Assessing time-by-covariate interactions in Cox proportional hazards regression models using cubic spline functions

This dissertation develops and explores the methodology for the use of cubic spline functions in assessing time-by-covariate interactions in Cox proportional hazards regression models. These interactions indicate violations of the proportional hazards assumption of the Cox model. Use of cubic spline functions allows for the investigation of the shape of a possible covariate time-dependence without having to specify a particular functional form. Cubic spline functions yield both a graphical method and a formal test for the proportional hazards assumption as well as a test of the nonlinearity of the time-by-covariate interaction. Five existing methods for assessing violations of the proportional hazards assumption are reviewed and applied along with cubic splines to three well known two-sample datasets. An additional dataset with three covariates is used to explore the use of cubic spline functions in a more general setting. ^

Simultaneous induction of NKG2D and NKG2D ligand for promoting immune surveillance by IL-12 plus doxorubicin treatment

NKG2D (natural killer group 2, member D) and its ligands interaction in tumor microenvironment directs tumor infiltrating immune cells to recognize tumor cells, stimulate cytotoxic effector immune cells, and therefore eradicate tumor cells. IL-12, a cytokine produced by antigen presenting cells, has remarkable antitumor effect by activating innate and adaptive immunity. Doxorubicin, a commonly used chemotherapeutic agent also boosts the host antitumor immune response to cause tumor cell death. Our previous publication suggests that IL-12 plus doxorubicin enhances NKG2D function-dependent inhibition of tumor progression and promotes CD8+T cells infiltrating into tumors. The purpose of this study is to determine the underlying mechanism. Our study reveals a novel function of doxorubicin, which is to augment IL-12–induced NKG2D expression in CD8+T cells but not in NK or CD4+T cells. This observation was further validated by NK and CD8+T cell-depletion studies, in which only depletion of CD8+T cells abolished the expression of NKG2D in lymphocytes. The induced NKG2D expression in CD8+T cells is tightly associated with tumor-specific localization of CD8+T cells and improved antitumor efficacy. The IL-12 plus doxorubicin treatment-induced antitumor efficacy is also due to NKG2D ligand Rae-1 induction in tumors. Rae-1 induction in tumors is a long term effect in multiple tumor models, but not in normal tissues. A novel CD8+T cell direct contact dependent mechanism accounts for Rae-1 induction in vivo and in vitro, and CD80 is the receptor through which CD8+T cells interplay with tumor cells to upregulate Rae-1 on tumor cells. In summary, increased NKG2D expression in CD8+T cells in response to IL-12 plus doxorubicin was closely associated with tumor-specific localization of CD8+T cells and greater antitumor efficacy of the combined regimen than either agent alone. NKG2D ligand Rae-1 induction is triggered by the interaction of CD80 on tumor cells with tumor infiltrating CD+8 T cells.

Planktonic foraminifera in the trans-tropical Pacific Ocean

Cores from four Ocean Drilling Program (ODP) sites were examined for planktonic foraminifers. One sample per core (from core-catchers in Holes 806B and 807B and from Section 4 in Holes 847B and 852B) was examined through the interval representing the last 5.8 m.y. Sites 806 (0°19.1'N; 159°21.7'E) and 847 (0o12.1'N; 95°19.2'W) are beneath the equatorial divergence zone. Sites 807 (3°36.4'N; 156°37.5'E) and 852 (5°19.6'N; 110°4.6'W) are located north of the equator in the convergence zone created by the interaction of the westward-flowing South Equatorial Current (SEC) and the eastward-flowing North Equatorial Countercurrent (NECC). Specimens were identified to species and then grouped according to depth habitat and trophic level. Species richness and diversity were also calculated. Tropical neogloboquadrinids have been more abundant in the eastern than in the western equatorial Pacific Ocean throughout the last 5.8 m.y. During the mid-Pliocene (3.8-3.2 Ma), their abundance increased at all sites, while during the Pleistocene (after ~ 1.6 Ma), they expanded in the east and declined in the west. This suggests an increase in surface-water productivity across the Pacific Ocean during the closing of the Central American seaway and an exacerbation of the productivity asymmetry between the eastern and western equatorial regions during the Pleistocene. This faunal evidence agrees with eolian grain-size data (Hovan, 1995) and diatom flux data (Iwai, this volume), which suggest increases in tradewind strength in the eastern equatorial Pacific that centered around 3.5 and 0.5 Ma. The present longitudinal zonation of thermocline dwelling species, a response to the piling of warm surface water in the western equatorial region of the Pacific, seems to have developed after 2.4 Ma, not directly after the closing of the Panama seaway (3.2 Ma). Apparently, after 2.4 Ma, the piling warm water in the west overwhelmed the upwelling of nutrients into the photic zone in that region, creating the Oceanographic asymmetry that exists in the modern tropical Pacific and is reflected in the microfossil record. In the upper Miocene and lower Pliocene sediments, the ratio of thermocline-dwelling species to mixed-layer dwellers is 60%:40%. During the mid-Pliocene, the western sites became 40% thermocline and 60% mixed-layer dwellers. Subsequent to -2.4 Ma, the asymmetry increased to 20%: 80% in the west and the reverse in the east. This documents the gradual thickening of the warm-water layer piled up in the western tropical Pacific over the last 5.8 m.y. and reveals two "steps" in the biotic trend that can be associated with specific events in the physical environment.

Initial biomass and biomass change of tundra and forest plants in three herbivore treatments in Norway and Sweden

Recent Pan-Arctic shrub expansion has been interpreted as a response to a warmer climate. However, herbivores can also influence the abundance of shrubs in arctic ecosystems. We addressed these alternative explanations by following the changes in plant community composition during the last 10 years in permanent plots inside and outside exclosures with different mesh sizes that exclude either only reindeer or all mammalian herbivores including voles and lemmings. The exclosures were replicated at three forest and tundra sites at four different locations along a climatic gradient (oceanic to continental) in northern Fennoscandia. Since the last 10 years have been exceptionally warm, we could study how warming has influenced the vegetation in different grazing treatments. Our results show that the abundance of the dominant shrub, Betula nana, has increased during the last decade, but that the increase was more pronounced when herbivores were excluded. Reindeer have the largest effect on shrubs in tundra, while voles and lemmings have a larger effect in the forest. The positive relationship between annual mean temperature and shrub growth in the absence of herbivores and the lack of relationships in grazed controls is another indication that shrub abundance is controlled by an interaction between herbivores and climate. In addition to their effects on taller shrubs (> 0.3 m), reindeer reduced the abundance of lichens, whereas microtine rodents reduced the abundance of dwarf shrubs (< 0.3 m) and mosses. In contrast to short-term responses, competitive interactions between dwarf shrubs and lichens were evident in the long term. These results show that herbivores have to be considered in order to understand how a changing climate will influence tundra ecosystems.

Towards a lightweight mobile semantic-based approach for enhancing interaction with smart objects

This work describes a semantic extension for a user-smart object interaction model based on the ECA paradigm (Event-Condition-Action). In this approach, smart objects publish their sensing (event) and action capabilities in the cloud and mobile devices are prepared to retrieve them and act as mediators to configure personalized behaviours for the objects. In this paper, the information handled by this interaction system has been shaped according several semantic models that, together with the integration of an embedded ontological and rule-based reasoner, are exploited in order to (i) automatically detect incompatible ECA rules configurations and to (ii) support complex ECA rules definitions and execution. This semantic extension may significantly improve the management of smart spaces populated with numerous smart objects from mobile personal devices, as it facilitates the configuration of coherent ECA rules.

Interacción combinada táctil 3D para manejo de colecciones de documentos

Actualmente existen varios dispositivos que aceptan gestos sobre superficies táctiles, sean celulares, tabletas, computadores, etc. a los cuales las personas se acostumbran rápidamente a su uso y los aceptan como herramientas necesarias en su vida. Del mismo modo existen algunas aplicaciones que manejan entornos en 3D, y permiten captar gestos realizados con las manos, cuerpo, cabeza. Estas técnicas se han desarrollado mucho por separado pero se ha podido evidenciar en base a los artículos revisados que no existen muchos estudios que combinen las aplicaciones táctiles con las 3D manejadas por gestos en el aire. El presente trabajo muestra un prototipo que permite la comunicación y coordinación entre dos aplicaciones, una que muestra documentos representados por esferas en una aplicación con interacción táctil desarrollada en Unity que funciona sobre Android, y una segunda aplicación desarrollada también en Unity que maneja un entorno 3D con el que se interactúa mediante gestos realizados en el aire. Luego de algunos intentos la interacción entre ambas aplicaciones fue lograda implementando comunicación por sockets entre la aplicación en el dispositivo Android y la aplicación 3D que se encuentra alojada en un computador con Windows 7. La captura de gestos en el aire se realiza mediante el sistema Tracking Tools desarrollado por la compañía Optitrack que captura los movimientos con cámaras infrarrojas y marcadores en los dedos. Este sistema envía los datos de los gestos a nuestra aplicación 3D. Estos equipos son de propiedad del laboratorio Decoroso Crespo de la Universidad Politécnica de Madrid. Una vez lograda la implementación e interacción entre las aplicaciones se han realizado pruebas de usabilidad con nueve estudiantes del Máster Universitario en Software y Sistemas de la Universidad Politécnica de Madrid. Cada uno ha respondido una serie de encuestas para poder obtener resultados sobre cuán usable es el prototipo, la experiencia del usuario y qué mejoras se podrían realizar sobre éste. En la parte final de este documento se presentan los resultados de las encuestas y se muestran las conclusiones y trabajo futuro.---ABSTRACT---Currently there are several devices that accept gestures on touch surfaces like phones, tablets, computers, etc. to which people quickly become accustomed to their use and accept them as necessary tools in their life. Similarly there are some applications that handle 3D environments and like televisions, holograms and allow capture gestures made with hands, body, and head. These techniques have been developed on a separated way but based on some research we may say that the are not many studies that combine touch with 3D applications handled by gestures in the air. This paper presents a prototype of the interaction of two issues of a 2D showing documents represented by spheres on a touch application developed in Unity that works on Android and allows communicating with the second application also developed in Unity that handles a 3D environment interaction of gestures made in air. After some attempts interaction was achieved by implementing communication sockets between the application on the Android device and 3D application that is hosted on a computer with windows 7, and gestures capturing in the air is done by the system Tracking Tools developed by the Optitrack company it captures movements with infrared cameras and markers on the fingers, which sends data to this application gestures, these equipment are owned by the Decoroso Crespo laboratory of the Polytechnic University of Madrid. Once achieved the interaction of applications has been conducted performance tests with ten students of the university master of the Universidad Politécnica de Madrid, each has answered a series of surveys to get results on how usable is the prototype, the user experience and that improvements could be made on this.

Force-mediated kinetics of single P-selectin/ligand complexes observed by atomic force microscopy

Leukocytes roll along the endothelium of postcapillary venules in response to inflammatory signals. Rolling under the hydrodynamic drag forces of blood flow is mediated by the interaction between selectins and their ligands across the leukocyte and endothelial cell surfaces. Here we present force-spectroscopy experiments on single complexes of P-selectin and P-selectin glycoprotein ligand-1 by atomic force microscopy to determine the intrinsic molecular properties of this dynamic adhesion process. By modeling intermolecular and intramolecular forces as well as the adhesion probability in atomic force microscopy experiments we gain information on rupture forces, elasticity, and kinetics of the P-selectin/P-selectin glycoprotein ligand-1 interaction. The complexes are able to withstand forces up to 165 pN and show a chain-like elasticity with a molecular spring constant of 5.3 pN nm−1 and a persistence length of 0.35 nm. The dissociation constant (off-rate) varies over three orders of magnitude from 0.02 s−1 under zero force up to 15 s−1 under external applied forces. Rupture force and lifetime of the complexes are not constant, but directly depend on the applied force per unit time, which is a product of the intrinsic molecular elasticity and the external pulling velocity. The high strength of binding combined with force-dependent rate constants and high molecular elasticity are tailored to support physiological leukocyte rolling.

Activation and inhibition of K-ATP currents by guanine nucleotides is mediated by different channel subunits

The ATP-sensitive potassium channel (K-ATP channel) plays a key role in insulin secretion from pancreatic β-cells. It is closed by glucose metabolism, which stimulates secretion, and opened by the drug diazoxide, which inhibits insulin release. Metabolic regulation is mediated by changes in ATP and MgADP concentration, which inhibit and potentiate channel activity, respectively. The β-cell K-ATP channel consists of a pore-forming subunit, Kir6.2, and a regulatory subunit, SUR1. The site at which ATP mediates channel inhibition lies on Kir6.2, while the potentiatory action of MgADP involves the nucleotide-binding domains of SUR1. K-ATP channels are also activated by MgGTP and MgGDP. Furthermore, both nucleotides support the stimulatory actions of diazoxide. It is not known, however, whether guanine nucleotides mediate their effects by direct interaction with one or more of the K-ATP channel subunits or indirectly via a GTP-binding protein. We used a truncated form of Kir6.2, which expresses independently of SUR1, to show that GTP blocks K-ATP currents by interaction with Kir6.2 and that the potentiatory effects of GTP are endowed by SUR1. We also showed that mutation of the lysine residue in the Walker A motif of either the first (K719A) or second (K1384M) nucleotide-binding domain of SUR1 abolished both the potentiatory effects of GTP and GDP on K-ATP currents and their ability to support stimulation by diazoxide. This argues that the stimulatory effects of guanine nucleotides require the presence of both Walker A lysines.

Regulation of transforming growth factor β- and activin-induced transcription by mammalian Mad proteins

Members of the transforming growth factor β (TGF-β) superfamily are involved in diverse physiological activities including development, tissue repair, hormone regulation, bone formation, cell growth, and differentiation. At the cellular level, these functions are initiated by the interaction of ligands with specific transmembrane receptors with intrinsic serine/threonine kinase activity. The signaling pathway that links receptor activation to the transcriptional regulation of the target genes is largely unknown. Recent work in Drosophila and Xenopus signaling suggested that Mad (Mothers against dpp) functions downstream of the receptors of the TGF-β family. Mammalian Mad1 has been reported to respond to bone morphogenetic protein (BMP), but not to TGF-β or activin. We report here the cloning and functional studies of a novel mammalian Mad molecule, Mad3, as well as a rat Mad1 homologue. Overexpression of Mad3 in a variety of cells stimulated basal transcriptional activity of the TGF-β/activin-responsive reporter construct, p3TP-Lux. Furthermore, expression of Mad3 could potentiate the TGF-β- and activin-induced transcriptional stimulation of p3TP-Lux. By contrast, overexpression of Mad1 inhibited the basal as well as the TGF-β/activin induced p3TP-Lux activity. These findings, therefore, support the hypothesis that Mad3 may serve as a mediator linking TGF-β/activin receptors to transcriptional regulation.

Molecular mechanism of use-dependent calcium channel block by phenylalkylamines: Role of inactivation

The role of channel inactivation in the molecular mechanism of calcium (Ca2+) channel block by phenylalkylamines (PAA) was analyzed by designing mutant Ca2+ channels that carry the high affinity determinants of the PAA receptor site [Hockerman, G. H., Johnson, B. D., Scheuer, T., and Catterall, W. A. (1995) J. Biol. Chem. 270, 22119–22122] but inactivate at different rates. Use-dependent block by PAAs was studied after expressing the mutant Ca2+ channels in Xenopus oocytes. Substitution of single putative pore-orientated amino acids in segment IIIS6 by alanine (F-1499-A, F-1500-A, F-1510-A, I-1514-A, and F-1515-A) gradually slowed channel inactivation and simultaneously reduced inhibition of barium currents (IBa) by (−)D600 upon depolarization by 100 ms steps at 0.1 Hz. This apparent reduction in drug sensitivity was only evident if test pulses were applied at a low frequency of 0.1 Hz and almost disappeared at the frequency of 1 Hz. (−)D600 slowed IBa recovery after maintained membrane depolarization (1–3 sec) to a comparable extent in all channel constructs. A drug-induced delay in the onset of IBa recovery from inactivation suggests that PAAs promote the transition to a deep inactivated channel conformation. These findings indicate that apparent PAA sensitivity of Ca2+ channels is not only defined by drug interaction with its receptor site but also crucially dependent on intrinsic gating properties of the channel molecule. A molecular model for PAA-Ca2+ channel interaction that accounts for the relationship between drug induced inactivation and channel block by PAA is proposed.

Binding of Signal Recognition Particle Gives Ribosome/Nascent Chain Complexes a Competitive Advantage in Endoplasmic Reticulum Membrane Interaction

Most secretory and membrane proteins are sorted by signal sequences to the endoplasmic reticulum (ER) membrane early during their synthesis. Targeting of the ribosome-nascent chain complex (RNC) involves the binding of the signal sequence to the signal recognition particle (SRP), followed by an interaction of ribosome-bound SRP with the SRP receptor. However, ribosomes can also independently bind to the ER translocation channel formed by the Sec61p complex. To explain the specificity of membrane targeting, it has therefore been proposed that nascent polypeptide-associated complex functions as a cytosolic inhibitor of signal sequence- and SRP-independent ribosome binding to the ER membrane. We report here that SRP-independent binding of RNCs to the ER membrane can occur in the presence of all cytosolic factors, including nascent polypeptide-associated complex. Nontranslating ribosomes competitively inhibit SRP-independent membrane binding of RNCs but have no effect when SRP is bound to the RNCs. The protective effect of SRP against ribosome competition depends on a functional signal sequence in the nascent chain and is also observed with reconstituted proteoliposomes containing only the Sec61p complex and the SRP receptor. We conclude that cytosolic factors do not prevent the membrane binding of ribosomes. Instead, specific ribosome targeting to the Sec61p complex is provided by the binding of SRP to RNCs, followed by an interaction with the SRP receptor, which gives RNC–SRP complexes a selective advantage in membrane targeting over nontranslating ribosomes.

Phosphorylation of SNAP-23 by the Novel Kinase SNAK Regulates t-SNARE Complex Assembly

The docking and fusion of cargo-containing vesicles with target membranes of eukaryotic cells is mediated by the interaction of SNARE proteins present on both vesicle and target membranes. In many cases, the target membrane SNARE, or t-SNARE, exists as a complex of syntaxin with a member of the SNAP-25 family of palmitoylated proteins. We have identified a novel human kinase SNAK (SNARE kinase) that specifically phosphorylates the nonneuronal t-SNARE SNAP-23 in vivo. Interestingly, only SNAP-23 that is not assembled into t-SNARE complexes is phosphorylated by SNAK, and phosphorylated SNAP-23 resides exclusively in the cytosol. Coexpression with SNAK significantly enhances the stability of unassembled SNAP-23, and as a consequence, the assembly of newly synthesized SNAP-23 with syntaxin is augmented. These data demonstrate that phosphorylation of SNAP-23 by SNAK enhances the kinetics of t-SNARE assembly in vivo.

Regulation of CFTR Cl− channel gating by ATP binding and hydrolysis

Opening and closing of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl− channel is regulated by the interaction of ATP with its two cytoplasmic nucleotide-binding domains (NBD). Although ATP hydrolysis by the NBDs is required for normal gating, the influence of ATP binding versus hydrolysis on specific steps in the gating cycle remains uncertain. Earlier work showed that the absence of Mg2+ prevents hydrolysis. We found that even in the absence of Mg2+, ATP could support channel activity, albeit at a reduced level compared with the presence of Mg2+. Application of ATP with a divalent cation, including the poorly hydrolyzed CaATP complex, increased the rate of opening. Moreover, in CFTR variants with mutations that disrupt hydrolysis, ATP alone opened the channel and Mg2+ further enhanced ATP-dependent opening. These data suggest that ATP alone can open the channel and that divalent cations increase ATP binding. Consistent with this conclusion, when we mutated an aspartate thought to bind Mg2+, divalent cations failed to increase activity compared with ATP alone. Two observations suggested that divalent cations also stabilize the open state. In wild-type CFTR, CaATP generated a long duration open state, whereas ATP alone did not. With a CFTR variant in which hydrolysis was disrupted, MgATP, but not ATP alone, produced long openings. These results suggest a gating cycle for CFTR in which ATP binding opens the channel and either hydrolysis or dissociation leads to channel closure. In addition, the data suggest that ATP binding and hydrolysis by either NBD can gate the channel.

Genetic complexity of pathogen perception by plants: The example of Rcr3, a tomato gene required specifically by Cf-2

Genetic analysis of plant–pathogen interactions has demonstrated that resistance to infection is often determined by the interaction of dominant plant resistance (R) genes and dominant pathogen-encoded avirulence (Avr) genes. It was postulated that R genes encode receptors for Avr determinants. A large number of R genes and their cognate Avr genes have now been analyzed at the molecular level. R gene loci are extremely polymorphic, particularly in sequences encoding amino acids of the leucine-rich repeat motif. A major challenge is to determine how Avr perception by R proteins triggers the plant defense response. Mutational analysis has identified several genes required for the function of specific R proteins. Here we report the identification of Rcr3, a tomato gene required specifically for Cf-2-mediated resistance. We propose that Avr products interact with host proteins to promote disease, and that R proteins “guard” these host components and initiate Avr-dependent plant defense responses.

Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation

Modification of damaged replication forks is emerging as a crucial factor for efficient chromosomal duplication and the avoidance of genetic instability. The RecG helicase of Escherichia coli, which is involved in recombination and DNA repair, has been postulated to act on stalled replication forks to promote replication restart via the formation of a four-stranded (Holliday) junction. Here we show that RecG can actively unwind the leading and lagging strand arms of model replication fork structures in vitro. Unwinding is achieved in each case by simultaneous interaction with and translocation along both the leading and lagging strand templates at a fork. Disruption of either of these interactions dramatically inhibits unwinding of the opposing duplex arm. Thus, RecG translocates simultaneously along two DNA strands, one with 5′-3′ and the other with 3′-5′ polarity. The unwinding of both nascent strands at a damaged fork, and their subsequent annealing to form a Holliday junction, may explain the ability of RecG to promote replication restart. Moreover, the preferential binding of partial forks lacking a leading strand suggests that RecG may have the ability to target stalled replication intermediates in vivo in which lagging strand synthesis has continued beyond the leading strand.