIRPα) to inhibit macrophage activation and phagocytosis. In this study, we sought to investigate the role of CD47 in hepatosteatosis and fibrosis induced by a chronic high-fat diet (HFD), by comparing disease development in wild-type (WT) and CD47KO mice fed HFD for 40 weeks. The HFD induced remarkably more severe hepatic steatosis and fibrosis but less body weight gain and less subcutaneous fat accumulation in CD47KO mice compared to WT mice. Liver tissues from HFD-fed CD47KO mice exhibited enhanced inflammation characterized by increased proinflammatory cytokine production and increased nuclear factor-κB (NF-κB) activation compared to similarly fed WT mice. Although higher expression of apolipoproteins was observed in CD47KO mice compared to WT mice under a low-fat diet (LFD), HFD-fed WT and CD47KO mice showed comparably prominent downregulation of these apolipoprotein genes, suggesting that the marked difference observed in lipid accumulation and hepatosteatosis between these mice cannot be explained by changes in apolipoproteins. Like apolipoproteins, sirtuin 1 (SIRT1) and peroxisome proliferator activated receptor alpha (PPARα), which are involved in regulation of both lipid metabolism and inflammation, were more highly expressed in CD47KO than WT mice under LFD but more severely suppressed in CD47KO than in WT mice under HFD. Taken together, our results indicate that CD47 plays a significant role in the pathogenesis of HFD-induced hepatosteatosis and fibrosis through its role in regulation of inflammation and lipid metabolism.
Huntingtin-deficient zebrafish exhibit defects in iron utilization and development (2007)

Huntington's disease (HD) is one of nine neurodegenerative disorders caused by expansion of CAG repeats encoding polyglutamine in their respective, otherwise apparently unrelated proteins. Despite these proteins having widespread and overlapping expression patterns in the brain, a specific and unique subset of neurons exhibits particular vulnerability in each disease. It has been hypothesized that perturbation of normal protein function contributes to the specificity of neuronal vulnerability; however, the normal biological functions of many of these proteins including the HD gene product, Huntingtin (Htt), are unclear. To explore the roles of Htt, we have used antisense morpholino oligonucleotides to observe the effects of Htt deficiency in early zebrafish development. Knockdown of Htt expression resulted in a variety of developmental defects. Most notably, Htt-deficient zebrafish had hypochromic blood due to decreased hemoglobin production, despite the presence of iron within blood cells. Furthermore, transferrin receptor 1 transcripts were increased, suggesting cellular iron starvation. Provision of iron to the cytoplasm in a bio-available form restored hemoglobin production in Htt-deficient embryos. Since erythroid cells acquire iron via receptor-mediated endocytosis of transferrin, these results suggest a role for Htt in making endocytosed iron accessible for cellular utilization. Iron is required for oxidative energy production, and defects in iron homeostasis and energy metabolism are features of HD pathogenesis that are most pronounced in the major region of neurodegeneration. It is therefore plausible that perturbation of Htt's normal role in the iron pathway (by polyglutamine tract expansion) contributes to HD pathology, and particularly to its neuronal specificity.
Engineering of cytochrome P450 2B1 specificity. Conversion of an androgen 16 beta-hydroxylase to a 15 alpha-hydroxylase. (1993)

Six site-directed mutants of cytochrome P450 2B1 were constructed, and function was evaluated in COS cell microsomes by monitoring testosterone and androstenedione hydroxylation and inactivation by chloramphenicol. Mutants Ile-114-->Val and Ile-114-->Ala exhibited marked decreases in androgen 16 beta-OH:16 alpha-OH ratios and increases in 15 alpha-OH:16-OH ratios. Since substitution of Gly-478 with Ala or Ser reduces 16 beta-hydroxylation in favor of 15 alpha-hydroxylation, four double mutants containing Val or Ala at position 114 and Ala or Ser at position 478 were examined. For any given residue at position 114 (Ile, Val, or Ala), the 15 alpha-OH:16-OH ratio increased as residue 478 was changed from Gly to Ala to Ser, and for any residue at position 478, this ratio increased as residue 114 was changed from Ile to Val to Ala. As a consequence, the Ile-114-->Ala, Gly-478-->Ser mutant displayed an approximately 1000-fold higher androgen 15 alpha-OH:16-OH ratio compared with the parental enzyme and functionally resembles mouse P450 2A4 much more closely than P450 2B1. All three mutants with Val at position 114 retained susceptibility to inactivation by chloramphenicol, whereas inactivation was suppressed by Ala at this position. The results suggest the feasibility of an empirical approach to P450 engineering involving the appropriate combination of residues at a few critical sites to confer new regio- and stereoselectivity with retention of overall monooxygenase activity.
Solar simulator for solar dynamic space power system testing (1993)

Planned vacuum tank testing of a solar dynamic space power system requires a solar simulator. Several solar simulators were previously built and used for vacuum tank testing of various space systems. However, the apparent solar subtense angle, i.e., the angular size of the apparent sun as viewed from the experiment, of these solar simulators is too large to enable testing of solar dynamic systems. A new design was developed to satisfy the requirements of the solar dynamic testing. This design provides 1.8 kW/m(sup 2) onto a 4.5M diameter test area from a source that subtends only 1 deg, full cone angle. Key features that enable this improved performance are (1) elimination of the collimating mirror commonly used in solar simulators to transform the diverging beam into a parallel beam; (2) a redesigned lamp module that has increased efficiency; and (3) the use of a segmented reflective surface to combine beams from several individual lamp modules at the pseudosun. Each segment of this reflective surface has complex curvature to control the distribution of light. By developing a new solar simulator design for testing of the solar dynamic system instead of modifying current designs, the initial cost was cut in half, the efficiency was increased by 50 percent reducing the operating costs by one-third, and the volume occupied by the solar simulator was reduced by a factor of 10.
Three-dimensional echocardiographic evaluation of fetal heart anatomy and function: acquisition, analysis, and display. (1996)

The purpose of this work was to assess the functional dynamics and anatomy of the cardiac chambers and great vessels in the fetus (18 to 36 weeks) using in utero three-dimensional ultrasonographic imaging. Fifteen patients were studied using conventional two-dimensional sonographic equipment incorporating a position sensor attached to the transducer and a graphics workstation. Sonographic image data were acquired at 30 images per second and required less than 30 seconds per data set. Fetal heart rate and time in the cardiac cycle were determined and used to synchronize image data for reprojection into a volume at the appropriate part of the cardiac cycle. Volume data were analyzed, rendered, and displayed interactively. Three-dimensional sonographic volume data demonstrated fetal cardiac anatomy from multiple orientations and showed the myocardium, valves, ventricles, and atria clearly. The images showed good correlation with currently available embryologic-anatomic-pathologic data. Dynamic and spatial relationships among chambers, valves, and great vessels were readily appreciated. Three-dimensional sonographic imaging of the fetal heart provides both anatomic and functional information regarding the valves, myocardium, great vessels, and chamber dynamics. Interactive three-dimensional cinegraphic display enhances visualization of cardiac anatomy, which can be difficult to appreciate with two-dimensional methods. The methods presented in this work demonstrate the feasibility of three-dimensional fetal echocardiography.