gebhart/patrepeval huggingface dataset:
Supramolecular control of the photochemistry of stilbenes by cyclodextrins (1997)

Upon UV irradiation in the presence of β-cyclodextrin, (E)-4,4′-bis(dimethylammoniomethyl)stilbene is transformed to the (Z)-isomer, but in the presence of γ-cyclodextrin only the [2 + 2]-cycloaddition products are obtained; the products are a molecular imprint of the cavity of the cyclodextrin.
Enhanced Activation of T Cells by Dendritic Cells Engineered to Hyperexpress a Triad of Costimulatory Molecules (2000)

The ability of dendritic cells to activate both naive and effector T cells in vitro and in vivo can be enhanced with the use of poxvirus vectors that potentiate the hyperexpression of a triad of costimulatory molecules. Use of either rF-TRICOM or rV-TRICOM vectors significantly improved the efficacy of dendritic cells in priming specific immune responses. These studies have implications in vaccine strategies for both cancer and infectious diseases.
X-Ray Photoelectron Spectroscopy for the Investigation of Polymer Surfaces (1981)

Since the binding energies of electrons in core levels are characteristic of a particular element, X-ray photoelectron spectroscopy (XPS or ESCA) in its simplest form can be employed to produce an elemental analysis of a polymer surface. However a more detailed consideration of the information levels available from XPS has led to more comprehensive structural determinations for polymers, in terms of both the structural features present at the surface, and how the outermost few layers of the material differ from the subsurface and bulk sample. In this article a description of the application of XPS to the investigation of polymer surfaces is presented with the aid of some current examples. An emphasis is placed on the measurement of absolute and relative binding energies and, absolute and relative signal intensities, which is often sufficient to characterize a given polymer surface. For certain exceptions however it is also necessary to consider the
Color and luminance information in natural scenes (1998)

The spatial filtering applied by the human visual system appears to be low pass for chromatic stimuli and band pass for luminance stimuli. Here we explore whether this observed difference in contrast sensitivity reflects a real difference in the components of chrominance and luminance in natural scenes. For this purpose a digital set of 29 hyperspectral images of natural scenes was acquired and its spatial frequency content analyzed in terms of chrominance and luminance defined according to existing models of the human cone responses and visual signal processing. The statistical 1/f amplitude spatial-frequency distribution is confirmed for a variety of chromatic conditions across the visible spectrum. Our analysis suggests that natural scenes are relatively rich in high-spatial-frequency chrominance information that does not appear to be transmitted by the human visual system. This result is unlikely to have arisen from errors in the original measurements. Several reasons may combine to explain a failure to transmit high-spatial-frequency chrominance: (a) its minor importance for primate visual tasks, (b) its removal by filtering applied to compensate for chromatic aberration of the eye's optics, and (c) a biological bottleneck blocking its transmission. In addition, we graphically compare the ratios of luminance to chrominance measured by our hyperspectral camera and those measured psychophysically over an equivalent spatial-frequency range.
MHC Multimer-Guided and Cell Culture-Independent Isolation of Functional T Cell Receptors from Single Cells Facilitates TCR Identification for Immunotherapy (2013)

Adoptive therapy using T cells redirected to target tumor- or infection-associated antigens is a promising strategy that has curative potential and broad applicability. In order to accelerate the screening process for suitable antigen-specific T cell receptors (TCRs), we developed a new approach circumventing conventional in vitro expansion-based strategies. Direct isolation of paired full-length TCR sequences from non-expanded antigen-specific T cells was achieved by the establishment of a highly sensitive PCR-based T cell receptor single cell analysis method (TCR-SCAN). Using MHC multimer-labeled and single cell-sorted HCMV-specific T cells we demonstrate a high efficacy (approximately 25%) and target specificity of TCR-SCAN receptor identification. In combination with MHC-multimer based pre-enrichment steps, we were able to isolate TCRs specific for the oncogenes Her2/neu and WT1 even from very small populations (original precursor frequencies of down to 0.00005% of CD3(+) T cells) without any cell culture step involved. Genetic re-expression of isolated receptors demonstrates their functionality and target specificity. We believe that this new strategy of TCR identification may provide broad access to specific TCRs for therapeutically relevant T cell epitopes.
High‐Affinity Choline Transport Sites: Use of [3H]Hemicholinium‐3 as a Quantitative Marker (1993)

High-affinity choline transport (HAChT), the rate-limiting and regulatory step in acetylcholine (ACh) synthesis, is selectively localized to cholinergic neurons. Hemicholinium-3 (HC3), a potent and selective inhibitor of HAChT, has been used as a specific radioligand to quantify HAChT sites in membrane binding and autoradiographic studies. Because both HAChT velocity and [3H]HC3 binding change as in vivo activity of cholinergic neurons is altered, these markers are also useful measures of cholinergic neuronal activity. Evidence that [3H]HC3 is a specific ligand for HAChT sites on cholinergic terminals is reviewed. The ion requirements of HAChT and [3H]HC3 binding indicate that sodium and chloride are required for recognition of both choline and [3H]HC3. A common recognition site is also indicated by the close correspondence of the potency of HC3 and choline analogues for inhibiting both HAChT and [3H]HC3 binding. The parallel regional distributions of both markers in adult brain, during development and after specific lesions, all indicate specific cholinergic localization. The close association of HAChT and [3H]HC3 binding sites is also supported by parallel regulatory changes occurring after in vivo drug treatments and in vitro depolarization. Overall, the data indicate a close association between HAChT and [3H]HC3 binding and are consistent with the sites being identical. Methodologic considerations in using [3H]HC3 as a ligand and considerations in interpretation of results are also discussed.
Expression of ectonucleotidase CD39 by Foxp3+ Treg cells: hydrolysis of extracellular ATP and immune suppression (2007)

In the immune system, extracellular ATP functions as a "natural adjuvant" that exhibits multiple proinflammatory effects. It is released by damaged cells as an indicator of trauma and cell death but can be inactivated by CD39 (nucleoside triphosphate diphosphohydrolase-1 [NTPDase 1]), an ectoenzyme that degrades ATP to AMP. Here, we show that CD39 is expressed primarily by immune-suppressive Foxp3(+) regulatory T (Treg) cells. In mice, the enzyme is present on virtually all CD4(+)CD25(+) cells. CD39 expression is driven by the Treg-specific transcription factor Foxp3 and its catalytic activity is strongly enhanced by T-cell receptor (TCR) ligation. Activated Treg cells are therefore able to abrogate ATP-related effects such as P2 receptor-mediated cell toxicity and ATP-driven maturation of dendritic cells. Also, human Treg cells express CD39. In contrast to mice, CD39 expression in man is restricted to a subset of Foxp3(+) regulatory effector/memory-like T (T(REM)) cells. Notably, patients with the remitting/relapsing form of multiple sclerosis (MS) have strikingly reduced numbers of CD39(+) Treg cells in the blood. Thus, in humans CD39 is a marker of a Treg subset likely involved in the control of the inflammatory autoimmune disease.
Comparison of the cellular pharmacokinetics and toxicity of 2',2'-difluorodeoxycytidine and 1-beta-D-arabinofuranosylcytosine. (1988)

2',2'-Difluorodeoxycytidine (dFdC) is a new deoxycytidine analogue with good activity against human leukemic cell lines and murine solid tumors, while the activity of 1-beta-D-arabinofuranosylcytosine (ara-C) is established in experimental systems and for the treatment of human adult leukemia. This study compared the cellular metabolism and cytotoxic properties of dFdC and ara-C in Chinese hamster ovary cells. In wild-type cells, dFdC was significantly more cytotoxic than ara-C after both 4- and 18-h incubations. The 5'-triphosphate of dFdC (dFdCTP) was the major cellular metabolite (85-90%), reaching cellular concentrations up to 20-fold greater than those observed for ara-C 5'-triphosphate at equimolar concentrations of the parent drug. A deoxycytidine kinase-deficient mutant neither accumulated dFdCTP nor showed any cytotoxic response up to drug concentrations of 100 microM. The cytotoxicity of dFdC could be competitively reversed by deoxycytidine further suggesting that dFdC, like ara-C, required phosphorylation by deoxycytidine kinase for biological activity. Several explanations for the different cellular accumulation of the drug triphosphates were established: (a) nucleoside transport studies demonstrated that the membrane permeation of dFdC was 65% more rapid than that of ara-C; (b) deoxycytidine kinase had a higher affinity for dFdC (Km = 3.6 microM) than for ara-C (Km = 8.8 microM), while the Km for deoxycytidine was 1.4 microM; (c) the elimination of intracellular dFdCTP was biphasic with t1/2 alpha = 3.9 and t1/2 beta greater than 16 h while the degradation of ara-CTP was monophasic and significantly faster (t1/2 = 0.7 h). The comparatively long half-life of dFdCTP was related to the prolonged inhibition of DNA synthesis after removal of exogenous nucleoside. Together these factors contribute to the more potent cytotoxicity of dFdC compared with ara-C.
What Is Materials Chemistry? (1991)

The increasingly chemical nature of forefront scientific opportunities and pressing technological needs has resulted in the development of a new interdisciplinary field, materials chemistry. Its principal characteristics are: a focus on solids with useful properties, an emphasis on synthesis, a long term goal of understanding structure-bonding-property relations, a frequent dependence on crystal growth for answering key questions and providing exploitable materials and a need to understand and optimize process physical chemistry. Selected subjects in electronic materials chemistry are used to illustrate these characteristics. Included are resist materials, III-V semiconductors, piezoelectric quartz hydrothermal single crystal synthesis, non-linear-optical potassium titanyl phosphate hydrothermal synthesis and optical fiber preparation. Finally, future challenges are discussed. This paper is based in part on an invited talk given by the author as recipient of the ACS Materials Chemistry Prize, Boston, April 1990.
A General Method for Designing Combinatorial Peptide Libraries Decodable by Amino Acid Analysis (2007)

Herein we describe an algorithm for designing combinatorial peptide libraries for split-and-mix synthesis on solid support that are decodable by amino acid analysis (AAA) of the beads. AAA is a standard service analysis available in most biochemical laboratories, and it allows one to control the quality of the peptide on each bead, an important feature that is missing from most library decoding protocols. In the algorithm, each AA is assigned to two variable positions in the sequence grouped in a "unique pair". This arrangement limits sequence design because both the number of unique pairs U (setting the maximum number of variable AA) and the maximum number S of different AA per variable position depend on the peptide length N (U=N(N-1)/2), S=N-1). The method is therefore only suitable for focused libraries. An application example is shown for the selection of peptides with N-terminal proline or hydroxyproline catalyzing an aldol reaction from a combinatorial library of 65536 octapeptides. A simple enumeration program is available to help design combinatorial libraries decodable by amino acid analysis. The method applies to linear and cyclic peptides, can be used for nonnatural building blocks, including beta-amino acids, and should help to explore the vast chemistry of linear and cyclic peptide for catalysis and bioactivity.
5′ Splice Site Mutations in tau Associated with the Inherited Dementia FTDP-17 Affect a Stem-Loop Structure That Regulates Alternative Splicing of Exon 10 (1999)

Missense and splice site mutations in the microtubule-associated protein tau gene were recently found associated with fronto-temporal dementia and parkinsonism linked to chromosome 17 (Poorkaj et al. (1998) Ann. Neurol. 43, 815-825; Hutton et al. (1998) Nature 393, 702-705; Spillantini et al. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 7737-7741). The mutations in the 5' splice site of exon 10 were shown to increase the ratio of tau mRNAs containing exon 10 and thus the proportion of Tau protein isoforms with 4 microtubule binding repeat domains, although how this increase leads to neurodegeneration is presently unclear. The mechanism by which these mutations increase tau exon 10 splicing was not determined, although the mutations were predicted to disrupt a potential stem-loop structure that was likely involved in the regulation of exon 10 alternative splicing. Here we describe in vitro splicing assays and RNA structural analysis that demonstrate that the mutations do indeed act through disruption of the stem-loop structure and that the stability of this secondary structure feature at least partially determines the ratio of tau exon 10+/- transcripts. In addition, we provide evidence that the stability of the stem-loop structure underlies the alternative splicing of this exon in other species.
Phosphate Transport in Rat Liver Mitochondria (1974)

Abstract Experiments using an inhibitor-stop assay and a rapid sampling technique were carried out to analyze and determine the kinetic parameters and energy requirements of the p-chloromercuribenzoate-sensitive phosphate transport process in rat liver mitochondria. Initial rates of phosphate transport were measured, under conditions where transport was the rate-limiting process. The Km and Vmax of transport were determined to be 1.84 ± 0.18 mm and 229 ± 19 nmoles x min-1 x mg-1, respectively, at 0°. Using the selective inhibitors N-ethylmaleimide and n-butyl malonate, the over-all phosphate transport activity can be resolved into two components. The kinetic parameters of these two activities at 0° are: for N-ethylmaleimide-sensitive transport, Km = 1.60 ± 0.19 mm and Vmax = 205 ± 19 nmoles x min-1 x mg-1; and for n-butyl malonate-sensitive transport, Km = 1.76 ± 0.29 mm and Vmax = 14.9 ± 2.2 nmoles x min-1 x mg-1. The rate of over-all transport can be accounted for by the sum of the two activities in the presence of N-ethylmaleimide or n-butyl malonate, but the apparent affinities of these two activities cannot be distinguished, within experimental error. Measurements of phosphate uptake, along with determinations of intramitochondrial volumes, show that the phosphate transport system catalyzes transport of phosphate against a concentration gradient at 0°. Inhibitors of respiration and ATP hydrolysis have no effect on this process; but the uncoupler 2,4-dinitrophenol causes a sharp decrease in phosphate uptake. Addition of inonophores which are postulated to allow uptake of H+ in exchange for intramitochondrial K+ (nigericin or 2,4-dinitrophenol plus valinomycin) further inhibit the uptake of phosphate seen in the presence of uncoupler, and phosphate is excluded from the intramitochondrial volume. These results are consistent with the hypothesis that concentrative uptake of phosphate can be driven by the pH gradient of the mitochondrial membrane.
2 Genetically Modified Organisms for Agricultural Food Production (2008)

Abstract Genetically modified (GM) crops are now part of mainstream agriculture, and the trend towards increased use of GM organisms in plant and animal agriculture will undoubtedly continue. This chapter provides a brief outline of the technologies used to produce GM crop plants and livestock, the means whereby GM products can be detected as minor contaminants in food, and some of the difficulties and paradoxes that must be faced in attempts to label products derived from GM organisms.
⅔ -Power Law for Copolymer Lamellar Thickness Implies a ⅓ -Power Law for Spinodal Decomposition (1988)

We demonstrate the relation $\ensuremath{\theta}=2\ensuremath{\varphi}$. Here the exponent $\ensuremath{\theta}$ is defined as $D\ensuremath{\sim}{N}^{\ensuremath{\theta}}$, where $D$ is the equilibrium lamellar thickness of the diblock copolymer ordered phase and $N$ is the molecular weight. The exponent $\ensuremath{\varphi}$ is defined as $l\ensuremath{\sim}{t}^{\ensuremath{\varphi}}$, where $l$ is the pattern size of the spinodally decomposing system (say, a binary alloy) and $t$ is the time.
Overexpression of Phytochrome B Induces a Short Hypocotyl Phenotype in Transgenic Arabidopsis. (1991)

The photoreceptor phytochrome is encoded by a small multigene family in higher plants. phyA encodes the well-characterized etiolated-tissue phytochrome. The product of the phyB gene, which has properties resembling those of "green tissue" phytochrome, is as yet poorly characterized. We have developed a phytochrome B overexpression system for analysis of the structure and function of this protein. Using newly generated polyclonal and monoclonal antibodies that are selective for phytochrome B, we have demonstrated high levels of expression of full-length rice and Arabidopsis phytochrome B under the control of the cauliflower mosaic virus 35S promoter in transgenic Arabidopsis. The overexpressed phytochrome is spectrally active, undergoes red/far-red-light-dependent conformational changes, is synthesized in its inactive red light-absorbing form, and is stable in the light. Overexpression of phytochrome B is tightly correlated with a short hypocotyl phenotype in transgenic seedlings. This phenotype is strictly light dependent, thus providing direct evidence that phytochrome B is a biologically functional photoreceptor. Based on similarities to phenotypes obtained by overexpression of phytochrome A, it appears that phytochromes A and B can control similar responses in the plant.
Identification of surface features on cold-rolled stainless steel strip (2000)

A novel method based on three-dimensional profilometry data and Matlab analysis software is described to identify surface features on cold-rolled stainless steel strip. The aim of the method is to detect automatically pits and roll marks that can be observed in optical or SEM micrographs. Pits are identified by locating regions which are significantly deeper than the immediately adjacent surface. Deep or steep features which extend a significant distance in the direction of rolling are identified as roll marks. Results for typical cold-rolled stainless steel sheet show that the algorithms are effective in identifying the more obvious pits and roll marks. By suitable adjustment of the tolerances used in the analysis, the method can be tailored to detect less severe features. Application of the method, either for research purposes or routine industrial inspection, will require tuning of these tolerances to detect pits of the severity relevant to the end use of the strip. The methodology has been applied to a series of rolled strip samples to track the evolution of pits and roll marks during a schedule. Results show how the initially large area of deep pits is rapidly eliminated and transformed into shallow pits. The pit identification method is used to estimate the effect of trapped oil on lubrication. Results suggest that this expelled oil will contribute significantly to the lubrication of the surrounding area. Finally, a good correlation is demonstrated between strip surface reflectance measurements and the estimated pit area.
Content creation and rights management: experiences of SCRAN (the Scottish Cultural Resources Access Network) (2000)

Perhaps the single greatest obstacle to the creation and use of digital content, is uncertainty over copyright issues, and in particular a fear that the new technologies may facilitate intellectual property theft. This paper draws on the experience of the Scottish Cultural Resources Access Network (SCRAN) to review some of the issues that should be addressed in this area.
Secure distribution of watermarked images for a digital library of ancient papers (1997)

The electronic publishing, storage and distribution of documents is growing increasingly important and will have profound implications for our economy, culture and society. The multimedia digitalisation of libraries and the distribution of the contents of museums is revolutionising these organisations and will make these resources available to a much wider audience than was previously possible.
Starburst: A hybrid algorithm for video-based eye tracking combining feature-based and model-based approaches (2006)

Knowing the user’s point of gaze has significant potential to enhance current human-computer interfaces, given that eye movements can be used as an indicator of the attentional state of a user. The primary obstacle of integrating eye movements into today’s interfaces is the availability of a reliable, low-cost open-source eye-tracking system. Towards making such a system available to interface designers, we have developed a hybrid eye-tracking algorithm that integrates feature-based and model-based approaches and made it available in an open-source package. We refer to this algorithm as "starburst" because of the novel way in which pupil features are detected. This starburst algorithm is more accurate than pure feature-based approaches yet is signi?cantly less time consuming than pure modelbased approaches. The current implementation is tailored to tracking eye movements in infrared video obtained from an inexpensive head-mounted eye-tracking system. A validation study was conducted and showed that the technique can reliably estimate eye position with an accuracy of approximately one degree of visual angle.
Differential Distribution of Proteins Expressed in Companion Cells in the Sieve Element-Companion Cell Complex of Rice Plants (2005)

Sieve tubes are comprised of sieve elements, enucleated cells that are incapable of RNA and protein synthesis. The proteins in sieve elements are supplied from the neighboring companion cells through plasmodesmata. In rice plants, it was unclear whether or not all proteins produced in companion cells had the same distribution pattern in the sieve element-companion cell complex. In this study, the distribution pattern of four proteins, beta-glucuronidase (GUS), green fluorescent protein (GFP), thioredoxin h (TRXh) and glutathione S-transferase (GST) were analyzed. The foreign proteins GUS and GFP were expressed in transgenic rice plants under the control of the TRXh gene promoter (PTRXh), a companion cell-specific promoter. Analysis of leaf cross-sections of PTRXh-GUS and PTRXh-GFP plants indicated high accumulation of GUS and GFP, respectively, in companion cells rather than in sieve elements. GUS and GFP were also detected in phloem sap collected from leaf sheaths of the transgenic rice plants, suggesting these proteins could enter sieve elements. Relative amounts of GFP and endogenous phloem proteins, TRXh and GST, in phloem sap and total leaf extracts were compared. Compared to TRXh and GST, GFP content was higher in total leaf extracts, but lower in phloem sap, suggesting that GFP accumulated mainly in companion cells rather than in sieve elements. On the other hand, TRXh and GST appeared to accumulate in sieve elements rather than in companion cells. These results indicate the evidence for differential distribution of proteins between sieve elements and companion cells in rice plants.