gebhart/patrepeval huggingface dataset:
Direct aperture optimization for online adaptive radiation therapy (2007)

This paper is the first investigation of using direct aperture optimization (DAO) for online adaptive radiation therapy (ART). A geometrical model representing the anatomy of a typical prostate case was created. To simulate interfractional deformations, four different anatomical deformations were created by systematically deforming the original anatomy by various amounts (0.25, 0.50, 0.75, and ). We describe a series of techniques where the original treatment plan was adapted in order to correct for the deterioration of dose distribution quality caused by the anatomical deformations. We found that the average time needed to adapt the original plan to arrive at a clinically acceptable plan is roughly half of the time needed for a complete plan regeneration, for all four anatomical deformations. Furthermore, through modification of the DAO algorithm the optimization search space was reduced and the plan adaptation was significantly accelerated. For the first anatomical deformation , the plan adaptation was six times more efficient than the complete plan regeneration. For the 0.50 and deformations, the optimization efficiency was increased by a factor of roughly 3 compared to the complete plan regeneration. However, for the anatomical deformation of , the reduction of the optimization search space during plan adaptation did not result in any efficiency improvement over the original (nonmodified) plan adaptation. The anatomical deformation of demonstrates the limit of this approach. We propose an innovative approach to online ART in which the plan adaptation and radiation delivery are merged together and performed concurrently—adaptive radiation delivery (ARD). A fundamental advantage of ARD is the fact that radiation delivery can start almost immediately after image acquisition and evaluation. Most of the original plan adaptation is done during the radiation delivery, so the time spent adapting the original plan does not increase the overall time the patient has to spend on the treatment couch. As a consequence, the effective time allotted for plan adaptation is drastically reduced. For the 0.25, 0.5, and anatomical deformations, the treatment time was increased by only 2, 4, and , respectively, as compared to no plan adaptation. For the anatomical deformation of the time increase was substantially larger. The anatomical deformation of represents an extreme case, which is rarely observed for the prostate, and again demonstrates the limit of this approach. ARD shows great potential for an online adaptive method with minimal extension of treatment time.
Binding of Granzyme B in the Nucleus of Target Cells (1996)

Granzyme B (cytotoxic cell proteinase 1) is a serine proteinase that has been implicated in cytotoxic T lymphocyte-induced apoptosis. In order to understand how granzyme B is involved in mechanisms of target cell destruction, characterization and identification of substrates are required. We have developed an in situ binding assay using permeabilized cells and recombinant granzyme B that allows us to visualize potential substrates after immunostaining with anti-granzyme B antiserum. Confocal laser scanning microscopy and immunoelectron microscopic analyses demonstrate that granzyme B recognizes a nuclear substrate. The labeling pattern observed corresponds with regions of positive staining with uranyl acetate which binds to heterochromatin in the nucleus. Positive labeling of target cells with granzyme B is dependent on the presence of a catalytically active proteinase, since an inactive proenzyme form of granzyme B fails to give rise to any binding in the target cells. Far-Western blotting and immunoprecipitation of subcellular fractions of target cells have shown that the putative substrate of catalytically active granzyme B is an 80-kDa nuclear protein. Minor cytosolic bands of 50 and 94 kDa are also observed. A cytoplasmic band of 69 kDa is detected by both active and zymogen forms of granzyme B.
Differential regulation of IL-1 production in human monocytes by IFN-gamma and IL-4. (1990)

We have demonstrated that IL-4 markedly inhibits IL-1 production by highly purified normal human monocytes. When added to monocyte cultures, IL-4 suppressed LPS-induced IL-1 production in a time- and dose-dependent manner. Concentrations of IL-4 as low as 100 pg/ml reduced IL-1 production by approximately 50%, and doses of 1 ng/ml or higher suppressed IL-1 production by more than 90%. Maximal inhibition required that IL-4 be added before or simultaneous with LPS. Northern dot blot analyses revealed that IL-4 not only dramatically reduced the steady-state IL-1 beta mRNA levels in LPS-stimulated monocytes, but also those of TNF-alpha and IL-6. The inhibitory effect was not stimulus-specific because IL-4 suppressed IL-1 production induced by a variety of monocyte activation stimuli, including LPS, PMA, and Staphylococcus aureus Cowan strain. Monocytes expressed a relatively small number of high affinity IL-4R (approximately 150/cell; Ka = 3.15 +/- 1.13 x 10(10) M-1) indicating that relatively few receptors are necessary to generate the inhibitory effect. IL-4 enhanced monocyte MHC class II Ag (HLA-DR) expression in a manner similar to that of IFN-gamma. However, although both IFN-gamma and IL-4 up-regulated HLA-DR expression, they exhibited opposite effects on IL-1 production: IFN-gamma significantly enhanced monocyte IL-1 production induced by submaximal concentrations of LPS; whereas, IL-4 suppressed IL-1 production. Moreover, IL-4 largely neutralized the potentiating effect of IFN-gamma suggesting that IL-4 may be an effective antagonist of certain IFN-gamma-induced effects. Together these findings demonstrate that the relative levels of IFN-gamma and IL-4 may profoundly influence the state of monocyte activation by differentially regulating the expression of IL-1.
Phylogeny.fr: robust phylogenetic analysis for the non-specialist (2008)

Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The 'One Click' mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The 'Advanced' mode uses the same pipeline but allows the parameters of each program to be customized by users. The 'A la Carte' mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/
Climate Change and Sustainable Development: Realizing the Opportunity (2006)

Manifold linkages exist between climate change and sustainable development. Although these are starting to receive attention in the climate exchange literature, the focus has typically been on examining sustainable development through a climate change lens, rather than vice versa. And there has been little systematic examination of how these linkages may be fostered in practice. This paper examines climate change through a sustainable development lens. To illustrate how this might change the approach to climate change issues, it reports on the findings of a panel of business, local government, and academic representatives in British Columbia, Canada, who were appointed to advise the provincial government on climate change policy. The panel found that sustainable development may offer a significantly more fruitful way to pursue climate policy goals than climate policy itself. The paper discusses subsequent climate change developments in the province and makes suggestions as how best to pursue such a sustainability approach in British Columbia and other jurisdictions.
Evidence of homology in a high-sulphur protein fraction (SCMK-B2) of wool and hair α-keratins (1968)

Fractions corresponding to the S-carboxymethylated high-sulphur protein component SCMK-B2 isolated by Gillespie (1963) from Merino wool were prepared from five different wool samples and also from bovine hair. The six fractions showed great similarities in amino acid composition, and also gave very similar peptide ;maps' after tryptic and chymotryptic digestion. Some of the peptides were isolated from the different samples, and evidence is given that suggests that a sequence of at least 21 amino acids is common to all the fraction SCMK-B2 preparations. Further, all the fractions derived from the wool samples have the same acetylated heptapeptide for the N-terminal sequence, but one extra residue may be present in this N-terminal sequence in the protein from bovine hair. The general significance of these findings is discussed.
A new estra-1,3,5(10)-triene-3,17β-diol solvate: estradiol–methanol–water (3/2/1) (2003)

The title solvate of the steroid 17beta-estradiol (E(2)) with methanol and water, C(18)H(24)O(2).0.67CH(4)O.0.33H(2)O, is the first E(2) derivative to contain three crystallographically independent molecules in the asymmetric unit. The three steroid molecules, along with two methanol molecules and a water molecule, create a three-dimensional hydrogen-bonded system. Three-sided columns are formed, with the estradiol molecules aligned lengthwise parallel to (101), and joined by solvent molecules at both hydrophilic ends. The three estradiol molecules differ slightly in their ring-bowing angles, i.e. the angle between the mean plane of the A ring and that of the BCD ring; this angle ranges from 7.1 to 12.2 degrees.
Derivation and Evaluation of a Labeled Hedonic Scale (2009)

The objective of this study was to develop a semantically labeled hedonic scale (LHS) that would yield ratio-level data on the magnitude of liking/disliking of sensation equivalent to that produced by magnitude estimation (ME). The LHS was constructed by having 49 subjects who were trained in ME rate the semantic magnitudes of 10 common hedonic descriptors within a broad context of imagined hedonic experiences that included tastes and flavors. The resulting bipolar scale is statistically symmetrical around neutral and has a unique semantic structure. The LHS was evaluated quantitatively by comparing it with ME and the 9-point hedonic scale. The LHS yielded nearly identical ratings to those obtained using ME, which implies that its semantic labels are valid and that it produces ratio-level data equivalent to ME. Analyses of variance conducted on the hedonic ratings from the LHS and the 9-point scale gave similar results, but the LHS showed much greater resistance to ceiling effects and yielded normally distributed data, whereas the 9-point scale did not. These results indicate that the LHS has significant semantic, quantitative, and statistical advantages over the 9-point hedonic scale.
A helper T cell clone produces an antigen-specific molecule (T-ABM) which functions in the induction of suppression. (1987)

Among Ly-1+,2-T cells there appears to be two independent modes of antigen recognition. Helper and cytotoxic Ly-1 T cells recognize antigen only in the context of I region products whereas regulatory T cells, such as T suppressor inducer cells, produce antigen-specific, antigen-binding molecules (T-ABM). These T-ABM often have been found to form a part of biologically active, antigen-specific regulatory factors. A number of environmental conditions effect whether a foreign antigen will produce a positive response leading to immunity or a negative one leading to tolerance. Many of the conditions which favor the induction of suppressor T cells simultaneously preclude the proper interaction of antigen presenting cells with helper T cells. This parallel led us to ask whether helper T cells perform at least two, apparently opposite functions: a) under conditions favoring immunity helper T cells produce lymphokines to activate immune effector cells, and b) under conditions favoring suppression they produce molecules which function in suppressor cell induction. Therefore, this question relates to the mechanisms by which an immune response is switched into either a positive (help) or negative (suppressive) track. In addition, it begins to address the relationship between the different modes of antigen recognition exhibited by helper T cells vs. T suppressor inducer cells (see above). To explore this problem we employed an antigen-specific, I-Ak restricted helper T cell clone as the purest available source of helper T cells. We presented antigen to the cloned T cells under conditions which favor suppression rather than help (for example, by ultraviolet irradiation of the antigen-presenting cells) and collected supernatants 48 hrs later. The supernatants were then examined for activity in a functional assay for antigen-specific suppressor factors. Our results indicate that under conditions favoring suppression, a T-ABM was produced which functioned in the antigen-specific induction of suppression in vitro. The T-ABM had the same antigen specificity as that exhibited by the helper T cell and was therefore probably derived from the clone. This observation introduces the possibility that the interaction between antigen-presenting cells and helper T cells is a crucial decision point in the immune response which can lead to either immunity or suppression. The latter would be achieved through the production, by helper T cells, of an antigen-specific component of T suppressor inducer factor (i.e., the T-ABM). The possible relationship between T-ABMs and the T cell receptor is discussed.
A performance analysis and design of equalization with pilot aided channel estimation (2002)

This article presents some analysis and design rules for equalization in Rayleigh frequency-selective fading channels using training or pilot sequences. The union bounds of error probability performance are derived and are shown to be reasonably tight (especially for small constellations). These bounds can be used to predict the existence of an error floor. In addition, desirable properties for training sequences are established which may be used for training sequence design.
High‐Performance Flexible Broadband Photodetector Based on Organolead Halide Perovskite (2014)

Organolead halide perovskites have attracted extensive attentions as light harvesting materials for solar cells recently, because of its high charge‐carrier mobilities, high photoconversion efficiencies, low energy cost, ease of deposition, and so on. Herein, with CH 3 NH 3 PbI 3 film deposited on flexible ITO coated substrate, the first organolead halide perovskite based broadband photodetector is demonstrated. The organolead halide perovskite photodetector is sensitive to a broadband wavelength from the ultraviolet light to entire visible light, showing a photo‐responsivity of 3.49 A W −1 , 0.0367 A W −1 , an external quantum efficiency of 1.19×10 3 %, 5.84% at 365 nm and 780 nm with a voltage bias of 3 V, respectively. Additionally, the as‐fabricated photodetector exhibit excellent flexibility and robustness with no obvious variation of photocurrent after bending for several times. The organolead halide perovskite photodetector with high sensitivity, high speed and broad spectrum photoresponse is promising for further practical applications. And this platform creates new opportunities for the development of low‐cost, solution‐processed and high‐efficiency photodetectors.
NFAT5 binds to the TNF promoter distinctly from NFATp, c, 3 and 4, and activates TNF transcription during hypertonic stress alone (2005)

Tumor necrosis factor (TNF) is a pro-inflammatory cytokine that plays an important role in a variety of infectious and autoimmune disorders. Its transcription is regulated in a stimulus- and cell-type-specific manner via the recruitment of distinct DNA/activator complexes forming secondary structures or enhanceosomes. NFATp, a member of the nuclear factor of activated T cells (NFAT) family of transcription factors, plays a critical role in TNF gene regulation under a variety of conditions. In this study, we show that NFAT5, the most recently described NFAT family member, binds to the TNF promoter in a manner distinct from other NFAT proteins and is a key mediator in the activation of TNF gene transcription during hypertonic stress alone.
The inflammatory response to cardiopulmonary bypass and its impact on postoperative myocardial function (1995)

Cardiopulmonary bypass triggers a generalized inflammatory response that is largely mediated by activation of polymorphonuclear neutrophils, their adhesion to endothelial cells, and the subsequent release of cytotoxic products. It has been known for several years that the inflammatory response to extracorporeal circulation underlies the occasional development of postoperative organ--in particular, lung--dysfunction. It is now increasingly recognized that this response can adversely affect myocardial function as well. These harmful effects are exerted by a wide spectrum of compounds, regardless of whether they act as triggers (complement-derived anaphylatoxins), mediators (cytokines, adhesion molecules), or effectors (proteolytic enzymes, oxygen free radicals, leukotrienes) of the inflammatory cascade. These considerations suggest that future strategies of myocardial protection must not be limited to interventions targeted at the heart itself but should also encompass those designed to blunt the inflammatory response to cardiopulmonary bypass.
Electrical Properties of Sintered Lithium Titanium Phosphate Ceramics (Li1+XMXTi2−X(PO4)3, M3+ = Al3+, Sc3+, or Y3+) (1990)

Abstract Activation energies of electrical conduction for bulk and grain boundary in Li1+XMXTi2−X(PO4)3 (M = Al, Sc, or Y) systems were determined. The activation energy for the bulk kept constant in spite of the M3+ substitution, while that for the grain boundary appreciably decreased. The total conductivity enhancement by the M3+ substitution was attributed to the decrease in the activation energy of the grain boundary component.
Nine Ways to Use Visual Art as a Prewriting Strategy. (2007)

This article looks at the use of art in developing students’ prewriting ability. The activities, strategies, and objects used provide students with the background knowledge, motivation, vocabulary, structure, and fluency they need to compose and rehearse written pieces. The article describes research conducted on the effects of combining art with writing instruction. Finally, the article shows how various art activities and lessons help children develop strategies for improving their prewriting by providing a solid base of ideas and text structures at this initial stage.
Couture in the 21st century (2010)

This lavishly illustrated book features essays from 29 of the world's top designers, who talk about fashion in the first decade of the 21st century, with its emphasis on craftsmanship and traditional techniques, and pay loving homage to the iconic couturiers of the past, expressing how their creativity and attention to detail has forever shaped fashion's future. The book features personal essays on couture by today's most lauded contemporary designers, such as Giorgio Armani and Oscar de la Renta, plus the fresh faces who design for the top design houses: Marios Schwab, Jason Wu, and Maria Grazia Chiuri and Pier Paolo Piccioli for Valentino. Each designer describes their view of couture and the inspirations drawn from iconic figures such as Christian Dior, Yves Saint Laurent, Elsa Schiaparelli, Coco Chanel, Madeleine Vionnet, Madame Gres and Paul Poiret. Essays are complemented by photographs and fashion illustrations, plus an intimate portrait of the designer by photographer Rankin, world renowned for capturing the wit and personality of his subjects. Couture in the 21st Century beautifully captures the divine and sublime of couture fashion in the hands of the world's best-known designers.Couture in the 21st Century is an inspiring opportunity to delve into the archives of the likes of Christian Dior, Yves Saint Laurent and Coco Chanel.
DNA Hybridization with Hardjobovis-specific Recombinant Probes as a Method for Type Discrimination of Leptospira interrogans Serovar hardjo (1988)

Restriction endonuclease analysis of DNA of Leptospira interrogans, serovar hardjo, showed two distinct types within this serovar. These two types, hardjoprajitno and hardjobovis, cannot be differentiated by monoclonal antibodies. Application of 32P- or biotin-labelled total DNA probes in dot-blot or in situ hybridization assays showed a high sensitivity of the assays but also considerable cross-hybridization. Therefore, a genomic library of hardjobovis was constructed and a number of hardjobovis-specific recombinant clones were isolated. Finally, four clones were selected on the basis of a strong hybridization signal and a high specificity for hardjobovis as compared to hardjoprajitno. In a dot-blot assay as well as in in situ hybridization experiments all four clones gave strong signals, and no cross-hybridization with hardjoprajitno was observed in either type of assay. Our results indicate that specific recombinant DNA probes might provide tools for routine diagnosis and classification in cases of hardjo infections.
On the Stability of PtIV Pro‐Drugs with Haloacetato Ligands in the Axial Positions (2014)

The design of Pt(IV) pro-drugs as anticancer agents is predicated on the assumption that they will not undergo substitution reactions before entering the cancer cell. Attempts to improve the cytotoxic properties of Pt(IV) pro-drugs included the use of haloacetato axial ligands. Herein, we demonstrate that Pt(IV) complexes with trifluoroacetato (TFA) or dichloroacetato (DCA) ligands can be unstable under biologically relevant conditions and readily undergo hydrolysis, which results in the loss of the axial TFA or DCA ligands. The half-lives for Pt(IV) complexes with two TFA or DCA ligands at pH 7 and 37 °C range from 6 to 800 min, which is short relative to the duration of cytotoxicity experiments that last 24-96 h. However, complexes with two monochloroacetato (MCA) or acetato axial ligands are stable under biologically relevant conditions. The loss of the axial ligands depends primarily on the electron-withdrawing strength of the axial ligands, but also upon the nature of the equatorial ligands. We were unable to find obvious correlations between the structures of the Pt(IV) complexes and the rates of decay of the parent compounds. The X-ray crystal structures of the bis-DCA and bis-MCA Pt(IV) derivatives of oxaliplatin did not reveal any significant structural differences that could explain the observed differences in stability.