gebhart/patrepeval huggingface dataset:
Alloreactive 2C T cells recognize a self peptide in the context of the mutant Kbm3 molecule (1995)

Previous studies hav shown that 2C T cells have dual specificity for Ld and Kbm3 alloantigens and are positively selected in the context of Kb. Analysis of Kbm3-eluted peptides reveals a single HPLC fraction that is a central component of the Kbm3 allodeterminant. Peptides with biologic and biochemical properties indistinguishable from those of the Kbm3 allopeptide were also isolated from Kb and Kbm8, despite the fact that cells bearing these class I molecules are not efficient targets for 2C T cells. The allopeptide was isolated and compared with p2Ca, the Ld allopeptide recognized by 2C T cells in the context of Ld. The Kbm3 allopeptide was found to be biochemically and functionally different from p2Ca. Therefore, the 2C TCR has dual specificity for two different peptides presented in the context of two structurally distinct class I molecules. The possibility of a common peptide being bound by Kb, Kbm3, and Kbm8 suggests that the peptide defined as an allodeterminant in the context of Kbm3 may also function in the positive selection of 2C T cells when presented in the context of Kb and Kbm8 during thymic development. In support of this view, the allopeptide was also found in Kb and Kbm8 thymic peptide eluates.
Development, testing and application of a numerical simulator for predicting miscible flood performance (1971)

Variants of a 3-phase, 3-dimensional, compressible, numerical reservoir simulator have been developed which are capable of modeling the essential features of miscible displacement, while leaving the fine structure of unstable miscible flow unresolved. In the 3-component version, wetting (water) and nonwetting (hydrocarbon) phases are considered with 2-component miscible flow in the hydrocarbon phase. A mixing parameter model is used to represent viscous behavior of the oil and solvent as modified by dispersion at the flood front. Using the 4-component version, slug as well as continuous solvent injection may be examined. The efficiency of the 3-component simulator is demonstrated by comparison of predicted performance with experimental results from both linear and areal displacements in laboratory models. Predictions also are compared with reported results of miscible displacements conducted in a shallow, water-bearing sand. The application of the simulator is demonstrated by its use in the evaluation of alternate flooding configurations and operational policies for a field example. (21 refs.)
Fabrication of microfluidic systems in poly(dimethylsiloxane) (2000)

Microfluidic devices are finding increasing application as analytical systems, biomedical devices, tools for chemistry and biochemistry, and systems for fundamental research. Conventional methods of fabricating microfluidic devices have centered on etching in glass and silicon. Fabrication of microfluidic devices in poly(dimethylsiloxane) (PDMS) by soft lithography provides faster, less expensive routes than these conventional methods to devices that handle aqueous solutions. These soft-lithographic methods are based on rapid prototyping and replica molding and are more accessible to chemists and biologists working under benchtop conditions than are the microelectronics-derived methods because, in soft lithography, devices do not need to be fabricated in a cleanroom. This paper describes devices fabricated in PDMS for separations, patterning of biological and nonbiological material, and components for integrated systems.
Impact of Atrial Fibrillation on the Risk of Death (1998)

In subjects from the original cohort of the Framingham Heart Study, AF was associated with a 1.5- to 1.9-fold mortality risk after adjustment for the preexisting cardiovascular conditions with which AF was related. The decreased survival seen with AF was present in men and women and across a wide range of ages.
The Effects of Low-Level Energy Density Nd:YAG Irradiation on Calculus Removal (1992)

This study assessed the effects of using an Nd:YAG laser to remove dental calculus from root surfaces. Human extracted molar teeth, with extensive calculus attachment to root surfaces, were irradiated with an Nd:YAG beam [power densities (PD) = 1.09 W/cm 2 and 2.19 W/cm 2; energy densities (ED) = 49.2 J/cm 2 and 98.4 J/cm 2]. An additional group of teeth was instrumented with a Gracey 11/12 curette. A separate group of untreated specimens served as controls. Specimens were examined under scanning electron microscopy and rated as to the degree of calculus detachment from root surfaces. Nd:YAG irradiation at low ED did not appreciably affect the integrity of the calculus root surface attachment. The higher-ED Nd:YAG irradiation appeared to mimic the type of calculus removal depicted with conventional hand instrumentation. Root surface damage from both laser ablations was negligible.
Cartilage Tissue Engineering (2007)

The clinical goal of tissue engineering is to restore, repair, or replace damaged tissues in the body. Significant advances have been made in recent years using stem cells as a cell source for cartilage tissue engineering and reconstructive surgery applications. Embryonic stem cells have demonstrated the potential to self-renew and differentiate into a wide range of tissues including the chondrogenic lineage, depending on culture conditions. Three-dimensional scaffolds play an important role in tissue regeneration by providing attachment sites as well as bioactive signals for cells to grow and differentiate into specific lineages. The precise microenvironments required for optimal expansion or differentiation of stem cells are only beginning to emerge now, and the controlled differentiation of embryonic stem cells in tissue engineering remains a relatively unexplored field. Hydrogels are a class of polymer-based biomaterials that have been extensively utilized in tissue engineering as scaffolds. We have demonstrated that embryonic stem cells encapsulated within poly(ethylene glycol)-based (PEGDA) photopolymerizing hydrogels and cultured in an appropriate growth factor and medium conditions undergo chondrogenic differentiation with extracellular matrix deposition characteristic of neocartilage (Hwang et al., Stem Cells 24, 284-291). Another hydrogel that has been widely used for encapsulating chondrocytes in cartilage tissue engineering is alginate. This hydrogel also has potential for tissue engineering applications using stem cells. Here, we describe the three-dimensional culture of embryonic stem cell-derived embryoid bodies in hydrogels and their differentiation toward chondrogenic lineage in chemically defined chondrogenic medium in the presence of TGF-beta1 (chondrogenic inducing conditions). We also discuss various tools and assays used for characterizing the tissue-engineered cartilage.
5-Fluorouracil enhances azidothymidine cytotoxicity: in vitro, in vivo, and biochemical studies. (1990)

Preliminary in vitro studies suggest that the combination of 5-fluorouracil (FUra) and 3'-azido-3'-deoxythymidine (AZT) is more cytotoxic than either agent alone. Therefore, a biochemical and therapeutic evaluation of this combination was initiated. Quantitation of the cytotoxicity of FUra plus AZT against the growth of HCT-8 cells in vitro revealed that 1 microM FUra (approximately 10% inhibitory concentration) increased the cytotoxicity of AZT and decreased its 50% inhibitory concentration by 60%. Similarly, incubating HCT-8 cells in 5 microM AZT (approximately 10% inhibitory concentration) decreased the 50% inhibitory concentration of FUra by over 50%. Biochemical analysis indicated that AZT did not affect FUra-induced inhibition of thymidylate synthase or [3H]-FUra incorporation into nucleic acids. In contrast, incubation in 5 microM FUra increased the incorporation of [3H]-AZT (5 microM) into the nucleic acid fraction of these cells by 52% (P less than 0.05). Therapeutic evaluation of this combination in athymic (nude) mice bearing HCT-8 xenographs revealed that, while weekly FUra (85 mg/kg) or AZT (600 mg/kg) exerts minimal antineoplastic activity (after 4 courses, treatment/control = 0.81 and 0.70, respectively), their combination, at the same doses, inhibited tumor growth by nearly 70% (P less than 0.01 versus FUra alone). FUra-related host toxicity was not increased by the addition of AZT. Higher doses of FUra alone were not more effective than FUra plus AZT. In vivo, AZT did not affect the incorporation of [3H]-FUra into the nucleic acid fraction of various murine tissues, including HCT-8 xenografts. FUra, however, increased [3H]-AZT incorporation into nucleic acids in a tissue-specific manner. In the presence of FUra, the incorporation of [3H]-AZT in spleen, liver, and gut increased 40, 21, and 4%, respectively, while in HCT-8 xenografts [3H]-AZT incorporation increased more than 2-fold. Analysis of the activities of selected enzymes involved in pyrimidine metabolism suggests that this tissue-specific effect may be related to the pyrimidine salvage capacity of these tissues. These findings are described in light of their potential impact on human colon cancer chemotherapy.
Efficient exciplex emitting organic electroluminescent devices (2002)

Organic electroluminescent (EL) single-layer (SL) and double-layer (DL) light-emitting diodes were fabricated based on 4,4′,4″-tris[3-methylphenyl(phenyl)amino] triphenylamine (m-MTDATA) and 2-(biphenyl-4-yl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole (PBD) molecules incorporated in bisphenol-A-polycarbonate (PC) matrix. The external EL quantum efficiency of the dominating exciplex emission of the indium tin oxide (ITO)/m-MTDATA:PBD:PC/Ca SL structure is ≅0.4% photon/electron and that from the ITO/m-MTDATA:PC/PBD/Ca DL device exceeds 1% photon/electron. The operating voltage of the DL device at maximum efficiency is 4.8 V and the onset voltage of the EL is as low as 2.0 V. The photoluminesce quantum efficiency of the exciplex is greater than 17%. The high exciplex emission-based EL yield from the DL device is attributed to the narrow recombination zone imposed by the high energy barriers for the electron and hole transfer at the (m-MTDATA:PC)/PBD interface.
Iron deficiency intravenous substitution in a Swiss academic primary care division: analysis of practices (2016)

There was no clear overutilization of IV iron substitution. However, several steps of the iron deficiency management were not optimally documented, suggesting shortcuts in clinical reasoning.
Can Antibiotic Resistance be Controlled? (1994)

Several reports in this issue of the Journal deal with the potentially disastrous situation of antibiotic resistance13. The current antibiotic-resistance crisis differs from those of the past because several different organisms are involved and because there are no immediate solutions on the horizon. The consequences of resistance include higher mortality and greater morbidity, such as neurologic damage in children in whom meningitis is caused by a pneumococcus not recognized as resistant or for which alternatives to first-line antibiotic therapy are less effective. Infections with organisms resistant to antimicrobial agents lead to longer hospitalizations and greater expense,4 as exemplified . . .
Differential dependence of CD4 + CD25 + regulatory and natural killer-like T cells on signals leading to NF-κB activation (2004)

Natural killer-like (NK) T, regulatory T (TR), and memory type T cells display surface phenotypes reminiscent of activated T cells. Previously, we reported that the generation of TR cells and, to a lesser extent, of memory type T cells, depends on IkappaB kinase 2. Here, we show that T cell-specific ablation of IkappaB kinase 2, in addition, completely precludes NKT cell development. T cell antigen receptor (TCR)-induced signals to activate NF-kappaB are essential for mature T cell activation, leading us to hypothesize that this pathway could play an important role in the generation of the antigen-driven T cell subsets comprising TR, memory type T, and NKT cells. TCR-mediated NF-kappaB activation critically depends on Bcl10 and PKCtheta. By using mice deficient for these proteins, we demonstrate that the generation of TR and, to a lesser extent, of memory type T cells, depends on Bcl10 and PKCtheta, and therefore, most likely on NF-kappaB activation initiated by TCR engagement. NKT cells, on the other hand, require PKCtheta for thymic development, whereas absence of Bcl10 leads primarily to the reduction of peripheral NKT cell numbers.
Corneal blindness: a global perspective. (2001)

Diseases affecting the cornea are a major cause of blindness worldwide, second only to cataract in overall importance. The epidemiology of corneal blindness is complicated and encompasses a wide variety of infectious and inflammatory eye diseses that cause corneal scarring, which ultimately leads to functional blindness. In addition, the prevalence of corneal disease varies from country to country and even from one population to another. While cataract is responsible for nearly 20 million of the 45 million blind people in the world, the next major cause is trachoma which blinds 4.9 million individuals, mainly as a result of corneal scarring and vascularization. Ocular trauma and corneal ulceration are significant causes of corneal blindness that are often underreported but may be responsible for 1.5-2.0 million new cases of monocular blindness every year. Causes of childhood blindness (about 1.5 million worldwide with 5 million visually disabled) include xerophthalmia (350,000 cases annually), ophthalmia neonatorum, and less frequently seen ocular diseases such as herpes simplex virus infections and vernal keratoconjunctivitis. Even though the control of onchocerciasis and leprosy are public health success stories, these diseases are still significant causes of blindness--affecting a quarter of a million individuals each. Traditional eye medicines have also been implicated as a major risk factor in the current epidemic of corneal ulceration in developing countries. Because of the difficulty of treating corneal blindness once it has occurred, public health prevention programmes are the most cost-effective means of decreasing the global burden of corneal blindness.
Face Alignment at 3000 FPS via Regressing Local Binary Features (2014)

This paper presents a highly efficient, very accurate regression approach for face alignment. Our approach has two novel components: a set of local binary features, and a locality principle for learning those features. The locality principle guides us to learn a set of highly discriminative local binary features for each facial landmark independently. The obtained local binary features are used to jointly learn a linear regression for the final output. Our approach achieves the state-of-the-art results when tested on the current most challenging benchmarks. Furthermore, because extracting and regressing local binary features is computationally very cheap, our system is much faster than previous methods. It achieves over 3, 000 fps on a desktop or 300 fps on a mobile phone for locating a few dozens of landmarks.
Increase of the DNA strand assimilation activity of recA protein by removal of the C terminus and structure-function studies of the resulting protein fragment. (1988)

A proteolytic fragment of recA protein, missing about 15% of the protein at the C terminus, was found to promote assimilation of homologous single-stranded DNA into duplex DNA more efficiently than intact recA protein. This difference was not found if Escherichia coli single-stranded DNA binding protein was present. The ATPase activity of both intact recA protein and the fragment was identical. The difference in strand assimilation activity cannot be due to differences in single-stranded DNA affinity, since both the fragment and intact proteins bind to single-stranded DNA with nearly identical affinities. However, the fragment was found to bind double-stranded DNA more tightly and to aggregate more extensively than recA protein; both of these properties may be important in strand assimilation. Aggregation of the fragment was extensive in the presence of duplex DNA under the same condition where recA protein did not aggregate. The double-stranded DNA binding of both recA protein and the fragment responds to nucleotide cofactors in the same manner as single-stranded DNA binding, i.e. ADP weakens and ATP gamma S strengthens the association. The missing C-terminal region of recA protein includes a very acidic region that is homologous to other single-stranded DNA binding proteins and which has been implicated in DNA binding modulation. This C-terminal region may serve a similar function in recA protein, possibly inhibiting double-stranded DNA invasion. The possible role of the enhanced double-stranded DNA affinity of the fragment protein in the mechanism of strand assimilation is discussed.
Rapid Detection of Enterohemorrhagic Escherichia coli by Real-Time PCR with Fluorescent Hybridization Probes (2001)

In this report, we present a PCR protocol for rapid identification of enterohemorrhagic Escherichia coli on a LightCycler instrument. In a multiplex assay, the genes encoding Shiga toxin 1 and Shiga toxin 2 are detected in a single reaction capillary. A complete analysis of up to 32 samples takes about 45 min.
Engagement of CD44 modulates cyclooxygenase induction, VEGF generation, and cell proliferation in human vascular endothelial cells (2005)

CD44 is a receptor for hyaluronic acid and is found on the surface of hematopoetic cells and in mesenchymal tissue. It is also expressed on endothelial cells (EC). Cyclooxygenase (COX) is the rate-limiting enzyme in the production of prostaglandins in EC. Here we show that engagement of CD44 with signaling monoclonal antibodies (mAbs) or its natural ligand hyaluronic acid induces COX-2 and prostacyclin (PGI2) formation in human EC. This induction was blocked by mAbs that have been shown to inhibit CD44-mediated intracellular signaling. COX-1 induction was not observed after CD44 ligation. CD44-stimulated COX-2 activation/PGI2 production was accompanied by the production of the potent endothelial mitogen, vascular endothelial growth factor (VEGF) and was inhibited by a neutralizing VEGF antibody. Moreover, this COX-2 induction was also associated with an increase in EC proliferation that was inhibited by the blocking anti-CD44 mAbs and a COX-2-specific inhibitor. This is the first study to show that engagement of CD44 with mAbs or its natural ligand induces COX-2, generates VEGF, and thus leads to an increase in EC proliferation. Results from this study may have important and widespread implications for the development of novel therapeutic agents for modulating blood vessel growth during ischemic heart disease, during inflammation, or around solid tumors.
Long‐term effect of FTY720 on lymphocyte count and islet allograft survival in mice (2007)

This study was performed to observe the long-term effect of FTY720 on lymphocyte count change and islet allograft survival. Diabetic C57BL/6 mice were given FTY720 (group 1, 0.5 mg/kg/day; group 2, 1.0 mg/kg/day) or its vehicle (group 3, controls) after transplantation. Median graft survival time was prolonged in a dose-dependent manner (group 1, 84.5 days; group 2, >100 days, and group 3, 10 days, P < 0.01). Peripheral blood lymphocytes in groups 1 and 2 decreased to 23.81% and 12.59% compared with control group after FTY720 treatment. Lymphocytes from mesenteric lymph nodes and axillary nodes in groups 1 and 2 significantly increased on day 5, but decreased on day 14. Lymphocyte infiltration to the graft site was attenuated in groups 1 and 2. In conclusion, continuous FTY720 administration can induce and maintain lymphopenia, and inhibit lymphocytes from infiltrating the graft site so as to prolong islet allograft survival in mice.
Molecular Design of Anticancer Drug Leads Based on Three-Dimensional Quantitative Structure–Activity Relationship (2011)

Heat shock protein 90 (Hsp90) takes part in the developments of several cancers. Novobiocin, a typically C-terminal inhibitor for Hsp90, will probably used as an important anticancer drug in the future. In this work, we explored the valuable information and designed new novobiocin derivatives based on a three-dimensional quantitative structure-activity relationship (3D QSAR). The comparative molecular field analysis and comparative molecular similarity indices analysis models with high predictive capability were established, and their reliabilities are supported by the statistical parameters. Based on the several important influence factors obtained from these models, six new novobiocin derivatives with higher inhibitory activities were designed and confirmed by the molecular simulation with our models, which provide the potential anticancer drug leads for further research.
Ousting the "ouch factor" in drug delivery. (2007)

People just don’t like needles. But needles are what they’ll almost certainly get if they are candidates for a biologic therapy, as most are administered by intravenous infusion or subcutaneous injection.

Eliminating the “ouch” makes for a monster market opportunity, especially as more and more macromolecule biologics come to market. But it’s not just fear of needles that drives the search for new drug-delivery technologies. Infusion is inconvenient, time consuming, labor intensive, and costly; self-administered injection with a syringe depends on proper technique, accurate dosing, and is inconvenient at best. Ultimately, all of these factors adversely affect a patient’s adherence to therapy.

The most promising alternatives to infusion and syringe injection of biologic drugs appear to be pulmonary, “needle-free,” pen injection, and oral delivery methods. Other drug delivery technologies, such as depot injection and implants, still rely on needle injection or surgical implantation, but greatly reduce injection frequency (as with injectable extended-release technologies) or eliminate injection entirely (in the case of implants).
Automated refinement of protein models (1993)

An automated refinement procedure (ARP) for protein models is proposed, and its convergence properties discussed. It is comparable to the iterative least-squares minimization/difference Fourier synthesis approach for small molecules. ARP has been successfully applied to three proteins, and for two of them resulted in models very similar to those obtained by conventional least-squares refinement and rebuilding with FRODO. In real time ARP is about ten times faster than conventional refinement. In its present form ARP requires high (2.0 A or better) resolution data, which should be of high quality and a starting protein model having about 75% of the atoms in roughly the correct position. For the third protein at 2.4 A resolution, ARP was significantly less powerful but nevertheless gave definite improvement, in the density map at least.
Preparation of lotus-leaf-like polystyrene micro- and nanostructure films and its blood compatibility (2009)

The lotus-leaf-like polystyrene (PS) micro- and nanostructure film was prepared and characterised. This film reveals superhydrophobicity and good blood compatibility. The realization of this hierarchical PS nanostructure film could be important for further understanding non-wettability of biological surfaces with micro- and nanostructure and application in biomedical devices.