gebhart/patrepeval huggingface dataset:
Role of CD27 in T cell immune response. Analysis by recombinant soluble CD27. (1994)

CD27 is a disulfide-linked 120-kDa transmembrane glycoprotein expressed on the majority of T cells, B cells, and NK cells; it has homology to a family of molecules that includes the receptors for nerve growth factor and TNF. Previous studies strongly suggest that the CD27 molecule plays a key role in the process of T cell activation. To further determine its role in T cell activation, a recombinant soluble molecule composing only the extracellular domain of CD27 was produced by transfection of Chinese hamster ovary cells. We have defined the binding properties of recombinant soluble CD27 (rsCD27) to CD27 ligand (CD27L) cDNA transfected NIH 3T3 cells and have determined its functional effects on in vitro T cell activation as well as on PWM-driven B cell IgG synthesis. rsCD27 bound specifically to CD27L and the binding was inhibited by one of our anti-CD27 mAbs, anti-1A4, suggesting that the 1A4 epitope of CD27 plays a role in the binding to CD27L. Functionally, rsCD27 inhibited T cell proliferation induced by various stimuli, such as PHA, tetanus toxoid, and anti-CD2, as well as PWM-driven B cell IgG synthesis, similar to the effects of adding anti-1A4. Determination of CD27L expression showed that CD27L mRNA is induced rapidly on activated T and B cells. Taken together, these results provide direct evidence that CD27-CD27L interaction plays a critical role in T cell activation as well as in T cell-dependent B cell IgG synthesis, suggesting that the CD27-CD27L interaction may constitute a component of the T cell-T cell or T cell-B cell interaction seen after activation with Ag or mitogen.
Prenatally diagnosed balanced chromosome rearrangements: eight years' experience. (2006)

The incidences of prenatally diagnosed de novo reciprocal translocations, de novo Robertsonian translocations and de novo inversions were higher than those reported in previous, larger series. The major congenital anomaly rates for inherited and de novo chromosome rearrangements were higher than the 1.4% congenital anomaly rate in our general population. Consequently, detailed ultrasound examination and parental karyotyping should be viewed as essential measures in dealing with prenatally diagnosed balanced chromosome rearrangements.
Ontogeny of a biological clock in Drosophila melanogaster. (1992)

Drosophila melanogaster born and reared in constant darkness exhibit circadian locomotor activity rhythms as adults. However, the rhythms of the individual flies composing these populations are not synchronized with one another. This lack of synchrony is evident in populations of flies commencing development at the same time, indicating that a biological clock controlling circadian rhythmicity in Drosophila begins to function without a requirement for light and without a developmentally imparted phase. It is possible to synchronize the phases of rhythms produced by dark-reared flies with light treatments ending as early as the developmental transition from embryo to first-instar larva: Light treatments occurring at developmental times preceding hatching of the first-instar larva fail to synchronize adult locomotor activity rhythms, while treatments ending at completion of larval hatching entrain these rhythms. The synchronized rhythmic behavior of adult flies receiving such light treatments suggests that a clock controlling circadian rhythms may function continuously from the time of larval hatching to adulthood.
PTEN Mutation, EGFR Amplification, and Outcome in Patients With Anaplastic Astrocytoma and Glioblastoma Multiforme (2001)

PTEN mutation and EGFR amplification are important prognostic factors in patients with anaplastic astrocytoma and in older patients with glioblastoma multiforme, respectively.
The problem of anti‐pig antibodies in pig‐to‐primate xenografting: current and novel methods of depletion and/or suppression of production of anti‐pig antibodies (1999)

The role of antibodies directed against Galalpha1-3Gal (alpha-Gal) epitopes in porcine-to-primate xenotransplantation has been widely studied during the past few years. These antibodies (anti-alpha-Gal) have been associated with both hyperacute rejection and acute vascular rejection of vascularized organs. Depletion and (temporary or permanent) suppression of production of anti-alpha-Gal seem to be essential to the long-term survival of these organs, even when the ultimate aim is accommodation or tolerance. Although more than 95% depletion of anti-alpha-Gal can be achieved by the use of immunoaffinity column technology, to date no regimen has been successful in preventing the return of anti-alpha-Gal (from continuing production). In this review, we discuss current and novel methods for achieving depletion or inhibition (i.e. extracorporeal immunoadsorption, anti-idiotypic antibodies, the intravenous infusion of immunoglobulin or oligosaccharides) and suppression of production (i.e. irradiation, pharmacologic agents, specific monoclonal antibodies, immunotoxins) of anti-alpha-Gal antibodies.
Pharmacological studies of the new antiinflammatory agent 3-formylamino-7-methylsulfonylamino-6-phenoxy-4H-1-benzopyran-4-o ne. 1st communication: antiinflammatory, analgesic and other related properties. (1992)

The antiinflammatory, analgesic and antipyretic activities of 3-formylamino-7-methylsulfonylamino-6-phenoxy-4H-1-benzopyran-4-on e (T-614, CAS 123663-49-0) were investigated in various animal models and compared with those of nimesulide, indomethacin and ibuprofen. The antiinflammatory potency of T-614 on carrageenin-induced paw edema, paper disk granuloma and established adjuvant arthritis was greater than that of ibuprofen, but slightly lower than those of nimesulide and indomethacin. In acute inflammatory models, unlike indomethacin, T-614 suppressed the edemas provoked by dextran and bromelain in rats, but its inhibitory action on ultraviolet erythema in guinea-pigs was weak. Although the analgesic activity of T-614 was hardly demonstrated in writhing tests in mice, its potency against the inflammatory pain such as Randall-Selitto test, adjuvant-induced hyperalgesia and antigen-induced arthritic pain in rats was superior to that of ibuprofen. Moreover, it had a potent analgesic effect on urate-induced synovitis in dogs. T-614 exerted a prompt and strong antipyretic effect in both yeast-induced febrile rats and lipopolysaccharide-induced febrile rabbits. T-614 had virtually no gastrointestinal ulcerogenic action and did not affect water and sodium excretion in rats. T-614 is a novel antiinflammatory compound with different pharmacological properties from that of the reference drugs.
Scalable in situ single-cell profiling by electrophoretic capture of mRNA (2022)

Methods to spatially profile the transcriptome are dominated by a trade-off between resolution and throughput. Here, we developed a method named EEL FISH that can rapidly process large tissue samples without compromising spatial resolution. By electrophoretically transferring RNA from a tissue section onto a capture surface, EEL speeds up data acquisition by reducing the amount of imaging needed, while ensuring that RNA molecules move straight down towards the surface, preserving single-cell resolution. We applied EEL on eight entire sagittal sections of the mouse brain and measured the expression patterns of up to 440 genes to reveal complex tissue organisation. Moreover, EEL enabled the study of challenging human samples by removing autofluorescent lipofuscin, so that we could study the spatial transcriptome of the human visual cortex. We provide full hardware specification, all protocols and complete software for instrument control, image processing, data analysis and visualization.
Effect of Triton X-100 on the hydrolysis of sphingomyelin by sphingomyelinase of rat brain (1976)

Mixed dispersions of the nonionic detergent Triton X-100 and sphingomyelin were used as substrate for sphingomyelinase of rat brain. The dependence of the rate of hydrolysis on the concentration of sphingomyelin was measured in two ways: at a fixed concentration of Triton X-100 or at varying concentrations of this detergent, while maintaining a fixed molar ratio of Triton X-100 to sphingomyelin. In either case, the upsilon vs. S curves deviated from the hyperbolic shape predicted by the Michaelis-Menten kinetic theory. These deviations are discussed and interpreted on the basis of the physicochemical properties of the mixed dispersions of detergent and lipid studied in previous papers.
Scalable and expressive medical terminologies. (1996)

The K-Rep system, based on description logic, is used to represent and reason with large and expressive controlled medical terminologies. Expressive concept descriptions incorporate semantically precise definitions composed using logical operators, together with important non-semantic information such as synonyms and codes. Examples are drawn from our experience with K-Rep in modeling the InterMed laboratory terminology and also developing a large clinical terminology now in production use at Kaiser-Permanente. System-level scalability of performance is achieved through an object-oriented database system which efficiently maps persistent memory to virtual memory. Equally important is conceptual scalability-the ability to support collaborative development, organization, and visualization of a substantial terminology as it evolves over time. K-Rep addresses this need by logically completing concept definitions and automatically classifying concepts in a taxonomy via subsumption inferences. The K-Rep system includes a general-purpose GUI environment for terminology development and browsing, a custom interface for formulary term maintenance, a C+2 application program interface, and a distributed client-server mode which provides lightweight clients with efficient run-time access to K-Rep by means of a scripting language.
Design and Application of Basic Amino Acids Displaying Enhanced Hydrophobicity (2003)

Three noncoding basic amino acids, mono-, di-, and trimethyldiaminopropionic acid (mmdap, dmdap, and tmdap), have been synthesized for use in protein design. Covalent modification of a diaminopropionic acid (dap) side chain with an increasing number of methyl moieties results in a family of residues displaying short basic side chains with varying degrees of enhanced hydrophobic character. These residues may be used to introduce charged/polar interactions into the confining hydrophobic interior or interfacial spaces of proteins. As a demonstration of their utility, the ability of these residues to promote interior salt bridge formation at the helix/helix interface of GCN4-p1, a dimeric two-stranded coiled coil, was assessed. Heterodimerization mediated by buried salt bridge formation between a GCN4-based peptide containing either mmdap, dmdap, or tmdap at position 16 and an analogous peptide containing aspartic acid at the same position was studied. Mmdap-derived heterodimers are 0.5 kcal/mol more stable than the corresponding dap-derived heterodimers. This result indicates that the addition of one methyl group to the dap side chain can stabilize the heterodimeric fold. The stabilization can most likely be attributed to a decrease in the desolvation penalty incurred upon folding as well as enhanced van der Waals contacts in the folded state. The addition of three methyl groups to the dap side chain results in heterodimers that are significantly less stable than the corresponding dap-derived heterodimers, suggesting that increased steric bulk is not well accommodated in the interior of this protein. Unexpectedly, the addition of two methyl groups leads to homotrimerization of the dmdap-peptide. The resulting trimer is relatively stable (DeltaG(37)( degrees )(C) degrees = 11.8 kcal/mol) and undergoes cooperative thermal unfolding. The GCN4-p1 system exemplifies how small incremental changes in size and hydrophobicity can alter the folding preferences of a protein. Generally, this versatile suite of residues can be utilized in any protein and offer new options to the protein chemist.
Miniature all-fiber devices based on CO_2 laser microstructuring of tapered fibers (2001)

A focused carbon dioxide laser beam is used to microstructure fibers that have already been narrowed by conventional fiber tapering. We describe three new miniature devices made with this technique: a fused fiber microcoupler with an interaction length of 200 mum, a long-period grating made from a periodic chain of microtapers, and a new type of prolate whispering-gallery mode microcavity.
Binocular Stereopsis and Lane Marker Flow for Vehicle Navigation (1994)

We propose a new approach for vision based longitudinal and lateral vehicle control which makes extensive use of binocular stereopsis. Longitudinal control --- i.e. maintaining a safe, constant distance from the vehicle in front --- is supported by detecting and measuring the distances to leading vehicles using binocular stereo. A known camera geometry with respect to the locally planar road is used to map the images of the road plane in the two camera views into alignment. Any significant residual image disparity then indicates an object not lying in the road plane and hence a potential obstacle. This approach allows us to separate image features into those lying in the road plane, e.g. lane markers, and those due to other objects. The features which lie on the road are stationary in the scene and appear to move only because of the egomotion of the vehicle. Measurements on these features are used for dynamic update of (a) the camera parameters in the presence of camera vibration and changes in road slope (b) the lateral position of the vehicle with respect to the lane markers. In the absence of this separation, image features due to vehicles which happen to lie in the search zone for lane markers would corrupt the estimation of the road boundary contours. This problem has not yet been addressed by any lane marker based vehicle guidance approach, but has to be taken very seriously, since usually one has to cope with crowded traffic scenes where lane markers are often obstructed by vehicles. Lane markers are detected and used for lateral control, i.e. following the road while maintaining a constant lateral distance to the road boundary. For that purpose we model the road and hence the shape of the lane markers as clothoidal curves, the curvatures of which we estimate recursively along the image sequence. These curvature estimates also provide desirable look-ahead information for a smooth ride in the car.
The Problem of Surface Damage in Polyethylene Total Knee Components (1986)

Observations of surface damage on retrieved total knee polyethylene components have been combined with experimental and analytical studies of the contact problem to identify important clinical and design factors. The amount and severity of damage occurring on the articulating surfaces of knee components increases significantly with patient weight and with the length of time the component is implanted. The design variables that affect the amount of damage are component thickness, the conformity of the articulating surfaces, and the type of polyethylene material used. Surface damage will be more severe in thin (less than 4-6 mm) components and in components with relatively flat tibial articulating surfaces. Surface damage is also expected to be more extreme for carbon-reinforced polyethylene components than for components made from plain polyethylene.
Production of hepatitis B virus particles in Hep G2 cells transfected with cloned hepatitis B virus DNA. (1987)

The hepatoblastoma cell line Hep G2 was transfected with a plasmid carrying the gene that confers resistance to G418 and four 5'-3' tandem copies of the hepatitis B virus (HBV) genome positioned such that two dimers of the genomic DNA are 3'-3' with respect to one another. Cells of one clone that grew in the presence of G418 produce high levels of hepatitis B e antigen and of hepatitis B surface antigen. HBV DNA is carried by these cells as chromosomally integrated sequences and episomally as relaxed circular, covalently closed, and incomplete copies of the HBV genome. Viral DNA was detected also in conditioned growth medium at the buoyant densities characteristic for infectious Dane and immature core particles. Finally, HBV-specific components morphologically identical to the 22-nm spherical and filamentous hepatitis B surface antigen particles as well as 42-nm Dane particles were visualized by immunoelectron microscopic analysis. Therefore, we have demonstrated that the Hep G2 cell line can support the assembly and secretion not only of several of the replicative intermediates of HBV DNA but also of Dane-like particles. This in vitro system can now be used to study the life cycle of HBV and the reaction of immunocompetent cells with cells carrying HBV.
Relaxin Ameliorates Fibrosis in Experimental Diabetic Cardiomyopathy (2008)

Fibrosis (extracellular matrix accumulation) is the final end point in diabetic cardiomyopathy. The current study evaluated the therapeutic effects of the antifibrotic hormone relaxin (RLX) in streptozotocin-treated transgenic mRen-2 rats, which undergo pathological and functional features similar to human diabetes. Twelve-week-old hyperglycemic mRen-2 rats, normoglycemic control rats, and animals treated with recombinant human gene-2 (H2) RLX from wk 10-12 were assessed for various measures of left ventricular (LV) fibrosis, hemodynamics, and function, while the mechanism of RLX's actions was also determined. Hyperglycemic mRen-2 rats had increased LV collagen concentration (fibrosis) and gelatinase activity (all P < 0.05 vs. controls) but equivalent levels of interstitial collagenase and tissue inhibitor of metalloproteinase-1 to that measured in control rats. The increased LV fibrosis associated with diabetic animals led to significant alterations in the E/A wave ratio and E-wave deceleration time (both P < 0.05 vs. controls) in the absence of blood pressure changes, reflective of myocardial stiffness and LV diastolic dysfunction. H2-RLX treatment of diabetic rats led to significant decreases in interstitial and total LV collagen deposition (both P < 0.05 vs. diabetic group), resulting in decreased myocardial stiffness and improved LV diastolic function, without affecting nondiabetic animals. The protective effects of H2-RLX in diabetic rats were associated with a reduction in mesenchymal cell differentiation and tissue inhibitor of metalloproteinase-1 expression in addition to a promotion of extracellular matrix-degrading matrix metalloproteinase-13 (all P < 0.05 vs. diabetic group) but were independent of blood pressure regulation. These findings demonstrate that RLX is an antifibrotic with rapid-occurring efficacy and may represent a novel therapy for the treatment of diabetes.
INHIBITION OF HOST-VERSUS-GRAFT AND GRAFT-VERSUS-HOST RESPONSES AFTER SMALL BOWEL TRANSPLANTATION IN RATS BY RAPAMYCIN (1992)

The effect of rapamycin (RAPA) on both host-versus-graft (HVG) and graft-versus-host (GVH) immune responses was examined in small bowel transplant models using strongly histoincompatible donor-recipient combinations. Normal Wistar Furth (WFu; RT-1u) recipients rejected Buffalo (BUF; RT-1b) small bowel allografts within a mean survival time (MST) of 10.5 +/- 0.5 days. Administration of RAPA (0.8 mg/kg) by continuous intravenous infusion for 14 days via an osmotic pump prolonged graft survival to 25.0 +/- 4.6 days (P = 0.01). In a second strain combination, the 12.5 +/- 2.2 day survival of Brown Norway (BN; RT-1n) small bowel allografts in Lewis (RT-1l) recipients was prolonged to 21.6 +/- 2.0 and 28.5 +/- 2.8 days by 14 days of i.v. RAPA at doses of 0.8 and 1.6 mg/kg, respectively. In this model RAPA is five times more effective than cyclosporine, which at 4.0 mg/kg prolongs BN small bowel allografts in Lewis recipients to 21.6 +/- 6.3. To isolate HVG and GVH immune responses, (BN x Lewis)F1 hybrid rats served as the graft donor or host, respectively. In the HVG model, (BN x Lewis)F1 small bowel allografts, which were rejected by normal Lewis recipients at 12.2 +/- 3.6 days, were prolonged to 40.8 +/- 5.8 days (P = 0.001) by RAPA (0.8 mg/kg x 14 days). In the GVH model, the ability of Lewis small bowel allografts to produce severe GVH disease in untreated (BN x Lewis)F1 recipients at 12.3 +/- 2.8 days was delayed to 21.3 +/- 5.2 days by 0.8 mg/kg RAPA (P = 0.025). Thus, RAPA protects small bowel allografts more effectively against HVG than GVH immune responses.
Factor VII Deficiency Caused by a Structural Variant N57D of the First Epidermal Growth Factor Domain (1998)

We have previously described a kindred with factor VII (FVII) deficiency whose members exhibited reduced procoagulant activity relative to FVII antigen concentration. In this report, the molecular genetic basis of the FVII defect has been determined to be a heterozygous substitution of Asp for Asn at position 57 in the first epidermal growth factor (EGF) domain. Recombinant FVII (N57D) cDNA was created by site-directed mutagenesis and transiently expressed in human 293 cells. The transfected cells synthesized an immunoprecipitable protein with an apparent molecular weight of 50 kD. Quantitation of expression by FVII enzyme-linked immunosorbent assay indicated that mutant protein yields were consistently low, typically 10% to 30% of wild-type FVII. FVII (N57D) protein did not accumulate intracellularly, and Northern blot analysis indicated equivalent FVII mRNA levels in 293 cells expressing either wild-type FVII or FVII (N57D). Secreted FVII (N57D) protein did not bind tissue factor, exhibited no procoagulant activity, and failed to bind a conformation-dependent monoclonal antibody specific for the first EGF domain of FVII. Molecular modeling of the first EGF domain of FVII predicted that the N57D amino acid substitution would disrupt tertiary bonding structure. We conclude that the N57D mutation affects folding of the first EGF domain of FVII resulting in decreased cellular secretion of a mutant FVII molecule, which is unable to bind tissue factor and is therefore biologically inactive.
Significant reduction of cathodoluminescent degradation in sulfide-based phosphors (1998)

The degradation of cathodoluminescent (CL) brightness under prolonged electron-beam excitation of phosphors has been identified as one of the outstanding critical issues for flat-panel field-emission displays. In this letter, we have demonstrated that a TaSi2 coating on Y2O2S:Eu3+ phosphors substantially inhibits the cathodoluminescent degradation characteristics without reducing its efficiency. The coating was deposited by pulsed laser deposition of TaSi2 targets onto a fluidized bed containing phosphor particles. Cathodoluminescent degradation experiments conducted at 2 keV and at 150 μA/cm2, showed that the CL brightness decreased by more than 50% after a Coulomb load of 15 C/cm2 on the uncoated material. In contrast, the TaSi2-coated phosphor powders showed much less degradation, with CL brightness only decreasing by approximately 12% after electron irradiation with the same dose.
LogLuv Encoding for Full-Gamut, High-Dynamic Range Images (1998)

Abstract The human eye can accommodate luminance in a single view over a range of about 10,000:1 and is capable of distinguishing about 10,000 colors at a given brightness. By comparison, typical computer monitors have a luminance range less than 100:1 and cover about half of the visible color gamut. Despite this difference, most digital image formats are geared to the capabilities of conventional displays, rather than the characteristics of human vision. In this paper, we propose a compact encoding suitable for the transfer, manipulation, and storage of highdynamic range color images. This format is a replacement for conventional RGB images, and encodes color pixels as log luminance values and eIE (v′, v′) chromaticity coordinates. We have implemented and distributed this encoding as part of the standard TIFF I/O library available by anonymous ftp. After explaining our encoding, we describe its use within TIFF and present some techniques for handling high-dynamic range pixels, and demonstrate with an example image.