gebhart/patrepeval huggingface dataset:
A Method for Individualizing the Prediction of Immunogenicity of Protein Vaccines and Biologic Therapeutics: Individualized T Cell Epitope Measure (iTEM) (2010)

The promise of pharmacogenomics depends on advancing predictive medicine. To address this need in the area of immunology, we developed the individualized T cell epitope measure (iTEM) tool to estimate an individual's T cell response to a protein antigen based on HLA binding predictions. In this study, we validated prospective iTEM predictions using data from in vitro and in vivo studies. We used a mathematical formula that converts DRB1* allele binding predictions generated by EpiMatrix, an epitope-mapping tool, into an allele-specific scoring system. We then demonstrated that iTEM can be used to define an HLA binding threshold above which immune response is likely and below which immune response is likely to be absent. iTEM's predictive power was strongest when the immune response is focused, such as in subunit vaccination and administration of protein therapeutics. iTEM may be a useful tool for clinical trial design and preclinical evaluation of vaccines and protein therapeutics.
17.3: Highly Efficient Fluorescent/Phosphorescent OLED Devices Using Triplet Harvesting (2008)

Abstract We demonstrate efficient white and non‐white hybrid OLED devices operating by a triplet harvesting mechanism to create light. Triplet excited states are generated in a blue fluorescent light‐emitting layer (LEL) and utilized upon their diffusion to the phosphorescent LEL(s). At 1000 cd/m 2 a blue/yellow hybrid OLED device shows external quantum efficiency (EQE) of 13.6%, 3.8 V, 30.1 lm/W, and excellent color characteristics suitable for display application. Performance of non‐white‐emitting hybrids, RGB white, and a tandem hybrid device is discussed. The triplet harvesting mechanism in all hybrid devices was verified by several experimental methods (spectral analysis, time‐resolved electroluminescence (EL), magnetic field effect on EL).
Investigating CD99 Expression in Leukemia Propagating Cells in Childhood T Cell Acute Lymphoblastic Leukemia (2016)

A significant number of children with T-lineage acute lymphoblastic leukemia (T-ALL) fail to respond to therapy and experience early relapse. CD99 has been shown to be overexpressed on T-ALL cells and is considered to be a reliable detector of the disease. However, the relevance of CD99 overexpression in ALL has not been investigated in a functional context. The aim of this study was to investigate the functional capacity of CD99+ cells in childhood ALL and determine the suitability of CD99 as a therapeutic target. Flow cytometric analyses confirmed higher expression of CD99 in ALL blasts (81.5±22.7%) compared to normal hemopoietic stem cells (27.5±21.9%) and T cells (3.1±5.2%, P≤0.004). When ALL cells were sorted and assessed in functional assays, all 4 subpopulations (CD34+/CD99+, CD34+/CD99-, CD34-/CD99+ and CD34-/CD99-) could proliferate in vitro and establish leukemia in NSG mice. Leukemia propagating cell frequencies ranged from 1 in 300 to 1 in 7.4x104 but were highest in the CD34+/CD99- subpopulation. In addition, all four subpopulations had self-renewal ability in secondary NSG mice. Cells in each subpopulation contained patient specific TCR rearrangements and karyotypic changes that were preserved with passage through serial NSG transplants. Despite high levels of CD99 antigen on the majority of blast cells, leukemia initiating capacity in vivo was not restricted to cells that express this protein. Consequently, targeting CD99 alone would not eliminate all T-ALL cells with the ability to maintain the disease. The challenge remains to develop therapeutic strategies that can eliminate all leukemia cells with self-renewal capacity in vivo.
Upregulation of Pleiotrophin Gene Expression in Developing Microvasculature, Macrophages, and Astrocytes after Acute Ischemic Brain Injury (1998)

Pleiotrophin (PTN) is a heparin-binding, 18 kDa secretory protein that functions to induce mitogenesis, angiogenesis, differentiation, and transformation in vitro. PTN gene (Ptn) expression is highly regulated during development and is highest at sites in which mitogenesis, angiogenesis, and differentiation are active. In striking contrast, with the exception of the neuron, the Ptn gene is only minimally expressed in adults. We now demonstrate that Ptn gene expression is strikingly upregulated within 3 d in OX42-positive macrophages, astrocytes, and endothelial cells in areas of developing neovasculature after focal cerebral ischemia in adult rat. Ptn gene expression remains upregulated in these same cells and sites 7 and 14 d after ischemic injury. However, expression of the Ptn gene is significantly decreased in cortical neurons 6 and 24 hr after injury and is undetectable in degenerating neurons at day 3. Neurons in contralateral cortex continue to express Ptn in levels equal to control, uninjured brain. It is suggested that PTN may have a vital role in neovascular formation in postischemic brain and that postischemic brain is an important model in which to analyze sequential gene expression in developing neovasculature. In contrast, Ptn gene expression in injured neurons destined not to recover is strikingly reduced, and potentially its absence may contribute to the failure of the neuron to survive.
Preparation and properties of new lactose‐based surfactants (2001)

Abstract A new group of nonionic saccharide‐based surfactants, N ‐alkanoyl‐ N ‐methyllactitolamines (alkanoyl: decanoyl, lauroyl, myristoyl, palmitoyl, stearoyl), were synthesized and characterized. Surface properties such as critical micelle concentration, standard free energy of adsorption, standard free energy of micellization, surface tension reduction efficiency, effectiveness of surface tension reduction, surface excess concentration, and surface area demand per molecule as well as foaming properties (i.e., foam volume and foam stability), contact angle, antiraicrobial activity, and biodegradability were determined. The selected performance properties were evaluated in relation to commercially available alkyl polyglucosides (Glukopon 600 EC(HH)‐a Henkel product), and oligooxyethylenated decyl (C 10 E 4 ) and dodecyl (E 12 E 5 ) alcohols. The foaming‐stabilizing effect and contact angle suggest that the lactose‐derived surfactants that were studied share some common properties with alkyl polyglucosides that are different from those with an oligooxyethylene grouping. All tested N ‐alkanoyl‐ N ‐methyllactitolamines were practically nontoxic to bacteria and yeasts. These compounds are readily biodegradable in the Closed Bottle test inoculated with activated sludge. N ‐Alkanoyl‐ N ‐methyllactitolamines with lower chain lengths (C 10 –C 14 ) biodegraded at a slightly faster rate. Biological properties showed that this class of compounds fulfills all requirements needed for environmental acceptance.
Methicillin-Resistant, Quinupristin-Dalfopristin-Resistant <i>Staphylococcus aureus</i> with Reduced Sensitivity to Glycopeptides (2001)

Of 3,052 Staphylococcus aureus strains collected by the European SENTRY surveillance study, 35 were found to be nonsusceptible to quinupristin-dalfopristin (MIC of > or =2 mg/liter). These isolates originated from four hospitals in France and one in Spain. In isolates from two Parisian hospitals exhibiting the same SmaI macrorestriction pattern, streptogramin resistance was based on vatA and vgbA. One isolate from a hospital in Lyon and 22 from a hospital in Lille were of the vatB vgaB streptogramin A resistance genotype and possessed ermA and/or ermC. As deduced from the loss of either streptogramin A or streptogramin B resistance determinants in particular isolates, resistance to quinupristin-dalfopristin requires mechanisms conferring resistance to both compounds. The SmaI macrorestriction patterns of strains from hospitals in Lille and Lyon were different; however, similarity analysis suggested a relatedness of 20 methicillin-resistant S. aureus strains from the Lille hospital, a finding confirmed by PCR typing based on three different genomic polymorphisms. These groups of isolates were found to be hetero-glycopeptide-intermediate susceptible S. aureus. Information about the failure of glycopeptide chemotherapy has not been available.
Chemoenzymatic synthesis of discotic liquid crystals (1992)

Abstract Acylations at the 6-position of alkyl glycosides were obtained using the esterification potential of lipases. Thus, sugars with two alkyl chains result showing columnar discotic phases. The correlation between the configuration of the sugar moieties and the different clearing points can be understood on the basis of simple stereochemical assumptions.
A CMOS UWB On-Chip Antenna With a MIM Capacitor Loading AMC (2012)

A novel ultrawideband (UWB) on-chip antenna with metal-insulator-metal (MIM) capacitor loading artificial magnetic conductor (AMC) is presented using CMOS process. An equivalent resonant circuit model is proposed for understanding the physical insight of operating modes of the MIM-AMC. Based on the simulated results, comparisons of the bandwidth, transmission gain, and size of several different on-chip antennas are made. The effects of the lossy vias, the size and number of AMC patches, and the MIM capacitance on the performance of the antenna are analyzed. Within the resonant frequency band, a balanced optimized antenna is concluded based on the analysis, of which the radiation pattern is simulated to better understand the operating modes of the on-chip antenna. This antenna is fabricated in 0.18-μm CMOS with a size of 3.56 × 0.5 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ; a -10-dB S11 impedance bandwidth of 22.5-33.8 GHz; and a maximum -41.8-dB transmission gain at 25 GHz, which is measured with 5-mm interchip distance. The antenna can be used in UWB wireless inter-/intraconnects or a wireless chip area network.
Promising future biomarkers for anti-EGFR monoclonal antibody in colorectal cancer (2010)

Molecular targeted therapy has been a promising treatment for colorectal cancer today,which includes anti-EGFR(epithelial growth factor receptor) monoclonal antibody.How to select beneficial patients for this therapy,so as to avoid unnecessary toxicity and invalid expense,is a hotspot of research.The object of the review is to introduce some biomarkers which may predict efficacy of the anti-EGFR monoclonal antibody therapy.
Interpretation of Molecule Conformations from Drawn Diagrams (2008)

In chemistry, molecules are drawn on paper and chalkboards as diagrams consisting of lines, letters, and symbols which represent not only the atoms and bonds in the molecules but concisely encode cues to the 3D geometry of the molecules. Recent efforts into pen-based input methods for chemistry software have made progress at allowing chemists to input 2D diagrams of molecules into a computer simply by drawing them on a digitizer tablet. However, the task of interpreting these parsed sketches into proper 3D models has been largely unsolved due to the difficulty in making the models satisfy both the natural properties of molecule structure and the geometric cues made explicit in the drawing. 
This dissertation presents a set of techniques developed to solve this model construction problem within the context of an educational application for chemistry students. Our primary contribution is a framework for combining molecular structure knowledge and molecule diagram understanding via augmenting molecular mechanics equations to include drawing-based penalty terms. Additionally, we present an algorithm for generating molecule models from drawn diagrams which leverages domain-specific and diagram-driven heuristics. These heuristics make our process fast and accurate enough for molecule diagram drawing to be used as an interactive technique for model construction on modern Tablet PC computers.
Immunosuppressant PG490 (Triptolide) Inhibits T-cell Interleukin-2 Expression at the Level of Purine-box/Nuclear Factor of Activated T-cells and NF-κB Transcriptional Activation (1999)

PG490 (triptolide) is a diterpene triepoxide with potent immunosuppressive and antiinflammatory properties. PG490 inhibits interleukin(IL)-2 expression by normal human peripheral blood lymphocytes stimulated with phorbol 12-myristate 13-acetate (PMA) and antibody to CD3 (IC50 of 10 ng/ml), and with PMA and ionomycin (Iono, IC50 of 40 ng/ml). In Jurkat T-cells, PG490 inhibits PMA/Iono-stimulated IL-2 transcription. PG490 inhibits the induction of DNA binding activity at the purine-box/antigen receptor response element (ARRE)/nuclear factor of activated T-cells (NF-AT) target sequence but not at the NF-kappaB site. PG490 can completely inhibit transcriptional activation at the purine-box/ARRE/NF-AT and NF-kappaB target DNA sequences triggered by all stimuli examined (PMA, PMA/Iono, tumor necrosis factor-alpha). PG490 also inhibits PMA-stimulated activation of a chimeric transcription factor in which the C-terminal TA1 transactivation domain of NF-kappaB p65 is fused to the DNA binding domain of GAL4. In 16HBE human bronchial epithelial cells, IL-8 expression is regulated predominantly by NF-kappaB, and PG490 but not cyclosporin A can completely inhibit expression of IL-8. The mechanism of PG490 inhibition of cytokine gene expression differs from cyclosporin A and involves nuclear inhibition of transcriptional activation of NF-kappaB and the purine-box regulator operating at the ARRE/NF-AT site at a step after specific DNA binding.
Impaired Conditioned Fear and Enhanced Long-Term Potentiation in<i>Fmr2</i>Knock-Out Mice (2002)

FRAXE mental retardation results from expansion and methylation of a CCG trinucleotide repeat located in exon 1 of the X-linked FMR2 gene, which results in transcriptional silencing. The product of FMR2 is a member of a family of proteins rich in serine and proline, members of which have been associated with transcriptional activation. We have developed a murine Fmr2 gene knock-out model by replacing a fragment containing parts of exon 1 and intron 1 with the Escherichia coli lacZ gene, placing lacZ under control of the Fmr2 promoter. Expression of lacZ in the knock-out animals indicates that Fmr2 is expressed in several tissues, including brain, bone, cartilage, hair follicles, lung, tongue, tendons, salivary glands, and major blood vessels. In the CNS, Fmr2 expression begins at the time that cells in the neuroepithelium differentiate into neuroblasts. Mice lacking Fmr2 showed a delay-dependent conditioned fear impairment. Long-term potentiation (LTP) was found to be enhanced in hippocampal slices of Fmr2 knock-out compared with wild-type littermates. To our knowledge, this mouse knock-out is the first example of an animal model of human mental retardation with impaired learning and memory performance and increased LTP. Thus, although a number of studies have suggested that diminished LTP is associated with memory impairment, our data suggest that increased LTP may be a mechanism that leads to impaired cognitive processing as well.
Neural network optimization, components, and design selection (1990)

Neural Networks are part of a revived technology which has received a lot of hype in recent years. As is apt to happen in any hyped technology, jargon and predictions make its assimilation and application difficult. Nevertheless, Neural Networks have found use in a number of areas, working on non-trivial and noncontrived problems. For example, one net has been trained to "read", translating English text into phoneme sequences. Other applications of Neural Networks include data base manipulation and the solving of muting and classification types of optimization problems. Neural Networks are constructed from neurons, which in electronics or software attempt to model but are not constrained by the real thing, i.e., neurons in our gray matter. Neurons are simple processing units connected to many other neurons over pathways which modify the incoming signals. A single synthetic neuron typically sums its weighted inputs, runs this sum through a non-linear function, and produces an output. In the brain, neurons are connected in a complex topology: in hardware/software the topology is typically much simpler, with neurons lying side by side, forming layers of neurons which connect to the layer of neurons which receive their outputs. This simplistic model is much easier to construct than the real thing, and yet can solve real problems. The information in a network, or its "memory", is completely contained in the weights on the connections from one neuron to another. Establishing these weights is called "training" the network. Some networks are trained by design -- once constructed no further learning takes place. Other types of networks require iterative training once wired up, but are not trainable once taught Still other types of networks can continue to learn after initial construction. The main benefit to using Neural Networks is their ability to work with conflicting or incomplete ("fuzzy") data sets. This ability and its usefulness will become evident in the following discussion.
Optical intensity modulator with three−dimensional waveguide (1975)

A LiTaO3 optical waveguide modulator, in which a laser beam is confined in both transverse dimensions, has been fabricated. The three−dimensional waveguiding operation was achieved by using an ion−etched thin core slab and a slit metal cladding. Waveguide porperties for 0.633− and 1.15−μm laser beams and dc and rf modulation performance for a 1.15−μm beam are described.
CT-guided bone biopsy performed by means of a coaxial biopsy system with an eccentric drill. (1993)

Thirty-seven consecutive bone biopsies guided with computed tomography were performed in 32 patients by use of three different techniques to penetrate cortical bone and gain access to the lesion. The following instruments were used: a thin bone biopsy needle (12 biopsies), a conventional drill with an outer cannula (six biopsies), and a coaxial biopsy system that consists of a drill with an eccentric tip and an outer cannula (19 biopsies). This eccentric drill makes a hole in the bone larger than the diameter of the cannula and thereby makes it easy to advance the cannula over the drill until the cannula is anchored in the bone. One can then obtain multiple samples through the cannula. The thin bone biopsy needle could not penetrate thick (8 mm thick) cortical bone. The outer cannula was not anchored in the bone when the conventional drill was used. In 16 biopsies, the new coaxial biopsy system penetrated cortical bone with a thickness of 1-8 mm and was anchored there, and lesion samples were obtained through the anchored cannula.
The Use of Telemedicine in the Management of Diabetes-Related Foot Ulceration: A Pilot Study (2004)

These data appear to support the effectiveness of real-time interactive telemedicine consultation in the management of diabetes-related forefoot ulceration.
Host stromal versican is essential for cancer‐associated fibroblast function to inhibit cancer growth (2015)

The stroma provides a microenvironment that regulates tumor cell behavior. The extracellular matrix (ECM) has long been recognized to be important in tumor cell behavior, and previous studies have revealed the impact of individual matrix molecules on tumor progression. Although several reports have highlighted some central roles of tumor cell-expressed versican, the role of host stromal versican is not yet understood. In this study, we demonstrate that versican is an important molecule in the functional ECM structure and maintaining cancer-associated fibroblasts, using versican-negative QRsP11 fibrosarcoma cells. By their subcutaneous injection with cre-expressing adenoviruses to versican-floxed mice, we demonstrate that loss of host stromal versican facilitates tumor cell proliferation, and following angiogenesis, decreases cancer-associated fibroblasts, diminishes collagen fibers and alters hyaluronan distribution, concomitant with upregulation of hyaluronan, TGFβ and VEGF-mediated signaling. When the versican V3 variant consisting of G1 and G3 domains was expressed in tumor cells, it was integrated into the ECM, regained collagen fibers and cancer-associated fibroblasts and resulted in successful recovery of tumor growth inhibition, indicating that whatever cells produce, the G1 and G3 domains are adequate for versican function. Collectively, our results indicate a dynamic function of versican in the ECM that regulates tumor cell behavior. A greater understanding of the regulation of versican expression may contribute to the development of cancer therapies.
Effects of Diabetes Mellitus on Lactation in the Rat (1993)

Diabetes mellitus adversely affects the process of lactation. Although insulin administration restores lactation, the manner by which it does so is unknown. The goals of this study were to determine which phase of lactation, milk synthesis/supply (MS), and/or milk release (MR) was affected. Inasmuch as insulin, corticosterone, and prolactin, among other hormones, are involved in milk synthesis in vitro, this study investigated their probable roles in the suppression of lactation in diabetes in vivo. Diabetes was induced in rats on Day 3 postpartum with streptozotocin (50-60 mg/kg, ip). Milk synthesis/supply and milk release were indirectly monitored using body weight gain of pups during a timed-feeding period on postnatal Days 8/9 and 13/14. Plasma corticosterone, insulin, C-peptide, and prolactin were measured by radioimmunoassay in control, diabetic, and insulin-replaced diabetic animals. Insulin replacement was provided by means of an osmotic minipump implanted subcutaneously in the nape of the neck. In addition, several parameters of maternal behavior were monitored in order to determine whether diabetes affected maternal behavior and, therefore, whether such changes played a role in the alterations of lactation observed during diabetes. Diabetes significantly suppressed MS and MR. However, the decrease in MR, which was restored after partial insulin replacement, was a reflection of the reduced MS. There were no significant differences between the parameters of maternal behavior monitored in control and diabetic animals. Blood glucose in diabetic dams was significantly increased over that of controls. Although the levels of plasma glucose in the insulin-replaced groups were significantly lower than those of their uncontrolled diabetic counterparts, they also remained higher than that of controls. Corticosterone was not significantly altered after induction of diabetes. Insulin and C-peptide levels were significantly reduced in the uncontrolled diabetics; however, insulin levels were corrected in the insulin-replaced groups. Serum levels of prolactin decreased in all diabetic groups and insulin failed to restore these levels to those of control animals. In conclusion, it appears that diabetes decreases lactation through a suppressive effect on MS rather than on MR, with insulin replacement correcting for such deficiency. In addition, despite the lactogenic importance of glucocorticoids, prolactin and insulin demonstrated in vitro, lactation in vivo can be corrected without returning the levels of all three hormones to normal. The importance of another factor(s), such as normoglycemia, as essential to the observed defects, needs to be investigated.